base pairing

Summary

Summary: Pairing of purine and pyrimidine bases by hydrogen bonding in double-stranded DNA or RNA.

Top Publications

  1. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
  2. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
  3. pmc Expanding the microRNA targeting code: functional sites with centered pairing
    Chanseok Shin
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Mol Cell 38:789-802. 2010
  4. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
  5. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
  6. pmc Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 461:754-61. 2009
  7. pmc Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition
    Edze R Westra
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    PLoS Genet 9:e1003742. 2013
  8. pmc An alternative mode of microRNA target recognition
    Sung Wook Chi
    Laboratory of Neuro Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York, USA
    Nat Struct Mol Biol 19:321-7. 2012
  9. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
  10. ncbi Local RNA base pairing probabilities in large sequences
    Stephan H Bernhart
    Institut fur Theoretische Chemie, Universitat Wien, Währingerstr 17, A 1090 Wien, Austria
    Bioinformatics 22:614-5. 2006

Detail Information

Publications320 found, 100 shown here

  1. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  2. pmc Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    Adam Siepel
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, Santa Cruz, California 95064, USA
    Genome Res 15:1034-50. 2005
    ..Noncoding HCEs also show strong statistical evidence of an enrichment for RNA secondary structure...
  3. pmc Expanding the microRNA targeting code: functional sites with centered pairing
    Chanseok Shin
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Mol Cell 38:789-802. 2010
    ..This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many miRNAs are evolutionarily conserved...
  4. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  5. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
    ..Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active...
  6. pmc Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 461:754-61. 2009
    ..Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures...
  7. pmc Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition
    Edze R Westra
    Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
    PLoS Genet 9:e1003742. 2013
    ..into small RNAs that guide CRISPR-associated (Cas) proteins to invading nucleic acids by complementary base pairing. However, to avoid autoimmunity it is essential that these RNA-guides exclusively target invading DNA and not ..
  8. pmc An alternative mode of microRNA target recognition
    Sung Wook Chi
    Laboratory of Neuro Oncology, The Rockefeller University, Howard Hughes Medical Institute, New York, New York, USA
    Nat Struct Mol Biol 19:321-7. 2012
    ..We call position 6 the 'pivot' nucleotide and suggest a model in which a transitional 'nucleation bulge' leads to functional bulge mRNA-miRNA interactions, expanding the number of potential miRNA regulatory sites...
  9. ncbi Asymmetry in the assembly of the RNAi enzyme complex
    Dianne S Schwarz
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, 364 Plantation Street, Worcester, MA 01605, USA
    Cell 115:199-208. 2003
    ..Thus, the common step of RISC assembly is an unexpected source of asymmetry for both siRNA function and miRNA biogenesis...
  10. ncbi Local RNA base pairing probabilities in large sequences
    Stephan H Bernhart
    Institut fur Theoretische Chemie, Universitat Wien, Währingerstr 17, A 1090 Wien, Austria
    Bioinformatics 22:614-5. 2006
    ..Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window...
  11. doi Small RNA binding to 5' mRNA coding region inhibits translational initiation
    Marie Bouvier
    Max Planck Institute for Infection Biology, RNA Biology Group, Berlin D 10117, Germany
    Mol Cell 32:827-37. 2008
    ..This "five codon window" for translational control in the 5' coding region of mRNA not only has implications for sRNA target predictions but might also apply to cis-regulatory systems such as RNA thermosensors and riboswitches...
  12. pmc Tools for the automatic identification and classification of RNA base pairs
    Huanwang Yang
    Department of Chemistry and Chemical Biology, Rutgers University, NJ 08854 8087, USA
    Nucleic Acids Res 31:3450-60. 2003
    ..rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/...
  13. pmc Specificity of microRNA target selection in translational repression
    John G Doench
    Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 18:504-11. 2004
    ..Thus, predicted miRNA:mRNA interactions must be viewed in the context of other potential interactions and cellular conditions...
  14. ncbi tRNA's wobble decoding of the genome: 40 years of modification
    Paul F Agris
    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695 7622, USA
    J Mol Biol 366:1-13. 2007
    ....
  15. pmc Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals
    J V Chamary
    Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
    Genome Biol 6:R75. 2005
    ..Here we test whether synonymous mutations might be under selection owing to their effects on the thermodynamic stability of mRNA, mediated by changes in secondary structure...
  16. doi Revisiting the principles of microRNA target recognition and mode of action
    Peter Brodersen
    Institut de Biologie Moleculaire des Plantes, Centre National de la Recherche Scientifique, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
    Nat Rev Mol Cell Biol 10:141-8. 2009
    ..Generally thought to be merely a degradation mechanism, we propose that this might also be a biogenesis mechanism for biologically functional, non-coding RNA fragments...
  17. ncbi DNA replication fidelity
    Thomas A Kunkel
    Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    J Biol Chem 279:16895-8. 2004
  18. pmc Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA
    Kai Papenfort
    Institute for Molecular Infection Biology, University of Wurzburg, D 97080 Wurzburg, Germany
    Proc Natl Acad Sci U S A 107:20435-40. 2010
    ..microRNAs in their ability to control multiple genes at the posttranscriptional level by short and imperfect base pairing. In contrast to the universal length and seed pairing mechanism of microRNAs, the sRNAs are heterogeneous in ..
