nucleotides

Summary

Summary: The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)

Top Publications

  1. pmc Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
    Nucleic Acids Res 41:2073-94. 2013
  2. ncbi RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals
    P D Zamore
    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester 01655, USA
    Cell 101:25-33. 2000
  3. ncbi Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
    B C Meyers
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Plant J 20:317-32. 1999
  4. pmc Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide
    Shijun Mi
    National Institute of Biological Sciences, No 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
    Cell 133:116-27. 2008
  5. ncbi Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family
    Brad W Porter
    Department of Molecular Biosciences and Bioengineering, University of Hawai i at Manoa, Honolulu, HI 96822, USA
    Mol Genet Genomics 281:609-26. 2009
  6. ncbi Quantitative trait loci mapped to single-nucleotide resolution in yeast
    Adam M Deutschbauer
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 37:1333-40. 2005
  7. pmc ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
    Suzy M Vasa
    Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    RNA 14:1979-90. 2008
  8. pmc Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000325. 2009
  9. ncbi Membrane fusion: five lipids, four SNAREs, three chaperones, two nucleotides, and a Rab, all dancing in a ring on yeast vacuoles
    William Wickner
    Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755 3844, USA
    Annu Rev Cell Dev Biol 26:115-36. 2010
  10. pmc Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
    Thomas D Otto
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 26:1704-7. 2010

Detail Information

Publications361 found, 100 shown here

  1. pmc Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20984, USA
    Nucleic Acids Res 41:2073-94. 2013
    ..Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions...
  2. ncbi RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals
    P D Zamore
    Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester 01655, USA
    Cell 101:25-33. 2000
    ..During the RNAi reaction, both strands of the dsRNA are processed to RNA segments 21-23 nucleotides in length. Processing of the dsRNA to the small RNA fragments does not require the targeted mRNA...
  3. ncbi Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily
    B C Meyers
    Department of Vegetable Crops, University of California, Davis 95616, USA
    Plant J 20:317-32. 1999
    ..Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins...
  4. pmc Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5' terminal nucleotide
    Shijun Mi
    National Institute of Biological Sciences, No 7 Science Park Road, Zhongguancun Life Science Park, Beijing 102206, China
    Cell 133:116-27. 2008
    ..This suggests that specialization of AGO complexes might involve remodeling the 5' end-binding pocket to accept certain small RNA sequences, perhaps explaining the evolutionary drive for miRNAs to initiate with uridine...
  5. ncbi Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family
    Brad W Porter
    Department of Molecular Biosciences and Bioengineering, University of Hawai i at Manoa, Honolulu, HI 96822, USA
    Mol Genet Genomics 281:609-26. 2009
    ..Looking forward, the papaya NBS gene family is uniquely small in size but structurally diverse, making it suitable for functional studies aimed at a broader understanding of plant resistance genes...
  6. ncbi Quantitative trait loci mapped to single-nucleotide resolution in yeast
    Adam M Deutschbauer
    Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Genet 37:1333-40. 2005
    ..Our results provide the highest resolution to date of the molecular basis of a quantitative trait, showing that the interaction of a few genetic variants can have a profound phenotypic effect...
  7. pmc ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
    Suzy M Vasa
    Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    RNA 14:1979-90. 2008
    ..capillary electrophoresis and typically yields quantitative nucleotide flexibility information for 300-650 nucleotides (nt) per experiment...
  8. pmc Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics
    Barry J Grant
    Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California San Diego, La Jolla, California, United States of America
    PLoS Comput Biol 5:e1000325. 2009
    ....
  9. ncbi Membrane fusion: five lipids, four SNAREs, three chaperones, two nucleotides, and a Rab, all dancing in a ring on yeast vacuoles
    William Wickner
    Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755 3844, USA
    Annu Rev Cell Dev Biol 26:115-36. 2010
    ....
  10. pmc Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
    Thomas D Otto
    Parasite Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
    Bioinformatics 26:1704-7. 2010
    ..Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome ..
  11. pmc Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models
    Andreas Zwick
    Department of Entomology, State Museum of Natural History, Stuttgart, Germany
    PLoS ONE 7:e47450. 2012
    ..This study investigates the cause of that discrepancy...
  12. pmc Cryptic variation in the human mutation rate
    Alan Hodgkinson
    Centre for the Study of Evolution, School of Life Sciences, University of Sussex, Brighton, United Kingdom
    PLoS Biol 7:e1000027. 2009
    ..However, although this variation in the mutation rate is not associated with the adjacent nucleotides, we show that there are highly nonrandom patterns of nucleotides that extend approximately 80 base pairs on ..
  13. ncbi Development of polyphosphate parameters for use with the AMBER force field
    Kristin L Meagher
    Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church St, Ann Arbor, Michigan 48109 1065, USA
    J Comput Chem 24:1016-25. 2003
    ..These parameters are intended for use with the existing AMBER 94/99 force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems...
  14. ncbi Dietary nucleotides and early growth in formula-fed infants: a randomized controlled trial
    Atul Singhal
    Institute of Child Health, Medical Research Council Childhood Nutrition Research Center, 30 Guilford St, London WC1N 3EH, United Kingdom
    Pediatrics 126:e946-53. 2010
    Dietary nucleotides are nonprotein nitrogenous compounds that are found in high concentrations in breast milk and are thought to be conditionally essential nutrients in infancy...
  15. ncbi A new class of bacterial RNA polymerase inhibitor affects nucleotide addition
    Irina Artsimovitch
    Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA
    Science 302:650-4. 2003
    ..We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix...
  16. ncbi Extracellular nucleotides block bone mineralization in vitro: evidence for dual inhibitory mechanisms involving both P2Y2 receptors and pyrophosphate
    Isabel R Orriss
    Department of Anatomy and Developmental Biology, University College London, London WC1E 6BT, United Kingdom
    Endocrinology 148:4208-16. 2007
    Extracellular nucleotides, signaling through P2 receptors, may act as local regulators of bone cell function...
  17. ncbi The role of dietary nucleotides in reduction of DNA damage induced by T-2 toxin and deoxynivalenol in chicken leukocytes
    T Frankic
    Institute of Nutrition, Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230 Domzale, Slovenia
    Food Chem Toxicol 44:1838-44. 2006
    ..in spleen leukocytes and oxidative stress in chickens, and furthermore, to evaluate the potential of dietary nucleotides in reduction of toxin-induced DNA damage...
  18. pmc TRPM7 channel is regulated by magnesium nucleotides via its kinase domain
    Philippe Demeuse
    Laboratory of Cell and Molecular Signaling, Center for Biomedical Research at The Queen s Medical Center and John A Burns School of Medicine at the University of Hawaii, Honolulu, 96813, USA
    J Gen Physiol 127:421-34. 2006
    ..To obtain insight into these issues, we have determined the effect of purine and pyrimidine magnesium nucleotides on TRPM7 currents and investigated the possible involvement of the channel's kinase domain in mediating them...
