dna

Summary

Summary: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

Top Publications

  1. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
  2. doi DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
  3. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
  5. pmc DNA targeting specificity of RNA-guided Cas9 nucleases
    Patrick D Hsu
    1 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 3 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 4
    Nat Biotechnol 31:827-32. 2013
  6. pmc Human DNA methylomes at base resolution show widespread epigenomic differences
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 462:315-22. 2009
  7. doi A TALE nuclease architecture for efficient genome editing
    Jeffrey C Miller
    Sangamo BioSciences, Inc, Richmond, California, USA
    Nat Biotechnol 29:143-8. 2011
  8. pmc Quantitative visualization of DNA G-quadruplex structures in human cells
    Giulia Biffi
    Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nat Chem 5:182-6. 2013
  9. pmc The DNA damage response: making it safe to play with knives
    Alberto Ciccia
    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 40:179-204. 2010
  10. pmc Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    Juliane C Dohm
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 36:e105. 2008

Detail Information

Publications403 found, 100 shown here

  1. pmc Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    S F Altschul
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 25:3389-402. 1997
    The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities...
  2. doi DnaSP v5: a software for comprehensive analysis of DNA polymorphism data
    P Librado
    Departament de Genetica, Facultat de Biologia and Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
    Bioinformatics 25:1451-2. 2009
    DnaSP is a software package for a comprehensive analysis of DNA polymorphism data. Version 5 implements a number of new features and analytical methods allowing extensive DNA polymorphism analyses on large datasets...
  3. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large...
  4. pmc BLAT--the BLAST-like alignment tool
    W James Kent
    Department of Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Genome Res 12:656-64. 2002
    Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments...
  5. pmc DNA targeting specificity of RNA-guided Cas9 nucleases
    Patrick D Hsu
    1 Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 2 McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 3 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 4
    Nat Biotechnol 31:827-32. 2013
    ..We find that SpCas9 tolerates mismatches between guide RNA and target DNA at different positions in a sequence-dependent manner, sensitive to the number, position and distribution of ..
  6. pmc Human DNA methylomes at base resolution show widespread epigenomic differences
    Ryan Lister
    Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
    Nature 462:315-22. 2009
    b>DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease...
  7. doi A TALE nuclease architecture for efficient genome editing
    Jeffrey C Miller
    Sangamo BioSciences, Inc, Richmond, California, USA
    Nat Biotechnol 29:143-8. 2011
    ..We identify TALE truncation variants that efficiently cleave DNA when linked to the catalytic domain of FokI and use these nucleases to generate discrete edits or small deletions ..
  8. pmc Quantitative visualization of DNA G-quadruplex structures in human cells
    Giulia Biffi
    Cancer Research UK, Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nat Chem 5:182-6. 2013
    ..the generation and application of an engineered, structure-specific antibody employed to quantitatively visualize DNA G-quadruplex structures in human cells...
  9. pmc The DNA damage response: making it safe to play with knives
    Alberto Ciccia
    Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
    Mol Cell 40:179-204. 2010
    ..To respond to these threats, eukaryotes have evolved the DNA damage response (DDR)...
  10. pmc Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    Juliane C Dohm
    Max Planck Institute for Molecular Genetics, Ihnestr 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 36:e105. 2008
    ..Such biases have implications on the use and interpretation of Solexa data, for de novo sequencing, re-sequencing, the identification of single nucleotide polymorphisms and DNA methylation sites, as well as for transcriptome analysis.
  11. pmc Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1
    Mamta Tahiliani
    Department of Pathology, Harvard Medical School and Immune Disease Institute, 200 Longwood Avenue, Boston, MA 02115, USA
    Science 324:930-5. 2009
    b>DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development...
  12. doi Mechanism of eukaryotic homologous recombination
    Joseph San Filippo
    Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
    Annu Rev Biochem 77:229-57. 2008
    ..Two recombinases, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cells via a filamentous intermediate on ssDNA called the presynaptic filament...
  13. pmc Diversity and complexity in DNA recognition by transcription factors
    Gwenael Badis
    Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
    Science 324:1720-3. 2009
    Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome...
  14. pmc Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription
    Feng Zhang
    Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 29:149-53. 2011
    The ability to direct functional proteins to specific DNA sequences is a long-sought goal in the study and engineering of biological processes. Transcription activator-like effectors (TALEs) from Xanthomonas sp...
  15. ncbi Requirement for p53 and p21 to sustain G2 arrest after DNA damage
    F Bunz
    The Howard Hughes Medical Institute and The Johns Hopkins Oncology Center, 424 North Bond Street, Baltimore, MD 21231, USA
    Science 282:1497-501. 1998
    After DNA damage, many cells appear to enter a sustained arrest in the G2 phase of the cell cycle...
  16. pmc Systematic localization of common disease-associated variation in regulatory DNA
    Matthew T Maurano
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Science 337:1190-5. 2012
    ..We show that these variants are concentrated in regulatory DNA marked by deoxyribonuclease I (DNase I) hypersensitive sites (DHSs)...
  17. doi Linking DNA methylation and histone modification: patterns and paradigms
    Howard Cedar
    Department of Developmental Biology and Cancer Research, Hebrew University Medical School, Ein Kerem, Jerusalem 91120, Israel
    Nat Rev Genet 10:295-304. 2009
    Both DNA methylation and histone modification are involved in establishing patterns of gene repression during development...
  18. ncbi DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139
    E P Rogakou
    Laboratory of Molecular Pharmacology, Division of Basic Sciences, NCI, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Biol Chem 273:5858-68. 1998
    ..to as gamma, these components are formed in vivo by several procedures that introduce double-stranded breaks into DNA. gamma-Components, which appeared to be the only major novel components detected by mass or 32PO4 incorporation on ..
  19. doi DNA-binding specificities of human transcription factors
    Arttu Jolma
    Science for Life Center, Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
    Cell 152:327-39. 2013
    ..that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated...
  20. ncbi Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA
    J R Riordan
    Department of Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada
    Science 245:1066-73. 1989
    Overlapping complementary DNA clones were isolated from epithelial cell libraries with a genomic DNA segment containing a portion of the putative cystic fibrosis (CF) locus, which is on chromosome 7...
  21. pmc SSAHA: a fast search method for large DNA databases
    Z Ning
    Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 11:1725-9. 2001
    ..and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are preprocessed by breaking them into consecutive k-tuples of k contiguous bases and ..
  22. pmc High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity
    Vikram Pattanayak
    Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
    Nat Biotechnol 31:839-43. 2013
    The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA at sites complementary to a 20-base-pair guide RNA...
  23. pmc Personalized copy number and segmental duplication maps using next-generation sequencing
    Can Alkan
    Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
    Nat Genet 41:1061-7. 2009
    ..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...
  24. pmc Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers
    Adrian W Briggs
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
    Nucleic Acids Res 40:e117. 2012
    b>DNA built from modular repeats presents a challenge for gene synthesis...