  19. doi The Vibrio cholerae quorum sensing response is mediated by Hfq-dependent sRNA/mRNA base pairing interactions
    J Patrick Bardill
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332 0230, USA
    Mol Microbiol 80:1381-94. 2011
    ..These results demonstrate that the V. cholerae QS response is mediated by base pairing interactions between Qrr sRNAs and hapR mRNA.
  20. pmc Sequence- and structure-specific RNA processing by a CRISPR endonuclease
    Rachel E Haurwitz
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Science 329:1355-8. 2010
    ..The RNA recognition mechanism identified here explains sequence- and structure-specific processing by a large family of CRISPR-specific endoribonucleases...
  21. ncbi Analysis of RNA motifs
    Neocles B Leontis
    Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, Bowling Green, Ohio 43403, USA
    Curr Opin Struct Biol 13:300-8. 2003
    ..It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically...
  22. ncbi Recognition of cognate transfer RNA by the 30S ribosomal subunit
    J M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Science 292:897-902. 2001
    ..The third, or "wobble," position of the codon is free to accommodate certain noncanonical base pairs. By partially inducing these structural changes, paromomycin facilitates binding of near-cognate tRNAs...
  23. pmc The ribosome uses two active mechanisms to unwind messenger RNA during translation
    Xiaohui Qu
    Jason L Choy Laboratory of Single Molecule Biophysics and QB3 Institute, University of California, Berkeley, California 94720, USA
    Nature 475:118-21. 2011
    ..Our results establish a quantitative mechanical basis for understanding the mechanism of regulation of the elongation rate of translation by structured mRNAs...
  24. doi Prediction of RNA secondary structure using generalized centroid estimators
    Michiaki Hamada
    Mizuho Information and Research Institute, Inc, 2 3 Kanda Nishikicho, Chiyoda ku, Tokyo 101 8443, Japan
    Bioinformatics 25:465-73. 2009
    ..However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures...
  25. pmc Microsatellites in different eukaryotic genomes: survey and analysis
    G Toth
    Department of Genetics, Eotvos Lorand University, Budapest, Hungary
    Genome Res 10:967-81. 2000
    ..Our results suggest that strand-slippage theories alone are insufficient to explain microsatellite distribution in the genome as a whole. Other possible factors contributing to the observed divergence are discussed...
  26. doi Topology links RNA secondary structure with global conformation, dynamics, and adaptation
    Maximillian H Bailor
    Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
    Science 327:202-6. 2010
    ....
  27. pmc Topology of three-way junctions in folded RNAs
    Aurelie Lescoute
    Institut de Biologie Moleculaire et Cellulaire du CNRS, Bioinformatique, Modélisation et Simulations des Acides Nucléiques, UPR 9002 Architecture et Réactivité de l ARN, Universite Louis Pasteur, 15 rue Rene Descartes, 67084 Strasbourg Cedex, France
    RNA 12:83-93. 2006
    ..On the basis of the lengths of the linking segments, some guidelines could be deduced for choosing a topology for a three-way junction on the basis of a secondary structure. Examples and prediction bas'ed on those rules are discussed...
  28. pmc Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases
    Agnieszka Kiliszek
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 14, 61 704 Poznan, Poland
    Nucleic Acids Res 38:8370-6. 2010
    ..The CAG repeats and the previously examined CUG structures share a similar pattern of electrostatic charge distribution in the minor groove, which could explain their affinity for the pathogenesis-related MBNL1 protein...
  29. pmc Hfq proximity and orientation controls RNA annealing
    Subrata Panja
    T C Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
    Nucleic Acids Res 40:8690-7. 2012
    Regulation of bacterial gene networks by small non-coding RNAs (sRNAs) requires base pairing with messenger RNA (mRNA) targets, which is facilitated by Hfq protein...
  30. pmc A periodic pattern of mRNA secondary structure created by the genetic code
    Svetlana A Shabalina
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Nucleic Acids Res 34:2428-37. 2006
    ....
  31. pmc Base pairing small RNAs and their roles in global regulatory networks
    Chase L Beisel
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892 5430, USA
    FEMS Microbiol Rev 34:866-82. 2010
    ..Because most of these circuits were originally identified as network motifs in transcriptional networks, we also discuss why sRNAs may be used over protein transcription factors to help transduce environmental signals...
  32. pmc Base pairing between hepatitis C virus RNA and microRNA 122 3' of its seed sequence is essential for genome stabilization and production of infectious virus
    Tetsuro Shimakami
    Division of Infectious Diseases, Department of Medicine, Inflammatory Diseases Institute and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
    J Virol 86:7372-83. 2012
    ..This requires base pairing between the miR-122 "seed sequence" (nucleotides [nt] 2 to 8) and two sequences near the 5' end of the HCV RNA: ..