  19. ncbi The role of nucleotides in the immune and gastrointestinal systems: potential clinical applications
    Jennifer R Hess
    Nestle Nutrition R and D Centers, Minnetonka, MN 55343, USA
    Nutr Clin Pract 27:281-94. 2012
    b>Nucleotides are low molecular weight biological molecules key to biochemical processes. Sources include de novo synthesis, recovery via salvage mechanisms, and dietary intakes...
  20. ncbi The regulation of osteoblast function and bone mineralisation by extracellular nucleotides: The role of p2x receptors
    Isabel R Orriss
    Department of Cell and Developmental Biology, University College London, London, UK
    Bone 51:389-400. 2012
    Extracellular nucleotides, signalling through P2 receptors, regulate the function of both osteoblasts and osteoclasts...
  21. pmc Virtual terminator nucleotides for next-generation DNA sequencing
    Jayson Bowers
    Helicos BioSciences Corporation, Cambridge, Massachusetts, USA
    Nat Methods 6:593-5. 2009
    ..These were efficiently incorporated with high fidelity while preventing incorporation of additional nucleotides, and we used them to sequence canine bacterial artificial chromosomes in a single-molecule system that provided ..
  22. pmc Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle
    Chandar S Thakur
    Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences Bldg 296, College Park, MD 20742 3360, USA
    J Biomol NMR 48:179-92. 2010
    Escherichia coli (E. coli) is an ideal organism to tailor-make labeled nucleotides for biophysical studies of RNA. Recently, we showed that adding labeled formate enhanced the isotopic enrichment at protonated carbon sites in nucleotides...
  23. ncbi Progressive loss of mitochondrial DNA in thymidine kinase 2-deficient mice
    Xiaoshan Zhou
    Department of Laboratory Medicine, Karolinska Institute, S 141 86 Huddinge, Sweden
    Hum Mol Genet 17:2329-35. 2008
    ..We conclude that Tk2 has a major role in supplying deoxyribonucleotides for mtDNA replication and that other pathways of deoxyribonucleotide synthesis cannot compensate for loss of this enzyme...
  24. ncbi Osteoblast responses to nucleotides increase during differentiation
    Isabel R Orriss
    Department of Anatomy and Developmental Biology, University College London, London WC1E 6BT, UK
    Bone 39:300-9. 2006
    Accumulating evidence suggests that extracellular nucleotides, signaling through P2 receptors, play a role in modulating bone cell function...
  25. pmc Diversity in nucleotide binding site-leucine-rich repeat genes in cereals
    Jianfa Bai
    Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506 5502, USA
    Genome Res 12:1871-84. 2002
    ..The resistance gene repertoire of grasses has changed from that of dicots in their independent evolution since the two groups diverged. It is not clear whether this reflects a difference in downstream defense signaling pathways...
  26. pmc Using progenitor strain information to identify quantitative trait nucleotides in outbred mice
    B Yalcin
    Wellcome Trust Centre for Human Genetics, Oxford University, UK
    Genetics 171:673-81. 2005
    ....
  27. pmc Identification and characterization of endogenous small interfering RNAs from rice
    Ramanjulu Sunkar
    Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, 2150 Batchelor Hall, University of California, Riverside, CA 92521, USA
    Nucleic Acids Res 33:4443-54. 2005
    ..Using RNA ligase-mediated-5' rapid amplification of cDNA end assays, we validated three of the predicted targets and provided evidence for both cis- and trans-silencing of target genes by siRNAs-guided mRNA cleavage...
  28. ncbi Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs
    Z Kiss-László
    Laboratorie de Biologie Moléculaire Eucaryote du CNRS, Toulouse, France
    Cell 85:1077-88. 1996
    ..The conclusion that sno-RNAs function in covalent modification of the sugar moieties of ribonucleotides demonstrates that eukaryotic small nuclear RNAs have a more versatile cellular function than earlier anticipated...
  29. pmc Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis
    Xiaoping Tan
    The Genome Center, University of California, Davis, California 95616, USA
    BMC Plant Biol 7:56. 2007
    ..8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes...
  30. ncbi Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication
    Xiaohui Zhang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    Mol Genet Genomics 285:79-90. 2011
    ..It is important to determine the exact relative evolutionary rates of TNL, non-TNL, and non-NBS genes in order to understand how fast the host plant can adjust its response to rapidly evolving pathogens in a coevolutionary context...
  31. ncbi tRNA stabilization by modified nucleotides
    Yuri Motorin
    Laboratoire ARN RNP Maturation Structure Fonction, Enzymologie Moléculaire et Structurale AREMS, UMR 7214 CNRS UHP Faculté des Sciences et Techniques, Universite Henri Poincare, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre les Nancy, France
    Biochemistry 49:4934-44. 2010
    ..Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability...
  32. pmc Structural basis for allosteric regulation of human ribonucleotide reductase by nucleotide-induced oligomerization
    James Wesley Fairman
    Department of Biochemistry, University of Tennessee, Knoxville, TN, USA
    Nat Struct Mol Biol 18:316-22. 2011
    ..Site-directed mutagenesis and functional assays confirm that hexamerization is a prerequisite for inhibition by dATP. Our data indicate a mechanism for regulating RR activity by dATP-induced oligomerization...
  33. pmc Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
    A O Urrutia
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
    Genetics 159:1191-9. 2001
    ..The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans...
  34. pmc Site-specific labeling of DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs
    Young Jun Seo
    Department of Chemistry and Center for Protein and Nucleic Acid Research, The Scripps Research Institute, 10550 N Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 133:19878-88. 2011
    ....
  35. pmc Novel allosteric sites on Ras for lead generation
    Barry J Grant
    Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
    PLoS ONE 6:e25711. 2011
    ..We thus propose that the predicted allosteric sites are viable targets for the development and optimization of new drugs...
  36. pmc Genome-wide identification of NBS-encoding resistance genes in Brassica rapa
    Jeong Hwan Mun
    Genomics Division, Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin ro, Gwonseon gu, Suwon, 441 707, Korea
    Mol Genet Genomics 282:617-31. 2009
    ..Recent tandem duplication and ectopic deletion are likely to have played a role in the generation of novel Brassica lineage-specific resistance genes...
  37. pmc Characterization of an asymmetric occluded state of P-glycoprotein with two bound nucleotides: implications for catalysis
    Alena Siarheyeva
    Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
    J Biol Chem 285:7575-86. 2010
    ..We propose that this asymmetric state with two bound nucleotides represents the next intermediate on the path toward ATP hydrolysis after nucleotide binding, and an alternating ..
  38. pmc Stepwise mechanism for transcription fidelity
    Yulia Yuzenkova
    Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
    BMC Biol 8:54. 2010
    ..A flexible domain of the RNA polymerase active centre, the Trigger Loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive...
  39. pmc Patterns of nucleotide diversity in wild and cultivated sunflower
    Aizhong Liu
    Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
    Genetics 173:321-30. 2006
    ..Taken together, these results suggest that association-based approaches will provide a high degree of resolution for the mapping of functional variation in sunflower...