  25. doi Real-time DNA sequencing from single polymerase molecules
    JOHN EID
    Pacific Biosciences, 1505 Adams Drive, Menlo Park, CA 94025, USA
    Science 323:133-8. 2009
    We present single-molecule, real-time sequencing data obtained from a DNA polymerase performing uninterrupted template-directed synthesis using four distinguishable fluorescently labeled deoxyribonucleoside triphosphates (dNTPs)...
  26. pmc Loop-mediated isothermal amplification of DNA
    T Notomi
    Eiken Chemical Co Ltd, 1381 3 Shimoishigami, Ohtawara, Tochigi 324 0036, Japan, Department of Biochemistry and Molecular Biology, The University of Tokyo, Graduate School of Medicine, Bunkyo ku, Tokyo 113 0033, Japan
    Nucleic Acids Res 28:E63. 2000
    We have developed a novel method, termed loop-mediated isothermal amplification (LAMP), that amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions...
  27. pmc DNA transposons and the evolution of eukaryotic genomes
    CEDRIC FESCHOTTE
    Department of Biology, University of Texas, Arlington, TX 76019, USA
    Annu Rev Genet 41:331-68. 2007
    ..This review focuses on DNA-mediated or class 2 transposons and emphasizes how this class of elements is distinguished from other types of ..
  28. pmc ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions
    Terrence S Furey
    Department of Genetics, Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, CB 7264, Chapel Hill, North Carolina 27599, USA
    Nat Rev Genet 13:840-52. 2012
    Chromatin immunoprecipitation experiments followed by sequencing (ChIP-seq) detect protein-DNA binding events and chemical modifications of histone proteins...
  29. pmc Cyclic GMP-AMP synthase is a cytosolic DNA sensor that activates the type I interferon pathway
    Lijun Sun
    Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Science 339:786-91. 2013
    The presence of DNA in the cytoplasm of mammalian cells is a danger signal that triggers host immune responses such as the production of type I interferons...
  30. pmc Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
    Shinsuke Ito
    Howard Hughes Medical Institute and Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
    Science 333:1300-3. 2011
    5-methylcytosine (5mC) in DNA plays an important role in gene expression, genomic imprinting, and suppression of transposable elements. 5mC can be converted to 5-hydroxymethylcytosine (5hmC) by the Tet (ten eleven translocation) proteins...
  31. pmc Human CtIP promotes DNA end resection
    Alessandro A Sartori
    The Wellcome Trust and Cancer Research UK Gurdon Institute, and Department of Zoology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
    Nature 450:509-14. 2007
    In the S and G2 phases of the cell cycle, DNA double-strand breaks (DSBs) are processed into single-stranded DNA, triggering ATR-dependent checkpoint signalling and DSB repair by homologous recombination...
  32. pmc Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    Erez Lieberman-Aiden
    Broad Institute of Harvard and Massachusetts Institute of Technology MIT, MA 02139, USA
    Science 326:289-93. 2009
    ..The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes...
  33. pmc A simple salting out procedure for extracting DNA from human nucleated cells
    S A Miller
    Memorial Blood Center of Minneapolis, MN 55404
    Nucleic Acids Res 16:1215. 1988
  34. pmc Telomere measurement by quantitative PCR
    Richard M Cawthon
    Department of Human Genetics, University of Utah, 15 N 2030 E, Room 2100, Salt Lake City, UT 84112, USA
    Nucleic Acids Res 30:e47. 2002
    It has long been presumed impossible to measure telomeres in vertebrate DNA by PCR amplification with oligonucleotide primers designed to hybridize to the TTAGGG and CCCTAA repeats, because only primer dimer-derived products are expected...
  35. ncbi Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
    E Li
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
    Cell 69:915-26. 1992
    Gene targeting in embryonic stem (ES) cells has been used to mutate the murine DNA methyltransferase gene...
  36. pmc Megabase chromatin domains involved in DNA double-strand breaks in vivo
    E P Rogakou
    Laboratory of Molecular Pharmacology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    J Cell Biol 146:905-16. 1999
    The loss of chromosomal integrity from DNA double-strand breaks introduced into mammalian cells by ionizing radiation results in the specific phosphorylation of histone H2AX on serine residue 139, yielding a specific modified form named ..
  37. ncbi Highly efficient endogenous human gene correction using designed zinc-finger nucleases
    Fyodor D Urnov
    Sangamo BioSciences, Inc, Pt Richmond Tech Center 501, Canal Blvd, Suite A100 Richmond, California 94804, USA
    Nature 435:646-51. 2005
    ..Here we report a general solution using two fundamental biological processes: DNA recognition by C2H2 zinc-finger proteins and homology-directed repair of DNA double-strand breaks...
  38. pmc Mapping short DNA sequencing reads and calling variants using mapping quality scores
    Heng Li
    The Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
    Genome Res 18:1851-8. 2008
    New sequencing technologies promise a new era in the use of DNA sequence...
  39. pmc The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain
    Skirmantas Kriaucionis
    Laboratory of Molecular Biology, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA
    Science 324:929-30. 2009
    ..the abundance of 5-methylcytosine in Purkinje and granule cell nuclei, we detected the presence of an unusual DNA nucleotide...
  40. doi The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes
    Tian Peng Gu
    Group of DNA Metabolism, The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Nature 477:606-10. 2011
    ..The paternal genome in a zygote undergoes active DNA demethylation before the first mitosis...
  41. ncbi Chromatin modifications and their function
    Tony Kouzarides
    The Gurdon Institute and Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB21QN, UK
    Cell 128:693-705. 2007
    ..Their presence on histones can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA...
  42. pmc DNA secondary structures: stability and function of G-quadruplex structures
    Matthew L Bochman
    Department of Molecular Biology, Princeton University, 101 Lewis Thomas Laboratory, Washington Rd, Princeton, New Jersey 08544, USA
    Nat Rev Genet 13:770-80. 2012
    In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures...
  43. pmc AIM2 recognizes cytosolic dsDNA and forms a caspase-1-activating inflammasome with ASC
    Veit Hornung
    Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Nature 458:514-8. 2009
    ..Little is known about sensors for cytoplasmic DNA that trigger antiviral and/or inflammatory responses...
  44. pmc Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine
    Chun Xiao Song
    Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, USA
    Nat Biotechnol 29:68-72. 2011
    ..group can be chemically modified with biotin for detection, affinity enrichment and sequencing of 5-hmC-containing DNA fragments in mammalian genomes...
  45. pmc High-throughput droplet digital PCR system for absolute quantitation of DNA copy number
    Benjamin J Hindson
    Bio Rad Laboratories, Inc, Pleasanton, California 94566, United States
    Anal Chem 83:8604-10. 2011
    ..Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background...
  46. pmc FIMO: scanning for occurrences of a given motif
    Charles E Grant
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Bioinformatics 27:1017-8. 2011
    A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides...