  33. pmc Transient Hoogsteen base pairs in canonical duplex DNA
    Evgenia N Nikolova
    Department of Chemistry and Biophysics, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, USA
    Nature 470:498-502. 2011
    ..The methods presented here provide a new route for characterizing transient low-populated nucleic acid structures, which we predict will be abundant in the genome and constitute a second transient layer of the genetic code...
  34. pmc The base-pairing RNA spot 42 participates in a multioutput feedforward loop to help enact catabolite repression in Escherichia coli
    Chase L Beisel
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892 5430, USA
    Mol Cell 41:286-97. 2011
    ..Our results suggest that base-pairing RNAs in feedforward loops can help shape the steady-state levels and dynamics of gene expression...
  35. ncbi Functional siRNAs and miRNAs exhibit strand bias
    Anastasia Khvorova
    Amgen, Inc, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
    Cell 115:209-16. 2003
    ..Together, these results suggest that the thermodynamic properties of siRNA play a critical role in determining the molecule's function and longevity, possibly biasing the steps involved in duplex unwinding and strand retention by RISC...
  36. ncbi Selection of tRNA by the ribosome requires a transition from an open to a closed form
    James M Ogle
    MRC Laboratory of Molecular Biology, Hills Road, CB2 2QH, Cambridge, United Kingdom
    Cell 111:721-32. 2002
    ..We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity...
  37. pmc Defining a role for Hfq in Gram-positive bacteria: evidence for Hfq-dependent antisense regulation in Listeria monocytogenes
    Jesper Sejrup Nielsen
    Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
    Nucleic Acids Res 38:907-19. 2010
    ..Our findings indicate that modulation of translation by trans-encoded sRNAs may occur by both Hfq-dependent and -independent mechanisms, thus adding another layer of complexity to sRNA-mediated riboregulation in Gram-positive species...
  38. pmc New metrics for comparing and assessing discrepancies between RNA 3D structures and models
    Marc Parisien
    Institute for Research in Immunology and Cancer, Department of Computer Science and Operations Research, Universite de Montreal, Montreal, Quebec, Canada
    RNA 15:1875-85. 2009
    ..Our results show that there is little correlation between RMSD and interaction network fidelity. The deformation profile is a tool that allows for rapid assessment of the origins of discrepancies...
  39. pmc siRNAs can function as miRNAs
    John G Doench
    Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 17:438-42. 2003
    ..The use of siRNAs to study translational repression holds promise for dissecting the sequence and structural determinants and general mechanism of gene repression by miRNAs...
  40. pmc Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB
    Taras Afonyushkin
    Max F Perutz Laboratories, Department of Microbiology and Immunobiology, University Departments at the Vienna Biocenter Dr Bohrgasse 9 4, A 1030 Vienna, Austria
    Nucleic Acids Res 33:1678-89. 2005
    ..Moreover, RNase E cleavage can also occur at a cryptic site that becomes available upon sodB 5'-UTR/RyhB base pairing. We show that while playing an important role in facilitating the interaction of RyhB with sodB mRNA, Hfq is ..
  41. doi Binding of metal ions by pyrimidine base pairs in DNA duplexes
    Akira Ono
    Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, Yokohama 221 8686, Japan
    Chem Soc Rev 40:5855-66. 2011
    ..Oligonucleotides containing these bases are commercially available and can readily be applied in many scientific fields (86 references)...
  42. ncbi Rfold: an exact algorithm for computing local base pairing probabilities
    Hisanori Kiryu
    Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology AIST, 2 42 Aomi, Koto ku, Tokyo, Japan
    Bioinformatics 24:367-73. 2008
    b>Base pairing probability matrices have been frequently used for the analyses of structural RNA sequences...
  43. pmc PCR with an expanded genetic alphabet
    Denis A Malyshev
    Department of Chemistry and Center for Protein and Nucleic Acid Research, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    J Am Chem Soc 131:14620-1. 2009
    ..Importantly, the results reveal that the unnatural base pairs may function within an expanded genetic alphabet and make possible many in vitro applications...
  44. pmc Solution structure, mechanism of replication, and optimization of an unnatural base pair
    Denis A Malyshev
    Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
    Chemistry 16:12650-9. 2010
    ....
  45. pmc A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding
    H M Lim
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4255, USA
    Proc Natl Acad Sci U S A 98:14849-52. 2001
    ..Substitution of adenine by 2-AP at several other positions did not affect thymine unpairing. Changing the position of the amino group from C6 in adenine to C2 in 2-AP is mutational only at the master switch position, -11...
  46. pmc Ensemble of secondary structures for encapsidated satellite tobacco mosaic virus RNA consistent with chemical probing and crystallography constraints
    Susan J Schroeder
    Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
    Biophys J 101:167-75. 2011
    ..Multiple solutions to the genome packaging problem could be an evolutionary advantage for viruses. In such cases, an ensemble of structures that share favorable global features best represents the RNA fold...
  47. pmc Multiple factors dictate target selection by Hfq-binding small RNAs
    Chase L Beisel
    Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
    EMBO J 31:1961-74. 2012
    ..By modifying these features, we could impart Spot 42 regulation on non-target mRNAs. Our results thus provide valuable insights into the requirements for target selection by sRNAs...