  40. ncbi AtNUDX1, an 8-oxo-7,8-dihydro-2'-deoxyguanosine 5'-triphosphate pyrophosphohydrolase, is responsible for eliminating oxidized nucleotides in Arabidopsis
    Kazuya Yoshimura
    Department of Food and Nutritional Science, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto cho, Kasugai, Aichi, 487 8501 Japan
    Plant Cell Physiol 48:1438-49. 2007
    Cellular DNA, RNA and their precursor nucleotides are at high risk of being oxidized by reactive oxygen species...
  41. ncbi Transcript-assisted transcriptional proofreading
    Nikolay Zenkin
    Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Science 313:518-20. 2006
    ..We show that during transcription elongation, the hydrolytic reaction stimulated by misincorporated nucleotides proofreads most of the misincorporation events and thus serves as an intrinsic mechanism of transcription ..
  42. pmc Connections between alternative transcription and alternative splicing in mammals
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Genome Biol Evol 2:791-9. 2010
    ..Comparative analysis of the number of alternative nucleotides, isoforms, and introns per locus in genes with different types of alternative events suggests that ATI and ATT ..
  43. ncbi In vivo functional characterization of the Saccharomyces cerevisiae 60S biogenesis GTPase Nog1
    Jennifer L Fuentes
    Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 North University Avenue, Ann Arbor, MI 48109, USA
    Mol Genet Genomics 278:105-23. 2007
    ..Several conserved charge-to-alanine substitutions outside the GTPase domain display modest growth phenotypes indicating that these residues are not critical for function...
  44. ncbi Statistical analysis of atomic contacts at RNA-protein interfaces
    M Treger
    , , , 4 Rue Kirshleger, F-67000 Strasbourg, France
    J Mol Recognit 14:199-214. 2001
    ....
  45. ncbi Peptide-nucleotide microdroplets as a step towards a membrane-free protocell model
    Shogo Koga
    Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
    Nat Chem 3:720-4. 2011
    ....
  46. pmc Loop nucleotides control primary and mature miRNA function in target recognition and repression
    Si Biao Yue
    Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
    RNA Biol 8:1115-23. 2011
    ..We found that pri-let-7 loop nucleotides control the production of the 5' end of mature miRNAs and modulate the activity of the miRNA gene...
  47. ncbi Mechanisms of release of nucleotides and integration of their action as P2X- and P2Y-receptor activating molecules
    Eduardo R Lazarowski
    Department of Pharmacology, University of North Carolina School of Medicine, CB 7365, Chapel Hill, NC 27599, USA
    Mol Pharmacol 64:785-95. 2003
  48. ncbi Unique evolutionary pattern of numbers of gramineous NBS-LRR genes
    Jing Li
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
    Mol Genet Genomics 283:427-38. 2010
    ..In addition, the small proportion of conserved NBSs suggests that the loss of NBSs may be a general tendency in grass species...
  49. ncbi Modulation of the immune response mediated by dietary nucleotides
    A Gil
    Department of Biochemistry and Molecular Biology, University of Granada, Granada, Spain
    Eur J Clin Nutr 56:S1-4. 2002
    Dietary nucleotides have been reportedly beneficial, especially for infants, since they positively influence lipid metabolism, immunity, and tissue growth, development and repair...
  50. ncbi Crystal structures of MEK1 binary and ternary complexes with nucleotides and inhibitors
    Thierry O Fischmann
    Schering Plough Research Institute, Kenilworth, New Jersey 07033, USA
    Biochemistry 48:2661-74. 2009
    ..Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome...
  51. ncbi Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA
    L Aravind
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
    Proteins 48:1-14. 2002
    ..Thus, substantial evolutionary diversification of protein domains occurred well before the modern version of the protein-dependent translation machinery was established, i.e., still in the RNA world...
  52. pmc Structural evidence of a new catalytic intermediate in the pathway of ATP hydrolysis by F1-ATPase from bovine heart mitochondria
    David M Rees
    Medical Research Council Mitochondrial Biology Unit, Cambridge CB2 2XY, United Kingdom
    Proc Natl Acad Sci U S A 109:11139-43. 2012
    ..three states, hydrolyzing three ATP molecules, releasing the products and leaving the enzyme with two bound nucleotides. A transition-state analog structure, F(1)-TS, displays intermediate states between those observed in the ..
  53. ncbi Comparative analysis of NBS domain sequences of NBS-LRR disease resistance genes from sunflower, lettuce, and chicory
    Alex Plocik
    Department of Biology, University of Massachusetts, Boston, MA 02125 3393, USA
    Mol Phylogenet Evol 31:153-63. 2004
    ..These data suggest that NBS families in the Asteraceae family are ancient, but also that gene duplication and gene loss events occur and change the composition of these gene subfamilies over time...
  54. pmc Human branch point consensus sequence is yUnAy
    Kaiping Gao
    Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466 8550, Japan
    Nucleic Acids Res 36:2257-67. 2008
    ..We found that the branch points are located 21-34 nucleotides upstream of the 3' end of an intron in 83% clones...
  55. ncbi Adaptive evolution of non-coding DNA in Drosophila
    Peter Andolfatto
    Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
    Nature 437:1149-52. 2005
    ..I estimate that about 40-70% of nucleotides in intergenic regions, untranslated portions of mature mRNAs (UTRs) and most intronic DNA are evolutionarily ..
  56. pmc Rapid and simple ribozymic aminoacylation using three conserved nucleotides
    N V Chumachenko
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309 0347, USA
    J Am Chem Soc 131:5257-63. 2009
    ..from PheAMP in three cycles, yielding active RNAs (k(cat) = 12-20 min(-1)) using only three conserved nucleotides, acting independently of divalent ions...
  57. pmc Correlating SHAPE signatures with three-dimensional RNA structures
    Eckart Bindewald
    Basic Science Program, SAIC Frederick, Inc, NCI Frederick, Frederick, Maryland 21702, USA
    RNA 17:1688-96. 2011
    ..This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification...
  58. ncbi Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA
    Jesper Foged Havelund
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
    J Mol Biol 411:529-36. 2011
    ..Given the unstable nature of 5-hydroxycytidine, this modification might be found in other RNAs when applying the proper analytical conditions as described here...
  59. pmc Extracellular nucleotides as negative modulators of immunity
    Francesco Di Virgilio
    Department of Experimental and Diagnostic Medicine, Section of General Pathology, University of Ferrara, Italy
    Curr Opin Pharmacol 9:507-13. 2009
    b>Nucleotides are well known for being the universal currency of intracellular energy transactions, but over the past decade it has become clear that they are also ubiquitous extracellular messengers...
  60. pmc Intrinsic flexibility of B-DNA: the experimental TRX scale
    Brahim Heddi
    INSERM UMR S665, INTS, 75015 Paris, France
    Nucleic Acids Res 38:1034-47. 2010
    ..Thus, DNA flexibility captured by the TRX scale is relevant to nucleosome formation, suggesting that this scale may be of general interest to better understand protein-DNA recognition...