  47. pmc DNA interrogation by the CRISPR RNA-guided endonuclease Cas9
    Samuel H Sternberg
    1 Department of Chemistry, University of California, Berkeley, California 94720, USA 2
    Nature 507:62-7. 2014
    ..interspaced short palindromic repeats (CRISPR)-associated enzyme Cas9 is an RNA-guided endonuclease that uses RNA-DNA base-pairing to target foreign DNA in bacteria...
  48. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
    ..particle of chromatin shows in atomic detail how the histone protein octamer is assembled and how 146 base pairs of DNA are organized into a superhelix around it...
  49. pmc MEME-ChIP: motif analysis of large DNA datasets
    Philip Machanick
    Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Queensland, Australia
    Bioinformatics 27:1696-7. 2011
    ..While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets...
  50. pmc Targeting DNA double-strand breaks with TAL effector nucleases
    Michelle Christian
    Department of Plant Pathology, Iowa State University, Ames, Iowa 50011, USA
    Genetics 186:757-61. 2010
    Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis...
  51. pmc Repetitive DNA and next-generation sequencing: computational challenges and solutions
    Todd J Treangen
    McKusick Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nat Rev Genet 13:36-46. 2012
    Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs...
  52. pmc G-quadruplex structures are stable and detectable in human genomic DNA
    Enid Yi Ni Lam
    Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
    Nat Commun 4:1796. 2013
    The G-quadruplex is an alternative DNA structural motif that is considered to be functionally important in the mammalian genome for transcriptional regulation, DNA replication and genome stability, but the nature and distribution of G-..
  53. pmc MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences
    Sudhir Kumar
    Biodesign Institute, A240, Arizona State University, Tempe, AZ 85287 5301, USA
    Brief Bioinform 9:299-306. 2008
    ..families or from different species with a special emphasis on inferring evolutionary relationships and patterns of DNA and protein evolution...
  54. doi TAL effectors: customizable proteins for DNA targeting
    Adam J Bogdanove
    Department of Plant Pathology, 351 Bessey Hall, Iowa State University, Ames, IA 50011, USA
    Science 333:1843-6. 2011
    ..Progress has been made in engineering DNA binding domains to direct proteins to particular sequences for mutagenesis or manipulation of transcription; ..
  55. doi How shelterin protects mammalian telomeres
    Wilhelm Palm
    Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10021, USA
    Annu Rev Genet 42:301-34. 2008
    ..genomes of eukaryotes are organized on linear chromosomes, which require mechanisms to protect and replicate DNA ends...
  56. pmc Reprogramming towards pluripotency requires AID-dependent DNA demethylation
    Nidhi Bhutani
    Baxter Laboratory for Stem Cell Biology, Institute for Stem Cell Biology and Regenerative Medicine, Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305 5175, USA
    Nature 463:1042-7. 2010
    ..However, iPS cell generation is asynchronous and slow (2-3 weeks), the frequency is low (<0.1%), and DNA demethylation constitutes a bottleneck...
  57. pmc TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    ..The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html...
  58. doi Genome-wide DNA methylation profiling using Infinium® assay
    Marina Bibikova
    Illumina Inc, 9885 Towne Centre Dr, San Diego, CA 92121, USA
    Epigenomics 1:177-200. 2009
    Bisulfite sequence analysis of individual CpG sites within genomic DNA is a powerful approach for methylation analysis in the genome. The major limitation of bisulfite-based methods is parallelization...
  59. pmc Extracellular DNA traps promote thrombosis
    Tobias A Fuchs
    Immune Disease Institute, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 107:15880-5. 2010
    Neutrophil extracellular traps (NETs) are part of the innate immune response to infections. NETs are a meshwork of DNA fibers comprising histones and antimicrobial proteins...
  60. pmc The helicase DDX41 senses intracellular DNA mediated by the adaptor STING in dendritic cells
    Zhiqiang Zhang
    Department of Immunology, Center for Cancer Immunology Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
    Nat Immunol 12:959-65. 2011
    The recognition of pathogenic DNA is important to the initiation of antiviral responses...
  61. doi A logic-gated nanorobot for targeted transport of molecular payloads
    Shawn M Douglas
    Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, MA 02115, USA
    Science 335:831-4. 2012
    We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery...
  62. ncbi MODELTEST: testing the model of DNA substitution
    D Posada
    Department of Zoology, Brigham Young University, 574 WIDB, Provo, UT 84602 5255, USA
    Bioinformatics 14:817-8. 1998
    The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
  63. pmc PRDM9 is a major determinant of meiotic recombination hotspots in humans and mice
    F Baudat
    Institut de Genetique Humaine, UPR1142, CNRS, Montpellier, France
    Science 327:836-40. 2010
    ..First, two mouse strains that differ in hotspot usage are polymorphic for the zinc finger DNA binding array of PRDM9...
  64. pmc Ab initio gene finding in Drosophila genomic DNA
    A A Salamov
    The Sanger Centre, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 10:516-22. 2000
    ..The suite of gene identification programs is available through the WWW server of Computational Genomics Group at http://genomic.sanger.ac.uk/gf. html...
  65. pmc A chemical method for fast and sensitive detection of DNA synthesis in vivo
    Adrian Salic
    Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 105:2415-20. 2008
    We have developed a method to detect DNA synthesis in proliferating cells, based on the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) and its subsequent detection by a fluorescent azide through a Cu(I)-catalyzed [3 + 2] cycloaddition ..
  66. doi Targets and dynamics of promoter DNA methylation during early mouse development
    Julie Borgel
    Institute of Molecular Genetics, Centre National de la Recherche Scientifique CNRS UMR 5535, Universite Montpellier 2, Universite Montpellier 1, Montpellier, France
    Nat Genet 42:1093-100. 2010
    b>DNA methylation is extensively reprogrammed during the early phases of mammalian development, yet genomic targets of this process are largely unknown...
  67. doi Structural basis for CRISPR RNA-guided DNA recognition by Cascade
    Matthijs M Jore
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    Nat Struct Mol Biol 18:529-36. 2011
    ..Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner...
  68. ncbi Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    Weizhong Li
    Burnham Institute for Medical Research La Jolla, CA 92037, USA
    Bioinformatics 22:1658-9. 2006
    ..Cd-hit-2d compares two protein datasets and reports similar matches between them; cd-hit-est clusters a DNA/RNA sequence database and cd-hit-est-2d compares two nucleotide datasets...
  69. doi Transcription-coupled DNA repair: two decades of progress and surprises
    Philip C Hanawalt
    Department of Biology, Stanford University, 371 Serra Mall, Stanford, California 94305 5020, USA
    Nat Rev Mol Cell Biol 9:958-70. 2008
    Expressed genes are scanned by translocating RNA polymerases, which sensitively detect DNA damage and initiate transcription-coupled repair (TCR), a subpathway of nucleotide excision repair that removes lesions from the template DNA ..