  48. pmc Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
    Peter Yakovchuk
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 34:564-74. 2006
    Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases...
  49. ncbi Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
    A G Nackley
    Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
    Science 314:1930-3. 2006
    ..These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations...
  50. pmc Rapid binding and release of Hfq from ternary complexes during RNA annealing
    Julia F Hopkins
    Program in Cellular, Molecular and Developmental Biology and Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA
    Nucleic Acids Res 39:5193-202. 2011
    The Sm protein Hfq binds small non-coding RNA (sRNAs) in bacteria and facilitates their base pairing with mRNA targets...
  51. ncbi Quantitative analysis of nucleic acid three-dimensional structures
    P Gendron
    , , C.P. 6128, Succ. Centre-Ville, , , H3C 3J7, Canada
    J Mol Biol 308:919-36. 2001
    ..The question of whether the current database of RNA three-dimensional structures is complete is addressed...
  52. pmc The functional Hfq-binding module of bacterial sRNAs consists of a double or single hairpin preceded by a U-rich sequence and followed by a 3' poly(U) tail
    Hirokazu Ishikawa
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    RNA 18:1062-74. 2012
    ..We also demonstrate that increasing the spacing between the base-pairing region and the Hfq-binding module reduces or impairs the silencing ability. These findings allowed us to design synthetic Hfq-binding sRNAs to target desired mRNAs...
  53. ncbi The role of modifications in codon discrimination by tRNA(Lys)UUU
    Frank V Murphy
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Struct Mol Biol 11:1186-91. 2004
    ..These structures allow the rationalization of how modifications in the anticodon loop enable decoding of both lysine codons AAA and AAG...
  54. pmc TargetRNA: a tool for predicting targets of small RNA action in bacteria
    Brian Tjaden
    Computer Science Department, Wellesley College, Wellesley, MA 02481, USA
    Nucleic Acids Res 36:W109-13. 2008
    ..The predictive performance of TargetRNA has been validated experimentally in several bacterial organisms. TargetRNA is freely available at http://snowwhite.wellesley.edu/targetRNA...
  55. pmc Structural insights into CUG repeats containing the 'stretched U-U wobble': implications for myotonic dystrophy
    Agnieszka Kiliszek
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 14, 61 704 Poznan, Poland
    Nucleic Acids Res 37:4149-56. 2009
    ..The residue, which accepts the H-bond, is inclined towards the minor groove. This previously unreported base pairing can be described as 'stretched U-U wobble'...
  56. ncbi Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA
    Richard A Lease
    T C Jenkins Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218 2865, USA
    J Mol Biol 344:1211-23. 2004
    ..rpoS RNA complex. We conclude that recognition of rpoS mRNA is stimulated by binding of Hfq to free DsrA sRNA, followed by release of Hfq from the sRNA.mRNA complex...
  57. pmc The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator
    Maude Guillier
    Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Nucleic Acids Res 36:6781-94. 2008
    ..Since the OmpR transcriptional regulator activates expression of both omrA and omrB genes, this newly identified control should result in an autoregulatory loop limiting the amount of OmrA/B sRNAs...
  58. pmc The small RNA SgrS controls sugar-phosphate accumulation by regulating multiple PTS genes
    Jennifer B Rice
    Department of Microbiology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Nucleic Acids Res 39:3806-19. 2011
    ..A ptsG manXYZ double mutant is resistant to the stress, indicating that PTS transporters encoded by both SgrS targets are involved in taking up substrates that cause stress...
  59. ncbi Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
    Dominic Didiano
    Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, Howard Hughes Medical Institute, 701 W 168th Street, New York, New York 10032, USA
    Nat Struct Mol Biol 13:849-51. 2006
    ..We show that G.U base pairing is tolerated in the 'seed' region of the lsy-6 miRNA interaction with its in vivo target cog-1, and that 6- to ..
  60. ncbi The structure of DNA in the nucleosome core
    Timothy J Richmond
    ETH Zurich, Institut fur Molekularbiologie und Biophysik, ETH Honggerberg, CH 8093 Zurich
    Nature 423:145-50. 2003
    ....
  61. ncbi 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets
    Amanda Birmingham
    Dharmacon Research, 2650 Crescent Drive, 100, Lafayette, Colorado 80026, USA
    Nat Methods 3:199-204. 2006
    ..These findings have strong implications for future siRNA design and the application of RNAi in high-throughput screening and therapeutic development...
  62. pmc 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking
    J M Jean
    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 98:37-41. 2001
    ..The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields...
  63. pmc MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region
    Allison C Mallory
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142 1479, USA
    EMBO J 23:3356-64. 2004
    ....
  64. pmc Tertiary motifs revealed in analyses of higher-order RNA junctions
    Christian Laing
    Department of Chemistry, New York University, 251 Mercer Street, New York, NY 10012, USA
    J Mol Biol 393:67-82. 2009
    ..More generally, studies of RNA junctions and tertiary building blocks can ultimately help in the difficult task of RNA 3D structure prediction...