  61. pmc Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase?
    Craig E Cameron
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, United States
    Curr Opin Struct Biol 19:768-74. 2009
    ..Here we review some of the recent work with the RdRp that leads us to suggest that structure provides only a partial understanding of RdRp function and dynamics may be the missing link...
  62. ncbi Should immunonutrition become routine in critically ill patients? A systematic review of the evidence
    D K Heyland
    Angada 3, Kingston General Hospital, 76 Stuart St, Kingston, Ontario K7L 2V7, Canada
    JAMA 286:944-53. 2001
    ..Several nutrients have been shown to influence immunologic and inflammatory responses in humans. Whether these effects translate into an improvement in clinical outcomes in critically ill patients remains unclear...
  63. ncbi Extracellular nucleotides mediate LPS-induced neutrophil migration in vitro and in vivo
    Filip Kukulski
    Centre de Recherce en Rhumatologie et Immunologie, Centre Hospitalier Universitaire de Quebec, Universite Laval, 2705, boulevard Laurier, Local T1 49, Quebec, QC, G1V 4G2, Canada
    J Leukoc Biol 81:1269-75. 2007
    Extracellular nucleotides are emerging as important inflammatory mediators. Here, we demonstrate that these molecules mediate LPS-induced neutrophil migration in vitro and in vivo...
  64. pmc Growth of wildtype and mutant E. coli strains in minimal media for optimal production of nucleic acids for preparing labeled nucleotides
    Chandar S Thakur
    Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, 1115 Biomolecular Sciences, Bldg 296, College Park, MD 20742 3360, USA
    Appl Microbiol Biotechnol 88:771-9. 2010
    ..cellular processes, there is a need for synthesizing large amounts of RNAs made from stable isotope-labeled nucleotides to advance the study of their structure and dynamics by nuclear magnetic resonance (NMR) spectroscopy...
  65. ncbi Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS
    S Mariana Margarit
    Department of Molecular Genetics and Microbiology, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
    Cell 112:685-95. 2003
    ..These results demonstrate the existence of a positive feedback mechanism for the spatial and temporal regulation of Ras...
  66. ncbi Hydrophobicity, shape, and pi-electron contributions during translesion DNA synthesis
    Xuemei Zhang
    Departments of Pharmacology and Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    J Am Chem Soc 128:143-9. 2006
    ..However, the kinetic dissociation constants for the non-natural nucleotides are identical and indicate that pi-electron density does not directly influence ground-state binding opposite ..
  67. ncbi Optimization of non-natural nucleotides for selective incorporation opposite damaged DNA
    Diana Vineyard
    Department of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
    Org Biomol Chem 5:3623-30. 2007
    ..Kinetic analyses indicate that the overall catalytic efficiencies of all four nucleotides are related to their base-stacking properties...
  68. ncbi The hydrolysis of lysophospholipids and nucleotides by autotaxin (NPP2) involves a single catalytic site
    Rik Gijsbers
    Afdeling Biochemie, Faculteit Geneeskunde, University of Leuven, Herestraat 49, B 3000 Leuven, Belgium
    FEBS Lett 538:60-4. 2003
    ..The hydrolysis of nucleotides is a metal-assisted reaction that occurs via a nucleotidylated threonine in the catalytic site...
  69. pmc A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution
    Scott L Cockroft
    Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 130:818-20. 2008
    ..The system described thus represents a promising advance toward nanopore-mediated single-molecule DNA sequencing concept and, in addition, might be applicable to studying a number of other biopolymer-protein interactions and dynamics...
  70. pmc Structure of human DNA polymerase kappa inserting dATP opposite an 8-OxoG DNA lesion
    Rodrigo Vasquez-Del Carpio
    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY, USA
    PLoS ONE 4:e5766. 2009
    ....
  71. ncbi Sensitivity of the yeast mitochondrial RNA polymerase to +1 and +2 initiating nucleotides
    Elizabeth A Amiott
    Department of Biochemistry and Molecular Genetics and the Program in Molecular Biology, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado 80045, USA
    J Biol Chem 281:34982-8. 2006
    ..We asked how changes in the initiating (+1 and +2) nucleotides, conformation of the promoter DNA template, and mutation of the mitochondrial RNA polymerase (mtRNAP) affect ..
  72. pmc Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis
    Dong Wang
    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
    Cell 127:941-54. 2006
    ..A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription...
  73. ncbi Application of tetranucleotide frequencies for the assignment of genomic fragments
    Hanno Teeling
    Department of Molecular Ecology, Genomics Group, Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Environ Microbiol 6:938-47. 2004
    ....
  74. ncbi Substrate complexes of hepatitis C virus RNA polymerase (HC-J4): structural evidence for nucleotide import and de-novo initiation
    Damien O'Farrell
    Astbury Centre of Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
    J Mol Biol 326:1025-35. 2003
    ..The apo-polymerase structure provides unprecedented insights into potential non-nucleoside inhibitor binding sites located between palm and thumb near motif E, which is unique to RNA polymerases and reverse transcriptases...
  75. pmc Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles
    Michal Mokry
    Cancer Genomics Center, Department of Medical Genetics, Hubrecht Institute and University Medical Center Utrecht, Utrecht, The Netherlands
    PLoS ONE 5:e15092. 2010
    ..Although optimized for the AB/SOLiD platform, the same approach may be applied to other platforms...
  76. pmc Mammalian ribonucleotide reductase subunit p53R2 is required for mitochondrial DNA replication and DNA repair in quiescent cells
    Giovanna Pontarin
    Department of Biology, University of Padova, I 35131 Padua, Italy
    Proc Natl Acad Sci U S A 109:13302-7. 2012
    ..Supplementation by deoxynucleosides improved DNA repair. Our results show that in nontransformed cells only during quiescence, protein p53R2 is required for maintenance of mtDNA and for optimal DNA repair after UV damage...
  77. pmc Stable tRNA-based phylogenies using only 76 nucleotides
    Jeremy Widmann
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    RNA 16:1469-77. 2010
    ....
  78. pmc Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity
    Ibrahim M Moustafa
    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
    J Mol Biol 410:159-81. 2011
    ..A role for nanosecond timescale dynamics in RdRp fidelity is supported by the altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme...
  79. pmc ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle
    David M Smith
    Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
    Cell 144:526-38. 2011
    ..To clarify the role of ATP in proteolysis, we studied how nucleotides bind to PAN...
  80. ncbi Enzymatic incorporation of LNA nucleotides into DNA strands
    Rakesh N Veedu
    Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Chembiochem 8:490-2. 2007
  81. ncbi Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides
    Jing Song Fan
    Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
    J Mol Biol 388:1-10. 2009
    ..ScDbp5p) and X-ray crystal structure of Dbp5p from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA...
  82. pmc Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine
    Steven E Glynn
    Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 139:744-56. 2009
    ....
  83. pmc The effects of nucleoside analogs on telomerase and telomeres in Tetrahymena
    C Strahl
    Department of Microbiology and Immunology, University of California San Francisco 94143 0414
    Nucleic Acids Res 22:893-900. 1994
    ..However, AZT decreased the efficiency of programmed de novo telomere addition during macronuclear development in mating cells...