  70. doi Induction and repair of DNA double strand breaks: the increasing spectrum of non-homologous end joining pathways
    Emil Mladenov
    Institute of Medical Radiation Biology, University of Duisburg Essen Medical School, Hufelandstr 55, 45122 Essen, Germany
    Mutat Res 711:61-72. 2011
    A defining characteristic of damage induced in the DNA by ionizing radiation (IR) is its clustered character that leads to the formation of complex lesions challenging the cellular repair mechanisms...
  71. pmc Fanconi anaemia and the repair of Watson and Crick DNA crosslinks
    Molly C Kottemann
    Laboratory of Genome Maintenance, The Rockefeller University, New York 10065, USA
    Nature 493:356-63. 2013
    The function of Fanconi anaemia proteins is to maintain genomic stability. Their main role is in the repair of DNA interstrand crosslinks, which, by covalently binding the Watson and the Crick strands of DNA, impede replication and ..
  72. pmc Cooperative control of holliday junction resolution and DNA repair by the SLX1 and MUS81-EME1 nucleases
    Dennis Castor
    MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
    Mol Cell 52:221-33. 2013
    Holliday junctions (HJs) are X-shaped DNA structures that arise during homologous recombination, which must be removed to enable chromosome segregation...
  73. pmc The AIM2 inflammasome is essential for host defense against cytosolic bacteria and DNA viruses
    Vijay A K Rathinam
    Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
    Nat Immunol 11:395-402. 2010
    ..AIM2 has been shown to bind DNA and engage the caspase-1-activating adaptor protein ASC to form a caspase-1-activating inflammasome...
  74. ncbi Histone H4-K16 acetylation controls chromatin structure and protein interactions
    Michael Shogren-Knaak
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Science 311:844-7. 2006
    ....
  75. pmc MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings
    Mitch McVey
    Department of Biology, Tufts University, 165 Packard Avenue, Medford, MA 02155, USA
    Trends Genet 24:529-38. 2008
    b>DNA double-strand breaks are normal consequences of cell division and differentiation and must be repaired faithfully to maintain genome stability...
  76. pmc Widespread RNA and DNA sequence differences in the human transcriptome
    Mingyao Li
    Department of Biostatistics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
    Science 333:53-8. 2011
    The transmission of information from DNA to RNA is a critical process...
  77. pmc Structural basis for sequence-specific recognition of DNA by TAL effectors
    Dong Deng
    State Key Laboratory of Bio membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China
    Science 335:720-3. 2012
    TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats...
  78. pmc Absolute quantification of somatic DNA alterations in human cancer
    Scott L Carter
    The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 30:413-21. 2012
    ..a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations...
  79. ncbi Neutrophil extracellular traps kill bacteria
    Volker Brinkmann
    Microscopy Core Facility, Max Planck Institute for Infection Biology, Schumannstrasse 21 22, 10117 Berlin, Germany
    Science 303:1532-5. 2004
    ..NETs appear to be a form of innate response that binds microorganisms, prevents them from spreading, and ensures a high local concentration of antimicrobial agents to degrade virulence factors and kill bacteria...
  80. ncbi Oncogene-induced senescence is part of the tumorigenesis barrier imposed by DNA damage checkpoints
    Jirina Bartkova
    Institute of Cancer Biology and Centre for Genotoxic Stress Research, Danish Cancer Society, DK 2100 Copenhagen, Denmark
    Nature 444:633-7. 2006
    ..One such barrier involves DNA replication stress, which leads to activation of the DNA damage checkpoint and thereby to apoptosis or cell cycle ..
  81. doi G-quadruplex structures: in vivo evidence and function
    Hans J Lipps
    Institute of Cell Biology, University Witten Herdecke, Stockumer Str 10, 58448 Witten, Germany
    Trends Cell Biol 19:414-22. 2009
    Although many biochemical and structural studies have demonstrated that DNA sequences containing runs of adjacent guanines spontaneously fold into G-quadruplex DNA structures in vitro, only recently has evidence started to accumulate for ..
  82. ncbi Adaptive protein evolution at the Adh locus in Drosophila
    J H McDonald
    Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08544
    Nature 351:652-4. 1991
    ..b>DNA sequence data on the Adh locus (encoding alcohol dehydrogenase, EC 1.1.1...
  83. pmc Prevalence of quadruplexes in the human genome
    Julian L Huppert
    University Chemical Laboratory, University of Cambridge Lensfield Road, Cambridge CB2 1EW, UK
    Nucleic Acids Res 33:2908-16. 2005
    Guanine-rich DNA sequences of a particular form have the ability to fold into four-stranded structures called G-quadruplexes...
  84. ncbi Folding DNA to create nanoscale shapes and patterns
    Paul W K Rothemund
    Departments of Computer Science and Computation and Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
    Nature 440:297-302. 2006
    ..The self-assembly of DNA molecules provides an attractive route towards this goal...
  85. pmc Origins of specificity in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Annu Rev Biochem 79:233-69. 2010
    Specific interactions between proteins and DNA are fundamental to many biological processes...
  86. doi R loops: from transcription byproducts to threats to genome stability
    Andres Aguilera
    CABIMER, Universidad de Sevilla CSIC, Av Americo Vespucio s n, 41092 Sevilla, Spain
    Mol Cell 46:115-24. 2012
    RNA:DNA hybrid structures known as R loops were thought to be rare byproducts of transcription...
  87. ncbi Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays
    S A Bustin
    Academic Department of Surgery, St Bartholomew s and the Royal London School of Medicine and Dentistry, Queen Mary and Westfield College, London E1 1BB, UK
    J Mol Endocrinol 25:169-93. 2000
    ..It illustrates the usefulness of these assays by demonstrating the significantly different levels of transcription between individuals of the housekeeping gene family, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH)...
  88. ncbi Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization
    Ahmet Yildiz
    Center for Biophysics and Computational Biology, University of Illinois, Urbana Champaign, IL 61801, USA
    Science 300:2061-5. 2003
    ..These results strongly support a hand-over-hand model of motility, not an inchworm model...
  89. pmc Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
    Matthew Slattery
    Department of Biochemistry and Molecular Biophysics, Columbia University, 701 West 168 th Street, HHSC 1104, New York, NY 10032, USA
    Cell 147:1270-82. 2011
    Members of transcription factor families typically have similar DNA binding specificities yet execute unique functions in vivo...
  90. doi DNA methylome analysis using short bisulfite sequencing data
    Felix Krueger
    Bioinformatics Group, The Babraham Institute, Cambridge, UK
    Nat Methods 9:145-51. 2012
    Bisulfite conversion of genomic DNA combined with next-generation sequencing (BS-seq) is widely used to measure the methylation state of a whole genome, the methylome, at single-base resolution...
  91. pmc The role of DNA shape in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
    Nature 461:1248-53. 2009
    The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-..
  92. pmc Identification of Birds through DNA Barcodes
    Paul D N Hebert
    Department of Zoology, University of Guelph, Guelph, Ontario, Canada
    PLoS Biol 2:e312. 2004
    Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species...