  65. pmc Conformational analysis of nucleic acids revisited: Curves+
    R Lavery
    Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, 7 passage du Vercors, 69367 Lyon, France
    Nucleic Acids Res 37:5917-29. 2009
    ..With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics...
  66. pmc Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs
    Amanda S O'Toole
    Department of Chemistry, Allegheny College, 520 N Main Street, Meadville, PA 16335, USA
    Nucleic Acids Res 34:3338-44. 2006
    ..Thermodynamic parameters for 3' single terminal overhangs adjacent to a UA pair are also presented...
  67. pmc 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    Xiang Jun Lu
    Department of Chemistry and Chemical Biology, Wright Rieman Laboratories, Rutgers The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854 8087, USA
    Nucleic Acids Res 31:5108-21. 2003
    ..Regular helical models based on X-ray diffraction measurements of various repeating sequences can also be generated within the program...
  68. ncbi Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass
    Samer Lone
    Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, NY 10029, USA
    Mol Cell 25:601-14. 2007
    ....
  69. ncbi Structure of a DNA glycosylase searching for lesions
    Anirban Banerjee
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Science 311:1153-7. 2006
    ..MutM therefore actively interrogates the intact DNA helix while searching for damage...
  70. pmc Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 36:1770-82. 2008
    ..The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5' RNA...
  71. ncbi A microRNA in a multiple-turnover RNAi enzyme complex
    Gyorgy Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Lazare Research Building, Room 825, 364 Plantation Street, Worcester, MA 01605, USA
    Science 297:2056-60. 2002
    ..Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells...
  72. ncbi Diversity of base-pair conformations and their occurrence in rRNA structure and RNA structural motifs
    Jung C Lee
    The Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A4800, Austin, TX 78712 0159, USA
    J Mol Biol 344:1225-49. 2004
    ..Thus, each rare non-canonical conformation may be functionally and structurally important. Finally, the topology-based isostericity of base-pair conformations can rationalize base-pair exchanges in the evolution of RNA molecules...
  73. pmc Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level
    N M Luscombe
    Biomolecular Structures and Modelling Unit, Department of Biochemistry and Molecular Biology, University College, Gower Street, London WC1E 6BT, UK
    Nucleic Acids Res 29:2860-74. 2001
    ..An interactive Web-based atlas of side chain-base contacts provides access to the collected data, including analyses and visualisation of the three-dimensional geometry of the interactions...
  74. doi An allosteric self-splicing ribozyme triggered by a bacterial second messenger
    Elaine R Lee
    Department of Molecular, Cellular, and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
    Science 329:845-8. 2010
    ..Our findings indicate that some self-splicing ribozymes are not selfish elements but are harnessed by cells as metabolite sensors and genetic regulators...
  75. pmc Binary complex crystal structure of DNA polymerase β reveals multiple conformations of the templating 8-oxoguanine lesion
    Vinod K Batra
    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, P O Box 12233, Research Triangle Park, NC 27709 2233, USA
    Proc Natl Acad Sci U S A 109:113-8. 2012
    ..during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its anti- and syn-conformations, base pairing with cytosine and adenine, respectively...
  76. pmc Single-molecule measurements of synthesis by DNA polymerase with base-pair resolution
    Thomas D Christian
    Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
    Proc Natl Acad Sci U S A 106:21109-14. 2009
    ..This may represent a previously unobserved step in the mechanism of DNA synthesis that could be part of the proofreading process...
  77. pmc Long-distance base pairing in flock house virus RNA1 regulates subgenomic RNA3 synthesis and RNA2 replication
    Brett D Lindenbach
    Howard Hughes Medical Institute, University of Wisconsin Madison, Madison, Wisconsin 53706 1596, USA
    J Virol 76:3905-19. 2002
    ..5 kb upstream, at nt 1229 to 1239. Base pairing between these distal and proximal elements was shown to be essential for RNA3 production by covariation ..
  78. pmc Transition of a microRNA from repressing to activating translation depending on the extent of base pairing with the target
    Ashesh A Saraiya
    Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
    PLoS ONE 8:e55672. 2013
    ..This is the first report showing a correlation between the extent of base-pairing with the target and a change in miRNA function...
  79. pmc Essential role of cyclization sequences in flavivirus RNA replication
    A A Khromykh
    Sir Albert Sakzewski Virus Research Centre, Royal Children s Hospital, University of Queensland, Herston Rd, Herston, Brisbane, QLD 4029, Australia
    J Virol 75:6719-28. 2001
    ....
  80. pmc Unusual base pairing during the decoding of a stop codon by the ribosome
    Israel S Fernández
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
    Nature 500:107-10. 2013
    ..The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs. ..
  81. pmc Two distinct overstretched DNA states
    Hongxia Fu
    Research Centre of Excellence in Mechanobiology, 117543, Singapore
    Nucleic Acids Res 38:5594-600. 2010
    ....