  84. ncbi Impact of the deltaF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure
    Hal A Lewis
    Structural GenomiX, Inc, San Diego, California 92121, USA
    J Biol Chem 280:1346-53. 2005
    ....
  85. ncbi The functions and consensus motifs of nine types of peptide segments that form different types of nucleotide-binding sites
    T W Traut
    Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill 27599 7260
    Eur J Biochem 222:9-19. 1994
    ..g. transfer of the gamma-phosphate, or of the adenylate to an acceptor) and also with a particular spatial arrangement of the three Kinase segments evident in the linear sequence for the protein...
  86. pmc Processing mutations disrupt interactions between the nucleotide binding and transmembrane domains of P-glycoprotein and the cystic fibrosis transmembrane conductance regulator (CFTR)
    Tip W Loo
    Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
    J Biol Chem 283:28190-7. 2008
    ..These results suggest that establishment of NBD interactions with the opposite TMD is a key step in folding of ABC transporters...
  87. pmc Profiling of mismatch discrimination in RNAi enabled rational design of allele-specific siRNAs
    Huang Huang
    Institute of Molecular Medicine, Peking University, Beijing 100871, China
    Nucleic Acids Res 37:7560-9. 2009
    ..In summary, these findings could dramatically simplify the design of allele-specific siRNAs and might also provide guide to increase the specificity of therapeutic siRNAs...
  88. ncbi Structural basis for substrate loading in bacterial RNA polymerase
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, Alabama 35294, USA
    Nature 448:163-8. 2007
    ..Second, freezing of the preinsertion state is an attractive target for the design of novel antibiotics. Last, the TL emerges as a prominent target whose refolding can be modulated by regulatory factors...
  89. pmc Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase
    Guobin Luo
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 104:12610-5. 2007
    ..The high level of selectivity of incoming dNTPs pertinent to this conformational change is a major contributor to replicative fidelity...
  90. ncbi Solubilizing mutations used to crystallize one CFTR domain attenuate the trafficking and channel defects caused by the major cystic fibrosis mutation
    Luísa S Pissarra
    Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, 1749 016 Lisboa, Portugal
    Chem Biol 15:62-9. 2008
    ..Thus, the available crystal structure of F508del-NBD1 might correspond to a partially corrected conformation of this domain...
  91. pmc Molecular evolution of regulatory genes in spruces from different species and continents: heterogeneous patterns of linkage disequilibrium and selection but correlated recent demographic changes
    Marie Claire Namroud
    Arborea and Canada Research Chair in Forest and Environmental Genomics, Forest Research Centre and Institute for Systems and Integrative Biology, Universite Laval, Quebec, QC G1V 0A6, Canada
    J Mol Evol 70:371-86. 2010
    ..Such different signatures indicate differential subfunctionalization of gene family members in the three congeneric species...
  92. ncbi PHAPI, CAS, and Hsp70 promote apoptosome formation by preventing Apaf-1 aggregation and enhancing nucleotide exchange on Apaf-1
    Hyun Eui Kim
    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
    Mol Cell 30:239-47. 2008
    ..These studies indicated that PHAPI, CAS, and Hsp70 play an important regulatory role during apoptosis...
  93. pmc Mutational analysis of the influenza virus cRNA promoter and identification of nucleotides critical for replication
    Mandy Crow
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom
    J Virol 78:6263-70. 2004
    ..Moreover, nucleotides in the tetraloop at positions 4, 5, and 7 and nucleotides forming the 2-9 base pair of the 3' hairpin loop were ..
  94. pmc Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DinB-like DNA polymerase with lesion-bypass properties akin to eukaryotic poleta
    F Boudsocq
    Section on DNA Replication, Repair and Mutagenesis, National Institute of Child Health and Human Development, National Institutes of Health, MD 20892 2725, USA
    Nucleic Acids Res 29:4607-16. 2001
    ..Thus, although phylogenetically related to DinB polymerases, our studies suggest that the archaeal Dpo4 enzyme exhibits lesion-bypass properties that are, in fact, more akin to those of eukaryotic poleta...
  95. ncbi Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision
    A Y Lau
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Cell 95:249-58. 1998
    ..The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone...
  96. pmc Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity
    Etienne Decroly
    Architecture et Fonction des Macromolecules Biologiques, CNRS and Universités d Aix Marseille I et II, UMR 6098, ESIL case 925, 13288 Marseille, France
    J Virol 82:8071-84. 2008
    ....
  97. ncbi Nucleotide binding to DNA gyrase causes loss of DNA wrap
    Jonathan G Heddle
    Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK
    J Mol Biol 337:597-610. 2004
    ....
  98. ncbi Towards a structural classification of phosphate binding sites in protein-nucleotide complexes: an automated all-against-all structural comparison using geometric matching
    Andreas Brakoulias
    Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, England
    Proteins 56:250-60. 2004
    ..Similar classification schemes for nucleotide binding proteins have also been arrived at independently by others using different methods...
  99. pmc DNA polymerases provide a canon of strategies for translesion synthesis past oxidatively generated lesions
    Karl E Zahn
    Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
    Curr Opin Struct Biol 21:358-69. 2011
    ....
  100. ncbi The search for a potentially prebiotic synthesis of nucleotides via arabinose-3-phosphate and its cyanamide derivative
    Carole Anastasi
    School of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
    Chemistry 14:2375-88. 2008
    ..Conceptually, the simplest route to RNA involves nucleotide polymerisation. Activated pyrimidine nucleotides can be derived from arabinose-3-phosphate under potentially prebiotic conditions, but the prebiotic synthesis ..
  101. pmc New insights regarding the regulation of chemotaxis by nucleotides, adenosine, and their receptors
    Ross Corriden
    Institute of Cell Signalling, University of Nottingham, Nottingham, UK
    Purinergic Signal 8:587-98. 2012
    The directional movement of cells can be regulated by ATP, certain other nucleotides (e.g., ADP, UTP), and adenosine. Such regulation occurs for cells that are "professional phagocytes" (e.g...

Research Grants73

  1. 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. ..
  2. Gamma-Synuclein-Mediated Regulation of Norepinephrine Transporter
    Anita Sidhu; Fiscal Year: 2010
    ..Nylon membranes will be slot-blotted with 2.5 g of cDNA sequences encoding -Syn (nucleotides 49-432 of cDNA), or -actin (nucleotides 50-545 of cDNA), in separate wells...
  3. DNA methylation of extracellular superoxide dismutase in pulmonary hypertension
    EVA NOZIK GRAYCK; Fiscal Year: 2012
    ..including cytosine methylation within the promoter region, specifically cytosines adjacent to guanosine nucleotides (CpG islands)...
  4. Hydrodynamic forces modulate renal tubular function
    Rajeev Rohatgi; Fiscal Year: 2012
    ..In microperfused cortical CD (CCD), intercalated cells (ICs) release a greater concentration of nucleotides than principal cells (PCs), suggesting the apical cilium is not required for flow-induced nucleotide release...