  93. ncbi Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    Gordon Robertson
    British Columbia Cancer Agency Genome Sciences Centre, 675 West 10th Avenue, Vancouver, British Columbia V5Z 4S6, Canada
    Nat Methods 4:651-7. 2007
    ..ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo...
  94. pmc Targeting DNA topoisomerase II in cancer chemotherapy
    John L Nitiss
    Molecular Pharmacology Department, St Jude Children s Research Hospital, Memphis, TN 38105, USA
    Nat Rev Cancer 9:338-50. 2009
    ..studies have expanded the biological contexts in which topoisomerase II (TOP2) has crucial functions, including DNA replication, transcription and chromosome segregation...
  95. ncbi Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints
    Aziz Sancar
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27599 7260, USA
    Annu Rev Biochem 73:39-85. 2004
    b>DNA damage is a relatively common event in the life of a cell and may lead to mutation, cancer, and cellular or organismic death...
  96. ncbi Genome-wide mapping of in vivo protein-DNA interactions
    David S Johnson
    Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305 5120, USA
    Science 316:1497-502. 2007
    In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold...
  97. doi Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
    Radoje Drmanac
    Complete Genomics, Inc, 2071 Stierlin Court, Mountain View, CA 94043, USA
    Science 327:78-81. 2010
    ..probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs...
  98. pmc Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags
    PAUL A HOHENLOHE
    Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, Oregon, United States of America
    PLoS Genet 6:e1000862. 2010
    ....
  99. ncbi Mammalian telomeres end in a large duplex loop
    J D Griffith
    Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill and Curriculum in Genetics and Molecular Biology, 27599 7295, USA
    Cell 97:503-14. 1999
    ..Electron microscopy reported here demonstrated that TRF2 can remodel linear telomeric DNA into large duplex loops (t loops) in vitro...
  100. pmc Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
    Alberto Perez
    Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Barcelona 08028, Spain
    Biophys J 92:3817-29. 2007
    ..The set of validation simulations includes two of the longest trajectories published to date for the DNA duplex (200 ns each) and the largest variety of NA structures studied to date (15 different NA families and 97 ..
  101. pmc Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains
    Le Cong
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nat Commun 3:968. 2012
    Transcription activator-like effectors are sequence-specific DNA-binding proteins that harbour modular, repetitive DNA-binding domains...

Research Grants124 found, 100 shown here

  1. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2012
    ..Title: National Ophthalmic Genotyping and Phenotyping Network, Stage 1 - Creation of DNA Repository for Inherited Ophthalmic Diseases Number: 06-EI-0236 Summary: This study will collect blood and DNA ..
  2. STATISITICAL DESIGN, MONITORING &COORD. OF VISION CLINICAL TRIALS &EPIDEMIOLOGY
    Keri Hammel; Fiscal Year: 2013
    ..Title: National Ophthalmic Genotyping and Phenotyping Network, Stage 1 - Creation of DNA Repository for Inherited Ophthalmic Diseases Number: 06-EI-0236 Summary: This study will collect blood and DNA ..
  3. Genetic variation and regulatory networks: Mechanisms and complexity
    DANA PE ER; Fiscal Year: 2009
    ..Conversely, DNA sequence polymorphisms are effective perturb-agens which provide a rich source of variation to help uncover ..
  4. Variation in M. tuberculosis in response to host selection
    Sarah Fortune; Fiscal Year: 2009
    ..In these studies, we expect to provide fundamental insights into the mechanisms and targets of diversifying immune selection in M. tuberculosis. ..
  5. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  6. Prevention of Complications in Thalassemia
    Elliott P Vichinsky; Fiscal Year: 2011
    ..Long-term, prospective follow-up of newborns who have undergone DNA and genetic modifier diagnosis has enabled us to better understand the genotype/phenotype correlations20-23...
  7. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..d. Store and ensure that any data related to family structure, when available, are cross-referenced to any DNA samples and genotype data generated from the sample...
  8. Chymase-Mediated MMP Activation in Ishemia Reperfusion Injury
    LOUIS JOSEPH DELL'ITALIA; Fiscal Year: 2013
    ..the cardiomyocyte that cleaved myofibrils (4-6) and nuclear matrix protein poly ADP-ribose polymerase (PARP)-a DNA repair enzyme in cell survival during I/R (7)...
  9. Transcription factors regulating sensory gene expression and pain pathways
    Eric E Turner; Fiscal Year: 2011
    ..Our research has focused on the role of switching molecules, called transcription factors, which bind to DNA and regulate the expression of the functional proteins that define sensory neurons...
  10. Lauren Endres; Fiscal Year: 2014
    ..and electrophiles arising from endogenous and environmental sources can induce single and double strand breaks in DNA. These DNA lesions activate a multifaceted DNA damage response (DDR) to promote DNA repair by respective single and ..
  11. SHAOCHUNG VICTOR HSIA; Fiscal Year: 2016
    ..is supported by the literature and our observations: First, HSV-1 TK and ICP0 are important for efficient viral DNA replication and transcription within the infected neurons. Second, TR is present in sensory ganglia...
  12. NIEHS SUPPORT OF THE AHS COHORT STUDY AT NCI
    Charles Knott; Fiscal Year: 2010
    ..We are also collecting buccal cell samples as a source of genomic DNA for GXE studies and studies of epigenetic mechanisms...
  13. THE AGRICULTURAL HEALTH STUDY - FIELD STATIONS
    Charles Lynch; Fiscal Year: 2010
    ..We are also collecting buccal cell samples as a source of genomic DNA for GXE studies and studies of epigenetic mechanisms...
  14. Anti-tumor properties of curcumin in oral cancers: role of thioredoxin reductase
    STEPHEN WILLIAM TUTTLE; Fiscal Year: 2010
    ..an essential selenoprotein with defined roles in redox regulation of cell growth, death (apoptosis), transcription, DNA repair, and angiogenesis...
  15. Ian C Michelow; Fiscal Year: 2016
    ..mothers of infants with mild or no malaria. They will use a newly produced P. falciparum (3D7) malaria genomic DNA T7 phage display library as well as a wild type blood-stage complementary DNA T7 phage library for this purpose...
  16. Yun Fai Chris Lau; Fiscal Year: 2014
    ..prostatic oncogenesis in the TSPY-LADY bi-transgenic mice, in terms of tumor pathogenesis, transgene expression, DNA methylation status of the TSPY promoter and exon 1, and identification of transcription factors and repressors ..
  17. The Primate Corpus Luteum: Functional Regression and Cardiovascular Impacts
    Randy L Bogan; Fiscal Year: 2012
    ..isoform to promoter regions of known LXR target genes will be determined during spontaneous luteolysis in vivo, and DNA microarray assays will be performed on luteal cells containing both or individual LXR isoforms in the presence of ..