  82. pmc RNA/DNA hybrid binding affinity determines telomerase template-translocation efficiency
    Xiaodong Qi
    Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA
    EMBO J 31:150-61. 2012
    ..Our results provide new insights into the ancient RNA/DNA hybrid binding ability of telomerase and its role in template translocation...
  83. doi Formation of pearl-necklace monomorphic G-quadruplexes in the human CEB25 minisatellite
    Samir Amrane
    School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore
    J Am Chem Soc 134:5807-16. 2012
    ..Further, we demonstrate that such a monomorphic structure is formed within longer sequence contexts folding into a pearl-necklace structure...
  84. ncbi DNA nanotweezers studied with a coarse-grained model of DNA
    Thomas E Ouldridge
    Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP, United Kingdom
    Phys Rev Lett 104:178101. 2010
    ..We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA "tweezers," a simple machine driven by hybridization and strand displacement...
  85. pmc Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
    Joshua W Shaevitz
    Department of Physics, Stanford University, Stanford, California 94305, USA
    Nature 426:684-7. 2003
    ..Inosine triphosphate increased the frequency of backtracking pauses, whereas the accessory proteins GreA and GreB, which stimulate the cleavage of nascent RNA, decreased the duration of such pauses...
  86. pmc Structural features of metabolite-sensing riboswitches
    Catherine A Wakeman
    Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390 9038, USA
    Trends Biochem Sci 32:415-24. 2007
    ..Our knowledge of the mechanisms underlying genetic regulation by riboswitches has increased mightily in recent years and will continue to grow as new riboswitch classes and ligands are discovered and structurally characterized...
  87. pmc Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity
    Thidathip Wongsurawat
    Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore 138671
    Nucleic Acids Res 40:e16. 2012
    ..RLFSs could be used as a novel source of prospective therapeutic targets...
  88. ncbi Site-specific incorporation of a photo-crosslinking component into RNA by T7 transcription mediated by unnatural base pairs
    Michiko Kimoto
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Chem Biol 11:47-55. 2004
    ..The site-specific Iy incorporation into RNA was achieved by T7 transcription mediated by unnatural base pairing between Iy and its partner, 2-amino-6-(2-thienyl)purine (s)...
  89. pmc Highly specific unnatural base pair systems as a third base pair for PCR amplification
    Rie Yamashige
    RIKEN Systems and Structural Biology Center SSBC, 1 7 22 Suehiro cho, Tsurumi ku, Yokohama, Kanagawa 230 0045, Japan
    Nucleic Acids Res 40:2793-806. 2012
    ..Furthermore, >97% of the Ds-Px pair in DNA survived in the 10(28)-fold amplified products after 100-cycle PCR (10 cycles repeated 10 times). This highly specific Ds-Px pair system provides a framework for new biotechnology...
  90. pmc A complex system of small RNAs in the unicellular green alga Chlamydomonas reinhardtii
    Tao Zhao
    National Institute of Biological Sciences, Zhongguancun Life Science Park, Beijing 102206, China
    Genes Dev 21:1190-203. 2007
    ..Our findings suggest that the miRNA pathway and some siRNA pathways are ancient mechanisms of gene regulation that evolved prior to the emergence of multicellularity...
  91. pmc Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes
    Mark J Lawson
    Department of Computer Science, Virginia Tech, 655 McBryde, Blacksburg, VA 24060, USA
    Genome Biol 7:R14. 2006
    ..We have performed a detailed comparative study of the distribution of SSRs in the sequenced genomes of Arabidopsis thaliana and rice...
  92. 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...
  93. pmc The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1
    Laurent Houzet
    Molecular Virology Section, Laboratory of Molecular Microbiology National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 0460, USA
    Nucleic Acids Res 40:11684-96. 2012
    ..Antagomirs to miR-326 that knocked down this cell endogenous miRNA increased HIV-1 replication in cells, suggesting that miR-326 is physiologically functional in moderating HIV-1 replication in human cells...
  94. pmc Crystal structures of CGG RNA repeats with implications for fragile X-associated tremor ataxia syndrome
    Agnieszka Kiliszek
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 14, 61 704 Poznan, Poland
    Nucleic Acids Res 39:7308-15. 2011
    ..CGG helical structures appear relatively stable compared with CAG and CUG tracts. This could be an important factor in the RNA's ligand binding affinity and specificity...
  95. doi A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA
    Kimika Maki
    Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464 8602, Japan
    Mol Microbiol 76:782-92. 2010
    ..Interestingly, the 14 nt oligo efficiently inhibited ptsG translation without the high-temperature pre-treatment, suggesting that remodelling of structured SgrS is an important mechanism by which Hfq promotes the base pairing.
  96. ncbi Formation of silver(I)-mediated DNA duplex and triplex through an alternative base pair of pyridine nucleobases
    Kentaro Tanaka
    Contribution from the Department of Chemistry, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo ku, Tokyo 113 0033, Japan
    J Am Chem Soc 124:8802-3. 2002
    We have recently reported the first artificial nucleoside for alternative DNA base pairing through metal complexation (J. Org. Chem. 1999, 64, 5002-5003)...