  5. NITROGEN HETEROCYCLES: METABOLIC EFFECTS AND TOXICITY
    Raymond F Novak; Fiscal Year: 2010
    ..In contrast, glucagon antagonizes insulin effects through cyclic nucleotides and PKA...
  6. Folate Status, Genomic Uracil, and the Balance of Base Excision Repair Activity
    Michael D Wyatt; Fiscal Year: 2011
    ..At a biochemical level, folate derivatives are important sources of one-carbon units for de novo synthesis of nucleotides and are necessary for enzymatic methylation of CpG sequences for gene silencing...
  7. Novel Collagen II Alternative Transcripts and Mouse Skeletal Development
    Audrey McAlinden; Fiscal Year: 2010
    ..IIC mRNA contains only the first 34 nucleotides of exon 2 by use of an alternative splice site in exon 2 resulting in a premature termination codon...
  8. Regulation of IFN-beta induction by P2X7 purinergic receptor signaling
    JUDITH ANNE SMITH; Fiscal Year: 2011
    ..During inflammation, the occurrence of tissue damage leads to sufficient release of extracellular purine nucleotides to stimulate immune cells via purinergic receptors such as P2X7...
  9. Vitamin B6 Effects on One-Carbon Metabolism
    Jesse F Gregory; Fiscal Year: 2013
    ..Thus, B6 nutrition is linked many vital cellular processes such as the synthesis of nucleotides and glutathione, metabolism of most amino acids, including sulfur amino acids, methylation processes, and ..
  10. Myosin phosphatase autoinhibition in gastrointestinal smooth muscle contraction
    Avril V Somlyo; Fiscal Year: 2012
    ..Cyclic nucleotides are well established as physiologically important mediators of relaxation in GI SM...
  11. Analogs of GTP as novel inhibitors of bacterial c-di-GMP-synthesizing enzymes
    George E Wright; Fiscal Year: 2010
    ..We will capitalize on the applicant's background in synthesis and study of guanine nucleotides as inhibitors/alternate substrates of nucleic acid metabolizing enzymes and that of our subcontractor in ..
  12. Delineation of the molecular mechanisms underlying group A Streptococcus virulenc
    Paul Sumby; Fiscal Year: 2013
    ..iii) Specific nucleotides within FASX are required for activity...
  13. microRNA mediation of Endothelial Progenitor Cell function in Myocardial Ichemia
    Prasanna Krishnamurthy; Fiscal Year: 2013
    ..MicroRNAs (miRNA;20-25 nucleotides), are known to regulate several cellular processes such as proliferation, differentiation, cell metabolism, ..
  14. Regulation of Rhox5 Transcriptional Elongation
    Marcy E Richardson; Fiscal Year: 2013
    ..Pol) II is recruited to the Pp and short mRNAs are generated, but transcription does not propagate beyond ~100 nucleotides. Several lines of preliminary evidence suggest that escape from this transcriptional elongation block requires ..
  15. Fnip1 Function in Lymphocyte Development, Activation and Metabolism
    Brian M Iritani; Fiscal Year: 2013
    ..produces energy, to aerobic glycolysis, which generates bio-precursors (such as lipids, amino acids, and nucleotides) required to fuel cell division...
  16. RNA polymerase II Elongation Complex: Structure and Function
    Daniel Reines; Fiscal Year: 2013
    ..Regulation of this gene by nucleotides is seen in organisms from yeast to humans and IMP dehydrogenase is a biomedically important enzyme...
  17. Investigation on Oligosaccharides as Antimicrobial and Prebiotics
    Peng George Wang; Fiscal Year: 2013
    ..pathway where oligosaccharides are assembled together by specific glycosyltransferases using individual sugar nucleotides as building blocks...
  18. HYPOXIA AND CONTROL OF FETAL BREATHING MOVEMENTS
    Brian J Koos; Fiscal Year: 2010
    Extracellular adenine nucleotides, central adenosine (ADO) A2A receptors, and the parafascicular nuclear complex (Pf) of the thalamus are crucially involved in hypoxic inhibition of fetal breathing (FB)...
  19. MECHANISM AND CONTROL OF UREA BIOSYNTHESIS
    Frank M Raushel; Fiscal Year: 2011
    ..enzyme found in all organisms where it catalyzes the first committed step in the biosynthesis of pyrimidine nucleotides and in the detoxification of ammonia via the urea cycle...
  20. Purinergic Regulation of Bone Metabolism
    Bruce Neil Cronstein; Fiscal Year: 2013
    ..generation during bone remodeling using animals deficient in the enzymes that convert extracellular adenine nucleotides to adenosine (NPP-1, TNAP, CD39 and CD73)...
  21. Genetic toxicology of purine metabolism
    Peter C Dedon; Fiscal Year: 2010
    ..studies rely on sensitive analytical methodology to quantify the deamination products in nucleic acids and nucleotides in purine metabolism mutants...
  22. Redox Regulation of Kv Channels
    SRINIVAS TIPPARAJU; Fiscal Year: 2013
    ..We propose that the binding of pyridine nucleotides to the AKR domain of the 2-subunit imparts metabolic sensitivity to Kv channels, such that an increase in the ..
  23. Purinergic signaling in sleep apnea
    Elzbieta Kaczmarek; Fiscal Year: 2012
    ..We have recent evidence that extracellular nucleotides, such as ATP, ADP and UTP, acting via specific P2 purinergic receptors, decrease high glucose- induced ROS ..
  24. Regulation of guanylyl cyclase A and B by hormones, ATP and phosphorylation
    Lincoln Ross Potter; Fiscal Year: 2013
    ..Adenine nucleotides regulate GC-A and GC-B by binding unidentified intracellular high affinity activation and low affinity ..
  25. MicroRNA-21 in Renal Aging
    Markus Bitzer; Fiscal Year: 2012
    ..microRNAs (miRs), are small RNA molecules (19-22 nucleotides long) that coordinate pathways of gene expression via partial complementary to target mRNAs...
  26. DNA METHYLOME STUDY IN TYPE 1 DIABETES
    ART PETRONIS; Fiscal Year: 2009
    ..Our effort will be dedicated to a detailed DNA methylation analysis of several million nucleotides that surround the insulin gene...
  27. Regulation of Tumor Metabolism by Retinoblastoma Protein
    Brian F Clem; Fiscal Year: 2013
    ..and glutamine consumption required for increased energy production and to drive the de novo biosynthesis of nucleotides, amino acids, and lipids essential for cell division...
  28. Kinetics of DNA polymerase gamma upon mutation and nucleoside analog exposure
    CHRISTAL DYANE SOHL; Fiscal Year: 2013
    ..the steps in the catalytic cycle including the nucleotide incorporation efficiency, the affinity for incoming nucleotides and the DNA template, and the overall fidelity...