  18. Carole R Mendelson; Fiscal Year: 2016
    ..of O2 and inhibitory effects of glucocorticoids on SP-A expression are associated with changes in phosphorylation, DNA-binding and transcriptional activity of TTF-1 and NF-(B...
  19. Genome-wide recombination as a risk factor for nondisjunction
    NATASHA D HOLLIS; Fiscal Year: 2010
    ..at the University of Alabama-Birmingham where her research examined the effect of ozone exposure on mitochondrial DNA damage and TNFa response in c57 mice...
  20. Physiological role of PRDM16 in brown fat development and energy balance
    Patrick Seale; Fiscal Year: 2011
    ..by sequence comparisons and share significant sequence similarity especially within the two conserved zinc-finger DNA/protein binding domains...
  21. A Hybrid PARP Inhibitor and Redox Catalyst for Lung Transplantation
    GARRY JOHN SOUTHAN; Fiscal Year: 2012
    ..These oxidizing and nitrosating species induce DNA single strand breaks that activate poly(ADP-ribose) polymerase (PARP), a nuclear DNA repair enzyme that in turn ..
  22. Prostate, Lung, Colorectal and Ovarian (PLCO) Screening Trial
    Mona Fouad; Fiscal Year: 2013
    ..The usual care arm provided buccal cell DNA samples which are also stored in the PLCO Biorepository. The PLCO Biorepository currently has over 2...
  23. Prostate, Lung, Colorectal and Ovarian (PLCO) Screening Trial
    BARBARA O'BRIEN; Fiscal Year: 2013
    ..The usual care arm provided buccal cell DNA samples which are also stored in the PLCO Biorepository. The PLCO Biorepository currently has over 2...
  24. Role of SAMe on UBC9 and sumolyation in liver cancer and alcoholic liver injury
    Maria Lauda Tomasi; Fiscal Year: 2012
    ..Inactivating mutations of UBC9's SUMO conjugating activity enhances sensitivity to DNA damaging agents...
  25. Retinoid and Carotenoid Depletion in Patients at High-Risk for Liver Cancer
    Peter H Gann; Fiscal Year: 2010
    ..For Aim 2, we will measure oxidative damage to DNA via 8OHdG in urine (oxidized, excreted DNA bases) and the comet assay (DNA strand breaks in lymphocytes) to test ..
  26. Discovery of Small Molecule MBT Domain Antagonists
    STEPHEN VERNON FRYE; Fiscal Year: 2010
    ..1] The template upon which the epigenome is written is chromatin - the complex of histone proteins, RNA and DNA that efficiently package the genome in an appropriately accessible state within each cell...
  27. Jian Min Yuan; Fiscal Year: 2014
    ..case-control studies within the two cohorts to elucidate the role of environmental exposure, genetic variants and DNA methylation in the development of lung or liver cancer...
  28. Role of Txnip in adapting fuel metabolism to nutritional state
    SIMON HUI; Fiscal Year: 2013
    ..Cellular antioxidant and ROS defense system will be measured as well as the levels of oxidative modified proteins, DNA and lipids in the mitochondria...
  29. Non-viral Genetic Modification of Antigen-presenting Cells in Allografts
    Wilson S Meng; Fiscal Year: 2011
    ..gene particles will be applied to skin allografts ex vivo (prior to transplantation) using polymeric particles as a DNA carrier...
  30. A Redox-active PARP Inhibitor for Lung Transplantation
    ANDREW LURIE SALZMAN; Fiscal Year: 2012
    ..IRI i mediated in part by the synthesis of oxidative and nitrosative species that in turn induce DNA single strand breakage and triggering of the nuclear DNA repair enzyme, poly(ADP-ribose) polymerase-1 (PARP-1)...
  31. Impact of the P479L Variant in CPT1A on Infant Mortality in Alaska
    David M Koeller; Fiscal Year: 2011
    ..The affected infants are all of Alaska Native heritage, and homozygous for the same DNA sequence variant in the CPT1A gene (c...
  32. Polycyclic aromatic hydrocarbons and birth outcomes in Mexico City
    MARIE SYLVIA O'NEILL; Fiscal Year: 2013
    ..We will obtain biomarkers relevant to PAH exposure (DNA adducts) in blood samples provided by participants monthly during their pregnancies, and umbilical cord blood ..
  33. Enterococcus faecalis, Colorectal Cancer, and Bystander Effects
    Mark M Huycke; Fiscal Year: 2012
    ..faecalis is unique in generating extracellular superoxide, promoting oxidative stress, and damaging DNA. We propose a novel hypothesis for sporadic CRC that involves innate immune responses triggered by redox-active ..
  34. The role of Fli1 in T cell function and the pathogenesis of lupus
    Tamara K Nowling; Fiscal Year: 2011
    ..with co-factors of the proteins that control the Fli1 promoter by western immunoblots, real-time RTPCR, co-IP and DNA affinity assays in T cells...
  35. Inhibition of human neutrophil function by Francisella tularensis
    Lee Ann H Allen; Fiscal Year: 2012
    ..phagosome escape and PMN viability;in vitro kinase assays and immunoblotting to measure intracellular signaling;DNA microarrays to define changes in neutrophil gene expression;and both targeted allelic replacement strategies and ..
  36. Lung Lysyl Oxidase Regulation by Metal Ion Homeostasis
    Wande Li; Fiscal Year: 2013
    ..cognate cis-elements, and determining LO promoter methylation to provide evidence for Cd epigenetic damage to LO DNA;3) to identify mechanisms for Cd silencing of the LO gene at the posttranscriptional level by examining Cd effects ..
  37. Bradley P Dixon; Fiscal Year: 2014
    ..bladder microenvironment, and we have recently shown that this hyperosmolal stress disrupts gastrointestinal cell DNA damage signaling and repair...
  38. Genetics and Haloperidol Response
    Robert J Hitzemann; Fiscal Year: 2012
    ..stock [HS] animals, the integration of QTL analysis, sequence data and functional genomics, high throughput DNA sequencing, the use of short term selective breeding to confirm the role of Drd2 network coherence in haloperidol ..
  39. Michael Demetriou; Fiscal Year: 2014
    Genetic information flows from DNA to macromolecular structures;the dominant force in the molecular organization of life...
  40. Bayar Thimmapaya; Fiscal Year: 2016
    ..studies showing that adenovirally-driven overexpression of Med1 (adeno-Med1) in mouse liver stimulates hepatocyte DNA replication and regeneration...
  41. Translational Machinery in Stress Signaling and Tumor Suppression
    THOMAS J contact BEGLEY; Fiscal Year: 2010
    ..In general, adaptation to stress promotes the repair of protein and DNA damage and must occur rapidly...
  42. Role of Polyamines in MYCN-Amplified Neuroblastoma
    ANDRE BACHMANN; Fiscal Year: 2009
    ..studies, Western blot, yeast two-hybrid, co-immunoprecipitation, GST-pull down, site-directed mutagenesis, DNA cloning, confocal laser microscopy, enzyme and in vitro kinase assays, flow cytometry, and HPLC...