  97. pmc The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern
    Samantha Kendrick
    Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, Arizona 85724, USA
    J Am Chem Soc 131:17667-76. 2009
    ..Furthermore, the two adjacent large lateral loops in the i-motif structure provide an unexpected opportunity for protein and small molecule recognition...
  98. pmc Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion
    R Micura
    Institut fur Organische Chemie, Leopold Franzens Universitat, Innrain 52a, A 6020 Innsbruck, Austria
    Nucleic Acids Res 29:3997-4005. 2001
    ..Therefore, it can be concluded that nucleobase methylations at the Watson-Crick base pairing site provide the potential not only to modulate but to substantially affect RNA structure by formation of ..
  99. pmc Frnakenstein: multiple target inverse RNA folding
    Rune B Lyngsø
    Department of Statistics, University of Oxford, Oxford OX1 3TG, UK
    BMC Bioinformatics 13:260. 2012
    ..However, whereas the RNA folding problem from an algorithmic viewpoint has an elegant and efficient solution, the inverse RNA folding problem appears to be hard...
  100. doi Site-specific fluorescent probing of RNA molecules by unnatural base-pair transcription for local structural conformation analysis
    Yasushi Hikida
    TagCyx Biotechnologies, Yokohama, Kanagawa, Japan
    Nat Protoc 5:1312-23. 2010
    ..This is the first protocol for RNA transcript preparation with fluorescent labeling at a desired position. The procedure for s-containing RNA preparation takes about 2-3 d...
  101. pmc Mechanism of IS200/IS605 family DNA transposases: activation and transposon-directed target site selection
    Orsolya Barabas
    Laboratory of Molecular Biology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
    Cell 132:208-20. 2008
    ..Rather, cleavage site recognition occurs by complementary base pairing with a TnpA-bound subterminal transposon DNA segment...

Research Grants70

  1. 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. ..
  2. Weight Loss &Exercise Effects on Telomere Length in Postmenopausal Women
    ANNE M MCTIERNAN; Fiscal Year: 2012
    ..Shorter telomeres have been linked to cancer risk. The project includes 438 postmenopausal, overweight/obese, sedentary women who have already completed the trial from which blood samples will be used. ..
  3. Genomic Enhancers at 8q24 and Prostate Cancer
    Gerhard A Coetzee; Fiscal Year: 2013
    ....
  4. Delineation of the molecular mechanisms underlying group A Streptococcus virulenc
    Paul Sumby; Fiscal Year: 2013
    ..Public health may be enhanced through the long-term goal of translating knowledge of FASX regulatory pathways into new treatment and/or preventative regimes based upon the inhibition of these pathways by novel antimicrobial agents. ..
  5. Molecular Determinants of DNA Sliding and Hopping by a DNA Repair Glycosylase
    MENG MENG ROWLAND; Fiscal Year: 2013
    ....
  6. microRNA and Down Syndrome
    Karl H Obrietan; Fiscal Year: 2010
    ..Our project will define miRNA/mRNA targets responsible for DS and will potentially lead to novel therapeutic strategies to treat DS individuals in the perinatal period to change the course of pathogenesis. ..
  7. Genome Sequencer FLX Instrument
    ANNE VIRGINIA KANE; Fiscal Year: 2010
    ..The equipment will be housed in a pre-existing Core facility, a plan for its management has been developed, and institutional support has been pledged by both Tufts Medical Center and Tufts University School of Medicine. ..
  8. Contribution of Sperm Nucleus to Paternal DNA Replication
    WILLIAM S WARD; Fiscal Year: 2013
    ..This application proposes to test the idea that the sperm cell brings to the egg more than only the DNA, itself, but instructions on how to replicate it properly in the first embryonic cell division. ..
  9. Identification, Discovery, and Public Archiving of RNA Structural Motifs
    Shaojie Zhang; Fiscal Year: 2013
    ..we will develop a new computational search tool which will, in addition to 3D geometry, take into account base pairing (hydrogen bonding forces) and base stack- ing (magnetic and electrostatic forces) information...
  10. Genetic hearing screening for newborns
    Xi Lin; Fiscal Year: 2009
    ..The ultimate goal of the STTR project is to provide a cost-realistic implementation protocol for a DNA-based hearing screening method that will significantly enhance the current UNHS program. ..
  11. FUNCTION OF THE KINETOPLAST IN THE HEMOFLAGELLATES
    Larry Simpson; Fiscal Year: 2013
    ..of a new class of short RNAs (guide RAs or gRNAs) that contain the sequence information for editing by base pairing in trans brought this type of RNA modification into line with the central dogma...
  12. Group II Intron Mobility and Gene Targeting
    Alan M Lambowitz; Fiscal Year: 2012
    ..the excised intron RNA and uses both for DNA target site recognition, with most of the specificity coming from base pairing of the intron RNA to the DNA target sequence...
  13. MiR-181b, endothelial cells, and vascular inflammation
    Mark W Feinberg; Fiscal Year: 2013
    ..MicroRNAs (miRNAs) are small, single-stranded, non-coding RNAs capable of repressing gene expression by base pairing to the 3'untranslated regions (3'-UTRs) of mRNA targets and are involved in a variety of ..