  29. Determinants of Telomere Length in Chronic SCI: A Pilot Study
    Eric Garshick; Fiscal Year: 2012
    DESCRIPTION (provided by applicant): Telomeres are made up of repeat sequences of nucleotides at the ends of human chromosomes...
  30. Role of Non-Core RAG1 in DSB Repair, Cell Survival, and Cell Cycle Progression
    Julie Horowitz; Fiscal Year: 2013
    ..histones and interact with the additional ubuitylating enzymes to prevent aberrant deletion and/or insertion of nucleotides during repair of RAG-mediated DSBs...
  31. Molecular and functional properties of the TRPM2 catioin channel
    Reinhold Penner; Fiscal Year: 2010
    ..propose experiments in Specific Aim 1 that will focus on the function of TRPM2 in events initiated by adenine-nucleotides. We hypothesize that TRPM2 may function as dual calcium influx and calcium release channel by taking advantage ..
  32. MRP4 extrudes cAMP for localized regulation of calcium channel activity
    OLIVIA RUTH BUONARATI; Fiscal Year: 2013
    ..MRP4 is implicated in the transport of cyclic nucleotides and xenobiotic molecules at the blood-brain barrier, yet its role in neuronal activity remains unknown...
  33. Insulin Clearance: Candidate and Positional Genetic Determinants
    MARK GOODARZI; Fiscal Year: 2012
    ..Thus, the hypothesis underlying this proposal is that genes involved in the interconversion of adenine nucleotides (AMP, ADP, ATP) and cellular response to these molecules (AMPK system) are determinants of insulin clearance...
  34. Cell Models for Alzheimer's disease (AD): Lipids and Related Signaling Pathways
    Grace Y Sun; Fiscal Year: 2012
    ..of neuronal functions;(2) chronic inflammation in AD is mediated by P2Y2 receptors (P2Y2Rs) for cytokine-like nucleotides in astrocytes and cerebral microvessels through transactivation of integrins and growth factor receptors, and ..
  35. High Specificity HIV-1 Markers Predictive of Neuro-AIDS
    Brian Wigdahl; Fiscal Year: 2013
    ..from a large well studied HIV-1- infected cohort using bioinformatic tools to examine SNPs at any of the 634 nucleotides of the HIV-1 LTR, within the HIV-1 gp120, or within the HIV-1 gp41, (3) construct a parallel PCR product ..
  36. Intra- and Extra-Chromosomal Probes for Mutagenesis by Carcinogens
    John M Essigmann; Fiscal Year: 2013
    ..Genomes of viruses and plasmids will be re-engineered to contain gaps (e.g., 16 nucleotides) at specific sites...
  37. C. trachomatis-mediated signaling pathways required for Type I IFN responses
    JEFFREY RYAN BARKER; Fiscal Year: 2013
    ..My hypothesis is that Chlamydia c-di- nucleotides are detected through cytosolic sensing pathways, which are critical for the host Type I interferon response...
  38. Control of cap-independent translation by a viral 3'UTR
    WYATT ALLEN MILLER; Fiscal Year: 2013
    ..This will reveal the key nucleotides and amino acids required for interaction and translation function...
  39. Synergistic innate immune activation and cell killing by RIG-I ligands in HCV-HCC
    Lee Gehrke; Fiscal Year: 2013
    ..These RNAs have a 5'triphosphate, are about 100 nucleotides in length, and are described as polyU/UC or polyAG/A...
  40. Purine Pathways and Inhibitor Design in Plasmodium
    Vern L Schramm; Fiscal Year: 2012
    ..biosynthesis, orotate phosphoribosyltransferase (OPRT) is the essential first step to form all pyrimidine nucleotides. These transition state structures will be solved by frontier methods coupling kinetic isotope effects and ..
  41. Ribonucleotide Reductase: Structure and Function
    JoAnne Stubbe; Fiscal Year: 2013
    DESCRIPTION (provided by applicant): Ribonucleotide reductases (RNRs) catalyze the conversion of nucleotides to deoxynucleotides in all organisms and are responsible for the supply of monomeric precursors required for DNA replication ..
  42. Intervention of HBV DNA synthesis and transcription
    Aleem Siddiqui; Fiscal Year: 2013
    ..In the second R33 phase, we propose to define the changes in duplex DNA containing these nucleotides. We will synthesize several templates containing HPMPA or HPMPC and assess the NMR solution structures of their ..
  43. Novel Fluorescent Nucleotide Analogues to Probe Nucleic Acid Metabolism
    BYRON WILLIS PURSE; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): Fluorescent nucleotides are synthetic building blocks of DNA and RNA that, in addition to being artificial structural components, emit colored light when irradiated with light of a longer wavelength...
  44. Structure and mechanism of the dynein motor
    Ronald D Vale; Fiscal Year: 2013
    ..In summary, these studies will provide new information on dynein's structure, how it utilizes nucleotides and changes its conformation, and how it has adapted for unique transport functions in the cytoplasm and the ..
  45. Genetics and Molecular Biology of Striated Muscle Myosin
    Sanford I Bernstein; Fiscal Year: 2013
    ..We will test the hypothesis that distal arthrogryposis mutations cause abnormal interactions with nucleotides yielding enhanced ADP binding, reduced sliding velocity, slowed relaxation dynamics and hypercontraction and ..
  46. Let-7 miRNA control of heart development
    Cathy J Hatcher; Fiscal Year: 2010
    ..MicroRNAs (miRNAs) are endogenous ~22 nucleotides RNAs that regulate gene expression at the post-transcriptional level by binding the 3'UTR of target genes...
  47. Donor Stem Cells, Campath, T/B Cell Regulation In HLA-Identical Renal Transplants
    Joshua Miller; Fiscal Year: 2010
    ..cytokine gene promoter polymorphisms (CGP), including DMA restriction enzyme allelic polymorphisms of single nucleotides (SNP) and their tandem repeat intron characterization (VNTR) such as those for IL-1 alpha/beta (SNP), the IL-1 ..
  48. Somatic Hypermutation in SLE
    Lawrence J Wysocki; Fiscal Year: 2013
    ..transferase (Tdt) enabled us to identify every somatic mutation, even in CDR3, where untemplated addition of nucleotides during V gene assembly would otherwise obscure them...
  49. Gene-Nutrient Interactions in Neural Tube Defects
    Patrick J Stover; Fiscal Year: 2012
    Folate metabolism is required for the synthesis of nucleotides (purines and dTMP) and S- adenosylmethionine (AdoMet)...
  50. Translational partitioning of the SL RNA
    David A Campbell; Fiscal Year: 2010
    ..followed by the addition of seven methylations on the sugar and/or base moieties of the first four nucleotides, constituting the unique 'cap 4'...
  51. TLR-mediated Signaling Complex Formation and Regulation of Effector Functions
    Hans Haecker; Fiscal Year: 2012
    ..specifically recognize diverse pathogen constituents such as lipopolysaccharides (LPS), peptidoglycans (PGN), nucleotides and proteins...