  43. Investigating Mechanism of Intracellular Rotational Transport with Optical T
    Jeffrey N Anker; Fiscal Year: 2012
    ..This inflammation and associated overproduction of reactive oxygen species further oxidize RNA/DNA/proteins, leading to fibrosis, mutagenesis and lung cancer...
  44. Targeting Inflammation for the Amelioration of Cisplatin-Hearing Loss
    Vickram Ramkumar; Fiscal Year: 2011
    ..However, inhibition of caspases, p53, or activation of DNA repair enzymes may promote the development of tumors or promote tumor chemoresistance...
  45. Group A Streptococcus responses to oxidative stress
    Ioannis Gryllos; Fiscal Year: 2010
    ..Of these, polA.1 encodes DNA polymerase I, which has been implicated in DNA damage repair in several bacterial species, as well as in virulence ..
  46. Skeletal Muscle. Ca Release Control Inside the Sarcoplasmic Reticulum.
    Eduardo Rios; Fiscal Year: 2013
    ..These goals are now feasible in living animals thanks to a DNA transfection method that works with every protein and can be used also to prevent their synthesis...
  47. Vitamin D Hormone Signaling in Bone Mineral Homeostasis
    Mark R Haussler; Fiscal Year: 2010
    ..promoters, with 1,25(OH)2D3-VDR-RXR attracting comodulator protein/enzyme complexes that either repress or induce DNA transcription by chromatin remodeling and linkage to RNA polymerase II...
  48. DNA methylation of extracellular superoxide dismutase in pulmonary hypertension
    EVA NOZIK GRAYCK; Fiscal Year: 2012
    ..Based on these data, we hypothesize that DNA methylation of the EC-SOD promoter mediates silencing of this protective gene and contributes to the pathogenesis ..
  49. Vitamin D and Estrogen Action in Bone: Concerted Role for hnRNPs in the C Family
    John S Adams; Fiscal Year: 2013
    ..By virtue of their capacity to interact with single-strand DNA (ssDNA), ssRNA as well as double- strand DNA (dsDNA), these hnRNPs have the potential to exert control over gene ..
  50. Junxuan Lu; Fiscal Year: 2014
    ..We data suggest novel targets/pathways of PGG for chemoprevention include a rapid inhibition of DNA replicative synthesis, and an activation of the p53 tumor suppressor and inactivating the Stat3 oncogenic signaling,..
  51. Rajvir Dahiya; Fiscal Year: 2015
    ..of CpG Islands in putative promoter regions of miRNAs using sodium bisulfite methylation techniques and direct DNA sequencing...
  52. Epigenetics of Sex Differences in Brain and Behavior
    BRIDGET NUGENT; Fiscal Year: 2012
    ..b>DNA methylation is the epigenetic process by which a DNA methyltransferase (DNMT) enzyme covalently modifies cytosine ..
  53. THE ETHICS OF POST-CONFLICT AND POST-DISASTER DNA IDENTIFICATION
    Sarah Wagner; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Forensic DNA profiling is increasingly becoming a standard tool in the search for missing people in the aftermath of mass violence and mass disaster...
  54. SAMY LEWIZ HABIB; Fiscal Year: 2016
    ..Diabetes and hyperglycemia are associated with enhanced production of reactive oxygen species and induce DNA damage by several mechanisms...
  55. Charlotte Cunningham-Rundles; Fiscal Year: 2015
    ..proliferation inducing ligand (APRIL) up-regulate the expression of activation-induced cytidine deaminase (AID), a DNA-editing enzyme essential for both class switch recombination (CSR) and somatic hypermutation (SHM...
  56. INSULIN RECEPTORS AND THE GLUCOSE TRANSPORT SYSTEM
    JERROLD MICHAEL OLEFSKY; Fiscal Year: 2013
    ..can function as a direct transrepressor of PPAR3 activity through protein/protein in- teractions, independent of DNA binding...
  57. FREDERIC TREMAINE BILLINGS; Fiscal Year: 2016
    ..In other preliminary studies, leukocyte mitochondrial DNA (mtDNA) coy number was significantly lower in cardiac surgery patients that developed AKI, intraoperative arterial ..
  58. Systematics of medically important Dermacentor tick vectors
    Dmitry A Apanaskevich; Fiscal Year: 2011
    ..To develop a DNA barcode system for Dermacentor species;and Aim 4...
  59. Jefferey L Burgess; Fiscal Year: 2014
    ..Urinary 8- hydroxy-2'-deoxyguanosine (8-OHdG) will be assayed to assess oxidative DNA damage...
  60. Jianming Qiu; Fiscal Year: 2016
    ..Among DNA viruses, B19V has a unique feature in the processing of its precursor mRNA (pre-mRNA) in that all the viral mRNAs ..
  61. Novel DNA-Launched Attenuated Vaccine for VEE Virus
    PETER M PUSHKO; Fiscal Year: 2012
    ..Medigen has recently developed the "infectious DNA" (i-DNA) vaccination technology, which represents a unique combination of conventional DNA immunization with high ..
  62. Hepatic Steatosis Modulation by Apo B Gene Transcription
    JANET DEHOFF SPARKS; Fiscal Year: 2010
    ..Aim 3 examines the role of DNA methylation in regulating apob gene expression as a potential mechanism of betaine action by assessment of global ..
  63. Xianglin Shi; Fiscal Year: 2015
    ..We will investigate the effects of C3G on UVB-induced lipid peroxidation, protein oxidation, and oxidative DNA damage in KSH mice...
  64. Monitoring cellular redox signaling and oxidant stress in vivo
    Paul T Schumacker; Fiscal Year: 2010
    ..High levels of ROS cause oxidative damage to proteins, lipids and DNA. Oxidant stress has been implicated in the cellular dysfunction associated with ischemia- reperfusion injury, ..
  65. Howard B Lieberman; Fiscal Year: 2016
    DESCRIPTION (provided by applicant): When cells are exposed to physical or chemical agents that damage DNA, or develop damage during normal metabolic processes, deleterious effects can ensue, including mutation, cancer or death...
  66. Interplay Between Tissue Architecture and Nuclear Organization in the DNA Damage
    Pierre Alexandre Vidi; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Double-strand DNA breaks (DSBs) constitute a constant threat for genome integrity. In absence of accurate repair, they lead to mutations and chromosomal translocations promoting cancer progression...
  67. Identification of Proteins Important for Male Osteoporosis
    Hong Wen Deng; Fiscal Year: 2013
    ..In combination with our ongoing projects for identifying risk genes of osteoporosis through genome-wide DNA association scan and genome-wide mRNA expression study of osteogenic cells, this study will powerfully and ..
  68. Rebecca A Simmons; Fiscal Year: 2016
    ..In addition to testing the expression and DNA methylation of imprinted genes, we will assay genome-wide DNA methylation changes and key histone modifications in ..
  69. Chou Zen Giam; Fiscal Year: 2014
    ..They, however, develop dramatic nuclear abnormalities in the form of multinucleation and DNA aneuploidy...
  70. ERIC KIRK LAU; Fiscal Year: 2014
    ..Specifically how PKCepsilon phosphorylation affects the transcriptional and non-transcriptional DNA damage response functions of ATF2 is not known...
  71. Betty L Slagle; Fiscal Year: 2014
    ..The role of HBV in mediating carcinogenesis is complex and includes integration of viral DNA into host chromosomes, the host immune system, and expression of the viral regulatory HBx protein...
  72. Patrick Cahan; Fiscal Year: 2016
    ..Louis, where he investigated the functional consequences of DNA copy number variation in hematopoietic stem and progenitors...
  73. Dual-Receptor Targeted Nanoparticles for Photodynamic Therapy of Brain Cancer
    Ann Marie Broome; Fiscal Year: 2013
    ..the mechanism of Pc 4-mediated programmed cell death using a mitochondrial membrane potential assay, TUNEL and DNA fragmentation assays, and cell permeability assays, including trypan blue staining and Annexin V/ propidium iodide ..
  74. Epigenetic downregulation of the antibody response and inhibition of autoimmunity
    Paolo Casali; Fiscal Year: 2013
    ..of the antibody response and inhibition of autoimmunity Epigenetic marks (including histone modifications, DNA methylation and microRNAs) "interact" with genetic programs to regulate B cell functions, such as class switch DNA ..
  75. Claire Larmonier; Fiscal Year: 2014
    ..polymerases (PARPs) constitute a family of 18 cell signaling enzymes, which are involved in the regulation of DNA-binding proteins and DNA repair...
  76. Jeanette Gowen Cook; Fiscal Year: 2016
    DESCRIPTION (provided by applicant): Timely, complete, and precise DNA replication followed by accurate chromosome segregation is critical for controlling cell proliferation and genome stability...
  77. Leena A Hilakivi-Clarke; Fiscal Year: 2015
    ..In addition, we will investigate whether these transgenerational effects involve changes in DNA methylation...
  78. Paul M Lieberman; Fiscal Year: 2016
    ..EBNA1 is a multifunctional, sequence-specific DNA-binding protein that regulates viral DNA replication, episome maintenance, metaphase chromosome tethering, and ..
  79. The role of LKB1 in the maintenance of genomic stability.
    Zhi Xiang Xu; Fiscal Year: 2013
    ..We found that LKB1 interacts with ATM, BRCA1, and other DNA damage response (DDR) proteins in vivo...
  80. ANASTACIA GRIEGO; Fiscal Year: 2016
    DESCRIPTION (provided by applicant): Human papillomaviruses (HPVs) are small double-stranded DNA viruses that are highly species specific and possess a strict tropism for squamous epithelium...
  81. ALBERT HONG JAE KIM; Fiscal Year: 2016
    ..expertise in the latest transgenic mouse technology, transcriptome analyses, and methodologies to study protein-DNA interactions, as well as his knowledge of cohesion biology will provide the candidate with the research tools ..
  82. David M Lyons; Fiscal Year: 2014
    ..e., increased DNA methylation) and thereby increases anticipatory impulsivity. Specifically, we address the following three aims...
  83. Alexandra M Machikas; Fiscal Year: 2014
    ..First, an evaluation of all types of cell death will include infarct assessment using TTC TUNEL staining, DNA laddering, and western blotting for protein markers of cell death signaling pathways...
  84. Mitzi Nagarkatti; Fiscal Year: 2015
    ..of proinflammatory Th1/Th17cells and induction of T regs/Th2 cells via epigenetic regulatory mechanisms such as DNA methylation and miRNA dysregulation that block neuroinflammation...
  85. JASON MARK BECKTA; Fiscal Year: 2014
    ..ATM, a serine-threonine kinase, plays a major role in many intracellular signaling networks, such as the DNA damage response...
  86. Conrad Alano; Fiscal Year: 2016
    ..of reactive oxygen species (ROS) like superoxide and peroxynitrite, and is a principal factor in the damage to DNA that occurs in ischemic stroke. Therefore, regulation of ROS production is a key target for ischemic stroke therapy...
  87. Ke Jian Liu; Fiscal Year: 2016
    ..It is becoming increasingly appreciated that low and non-cytotoxic concentrations of arsenic can amplify the DNA damaging and carcinogenic potential of other genotoxic agents such as ultraviolet radiation, at least in part, ..
  88. Jac A Nickoloff; Fiscal Year: 2016
    DESCRIPTION (provided by applicant): Most cancer patients receive radio- and/or chemotherapy that causes DNA damage, which blocks DNA replication...
  89. Howard E Gendelman; Fiscal Year: 2016
    ..First, we seek to maximize viral clearance (measured reduction of integrated viral DNA) by developing a range of antiretroviral nanoformulated drugs used alone or in combination...
  90. Regulation of the VDJ recombinase during genotoxic stress
    Karla K Rodgers; Fiscal Year: 2013
    ..localization of the V(D)J recombinase is regulated during genotoxic stress, and if this correlates with reduced DNA cleavage activity...
  91. Transcriptional Control by the Global Regulator Spx
    PETER A ZUBER; Fiscal Year: 2013
    ..Its mechanism of control is unique in that free Spx does not exhibit DNA-binding activity, but when bound to RNA polymerase (RNAP) in its oxidized disulfide form, it directs the enzyme to ..
  92. Gerald Shadel; Fiscal Year: 2016
    ..g. muscle, nerves, and major organs such as heart and brain). Mitochondria contain a DNA genome (mtDNA), which in humans encodes thirteen essential protein components of the mitochondrial OXPHOS complexes ..
  93. Kinga Szigeti; Fiscal Year: 2014
    ..Subjects consented to genetic testing and DNA was extracted and banked. The protocol will be amended with the olfactory phenotyping...
  94. David A Sinclair; Fiscal Year: 2016
    ..SIRT1 is the best studied. Major processes controlled by SIRT1 include DNA repair, protein folding, fatty acid and glucose metabolism, hypoxic responses, autophagy, and anti-apoptotic ..
  95. Carl W White; Fiscal Year: 2015
    ..SM analog CEES (2-chloroethyl ethylsulfide) caused inflammation, DNA damage (8-hydroxydeoxy-guanosine accumulation;comet assay;ATM/ATR activation and downstream signaling) and lipid ..
  96. Luzhe Sun; Fiscal Year: 2016
    ..be tested for this specific aim is that the transforming activity of BPA may be more evident in combination with a DNA damaging agent such as ionizing radiation, which is a known risk factor for breast cancer...
  97. Maria Lauda Tomasi; Fiscal Year: 2016
    ..such as signal transduction, stress responses, cellular trafficking, protein-protein interactions, protein-DNA interactions and transcriptional activity...