  52. Determination of histone modifications necessary for DNA base excision repair in
    JOHN MICHAEL HINZ; Fiscal Year: 2013
    ..Humans possess different systems of proteins that physically interact with DNA to remove damaged nucleotides and replace them in an ordered multi-step process called DNA repair...
  53. microRNAs in Developmental Toxicology
    Mark E Hahn; Fiscal Year: 2010
    ..MicroRNAs are single-stranded RNA molecules of ~22 nucleotides that regulate the expression of mRNAs by inhibiting their translation into proteins and promoting their ..
  54. Molecular Pathways Regulating Airway Goblet Cell Mucin Secretion
    Burton F Dickey; Fiscal Year: 2013
    ..Activation of P2Y2 receptors by nucleotides in the airway liquid layer leads to generation of the second messengers diacylglyerol (DAG) and calcium (Ca2+) ..
  55. Mitochondrial aconitase: Fe-S cluster biogenesis and interaction with mtDNA
    Debkumar Pain; Fiscal Year: 2012
    ..b>Nucleotides and/or redox status of the matrix may play a critical role in distributing aconitase between the TCA cycle and ..
  56. miRNA Biomarkers from FFPE Tissue for Early Breast Cancer Detection
    Sidney W Fu; Fiscal Year: 2013
    ..provided by applicant): MicroRNAs (miRNAs) are a highly abundant class of endogenous non-coding RNAs (18-25 nucleotides in length), which contributes to cancer initiation and progression, and are differentially expressed in normal ..
  57. High-Throughput Assay for the Discovery of Small Molecule Inhibitors of microRNA
    Alexander Deiters; Fiscal Year: 2011
    DESCRIPTION (provided by applicant): MicroRNAs (miRNAs) are short, single-stranded RNAs of 21-23 nucleotides that are enzymatically processed from stem-loop precursors encoded within the human genome...
  58. Cyclic nucleotide permeability of connexin mutants related to genetic disease
    Virginijus Valiunas; Fiscal Year: 2013
    ..The cyclic nucleotides, cAMP and cGMP are of particular interest as both are important in normal bone development and play a role in ..
  59. Structural Analysis of Mechanism and Regulation of Glutamine Amidotransferases
    AMBER MARIE SMITH; Fiscal Year: 2013
    ..glutaminase domain is combined with acceptor substrates for the synthesis of amino acids, purine and pyrimidine nucleotides, amino sugars and coenzymes...
  60. Identification of XX DSD Mutations by RNA-seq and Comparative Genomics
    Vicki N Meyers-Wallen; Fiscal Year: 2013
    ..will identify orthologs in XX DSD individuals (humans and dogs) that are evolutionarily conserved, yet contain nucleotides that are different from the reference genomes. Those nucleotide differences will be our candidate mutations...
  61. The role of peroxidasin in Goodpasture's disease
    ABRAHAM SCOTT MCCALL; Fiscal Year: 2013
    ..We hypothesize peroxidasin uses O2 and extracellular nucleotides as initial oxidants to form HOBr for the biosynthesis of the S=N bond...
  62. Identifying a network of microRNAs and genes that regulate breast tumor metastasi
    Huiping Liu; Fiscal Year: 2012
    ..Endogenous single strand small RNAs of 20- 22 nucleotides in length, known as microRNAs (miRNAs, miRs), have emerged to be powerful regulators of tumor progression...
  63. CELLULAR EFFECTS OF INHIBITION OF THYMIDYLATE SYNTHASE
    RICHARD MORAN; Fiscal Year: 1993
    ..normal and neoplastic stem cells to pharmacologically induced cellular deficiencies in the supply of thymidine nucleotides. This application proposes to study the biochemcial phenomena initiated by inhibition of TS that cause cell ..
  64. LIPID & PROTEIN PO4 TURNOVER IN IRIS OF THE EYE
    ATA ABDEL LATIF; Fiscal Year: 2002
    ..we propose to address the following specific aims: AIM-I will investigate the cross talk between the cyclic nucleotides (cAMP, cGMP) and the activation of the phospholipase C-beta isoforms (beta1, beta2, beta3), and their ..
  65. Potential Therapeutic Applications of Ecto-Nucleotidases in Lithium-induced NDI
    Bellamkonda K Kishore; Fiscal Year: 2010
    ..We further propose that therapeutic scavenging of the extracellular nucleotides by native and engineered ecto-nucleotidases should offer an efficacious and safer approach for the treatment of ..
  66. CYCLIC NUCLEOTIDES, CYCLOPHOSPHAMIDES, AND ANTIVIRALS
    WESLEY BENTRUDE; Fiscal Year: 1993
    ..One long range goal is a better understanding of the role of cyclic nucleotides (cAMP in particular and also cGMP) in cell proliferation and maligant transformation through a detailed ..
  67. MECHANISM OF CORONARY ENDOTHELIUM MEDIATED VASODILATION
    Pin Lan Li; Fiscal Year: 2000
    ..in the gating of K+ channel in coronary vascular smooth muscle and EETs alter the metabolism of these signaling nucleotides. The purpose of the proposed studies is to determine the role of cyclic ADP-ribose and ADP-ribose in the gating ..
  68. Role of Cellular P-bodies and Hantavirus Nucleocapsid Protein in Viral mRNA "cap
    MOHAMMAD AYOUB MIR; Fiscal Year: 2010
    ..The protected 5'capped oligos of at least 180 nucleotides in length are stored in cellular P bodies by N...
  69. DYNAMICS OF MICROTUBULE ASSEMBLY/DISASSEMBLY
    JOHN CORREIA; Fiscal Year: 1993
    ..We will perform extensive thermodynamic and kinetic studies of the binding of guanine nucleotides and their analogues to the tubulin heterodimer over a wide range of temperatures and assembly conditions...
  70. ALLOSTERIC INHIBITION OF GUANYLYL CYCLASE BY NUCLEOTIDES
    Scott Waldman; Fiscal Year: 2000
    ..Indeed, 2-substituted adenine nucleotides prevent the activation of G Cyclase-C by ST in an allosteric and guanine nucleotide-dependent fashion...
  71. GENETIC EFFECTS-FOLATE-DEPENDENT ONE-CARBON METABOLISM
    JESSE GREGORY; Fiscal Year: 2004
    ..We also hypothesize that the rate of folate-dependent synthesis of nucleotides (purines and thymidylate) will be reduced in folate deficiency but may be enhanced by the C677T mutation...
  72. Inosine Monophosphate Dehydrogenase: Regulation and Function
    Beverly Mitchell; Fiscal Year: 2007
    Inosine monophosphate dehydrogenase (IMPDH) catalyzes the first step in the de novo synthesis of guanine nucleotides and this enzyme activity is essential for cell proliferation...
  73. 'RECODING: DYNAMIC REPROGRAMMING OF GENETIC READOUT'
    John Atkins; Fiscal Year: 2004
    ..T4 gene 60 represents the efficient synthesis of one protein from two coding sequences that are separated by 50 nucleotides in mature mRNA...