  14. Role of microRNA in HIV associated neurological disorder (HAND).
    Bassel E Sawaya; Fiscal Year: 2013
    ..Outcome from these studies will serve to prevent and/or delay neuronal deregulation and disorders observed in AIDS patients. ..
  15. Structural and Mechanistic Characterization of the Histone Chaperone FACT
    Duane David Winkler; Fiscal Year: 2012
    ..Insights from these proposed aims could aid in the development of specific FACT inhibitors that have the potential to increase chemotherapy effectiveness while decreasing aberrant cancer-related processes. ..
  16. DNA REPLICATION AND CHROMOSOME STRUCTURE IN YEAST
    Virginia A Zakian; Fiscal Year: 2013
    ..These studies will lay the groundwork for the identification and analysis of human proteins with similar functions. ..
  17. Control of cap-independent translation by a viral 3'UTR
    WYATT ALLEN MILLER; Fiscal Year: 2013
    ..In NIH-funded research the PI's lab showed that this is facilitated by long-distance base pairing between the 3'CITE, which binds a translation initiation factor, and the 5'untranslated region...
  18. MiR-26a, endothelial cells, and neovascularization
    Mark W Feinberg; Fiscal Year: 2013
    ..MicroRNAs (miRNAs) are small, single-stranded, non-coding RNAs capable of repressing gene expression by base pairing to the 3'untranslated regions (3'-UTRs) of mRNA targets and are involved in a variety of ..
  19. Atrial Fibrillation: Bridging genetic discovery and clinical associations
    Steven A Lubitz; Fiscal Year: 2013
    ....
  20. A Novel Approach to Decoding Vertebrate Gene Regulation
    SAMANTHA JEAN RIESENFELD; Fiscal Year: 2013
    ..In addition, it will pave the way for gene therapy by genetically engineering regulatory elements that drive compounds to specific tissues at different time points. ..
  21. Role of microRNAs in skeletal development
    Tatsuya Kobayashi; Fiscal Year: 2013
    ..This proposal is aimed to establish the role of microRNAs in the skeletal system and to provide a basis for potential therapeutic interventions for skeletal diseases. ..
  22. Dynamics of nucleosome positioning and the role of chromatin in myogenesis
    DUSTIN EDWARD SCHONES; Fiscal Year: 2013
    ..These studies will lead to a greater understanding of the mechanisms responsible for the organization of nucleosomes across the genome and further elucidate the role of chromatin in the regulation of transcription. ..
  23. Micro-RNA 122 and Chronic Hepatitis C
    Stanley M Lemon; Fiscal Year: 2013
    ..The studies proposed will provide novel insight into how it functions in HCV replication and in the pathogenesis of chronic hepatitis C, thereby enhancing the scientific background on which it can be exploited as a therapeutic target. ..
  24. DNA damage recognition by nucleotide excision repair proteins
    Bennett Van Houten; Fiscal Year: 2013
    ..This project will gain insight into how these repair proteins detect and remove DNA damage. ..
  25. Coordinating Translesion DNA Synthesis Opposite Damaged DNA
    Robert L Eoff; Fiscal Year: 2013
    ..The goals of our research seek to answer questions related to how different types of "DNA making" enzymes function to maintain the integrity of our genetic material. ..
  26. Altered miRNA expression in mesangial cells in lupus mice
    CHRISTOPHER MICHAEL REILLY; Fiscal Year: 2011
    ..of microRNAs (miRNAs) which are short noncoding RNA molecules that inhibit gene expression through incomplete base pairing with the 30- untranslated region (30-UTR) of target mRNAs have initiated a flurry of investigations into how ..
  27. Transcriptional elongation and splicing in human genes in situ
    Richard A Padgett; Fiscal Year: 2013
    ..These studies will advance our understanding of human gene expression which is of major relevance to both normal and pathological cell growth and development. ..
  28. Expanding the Genetic Alphabet by Design and Selection
    Floyd E Romesberg; Fiscal Year: 2013
    ..Completion of the proposed work will also position us at the doorstep of creating the first semi-synthetic organism, able to store, retrieve, and evolve, with more information than natural organisms. ..
  29. REGULATION OF BACILLUS SUBTILIS TRNA SYNTHETASE GENES
    Tina M Henkin; Fiscal Year: 2012
    ....
  30. Mechanisms of CRISPR Interference
    Erik J Sontheimer; Fiscal Year: 2013
    ..self" DNA (the CRISPR locus) from targeted "non-self" DNA (plasmids and phage genomes) by differential base pairing outside of the spacer region...
  31. Regulation of plasma lipids and atherosclerosis by miR-30c
    M Mahmood Hussain; Fiscal Year: 2013
    ..If proven, miR-30c might serve as a potentially new therapeutic agent to treat hyperlipidemia, atherosclerosis and other related metabolic disorders. ..
  32. Regulation of Nucleosome Assembly
    Zhiguo Zhang; Fiscal Year: 2013
    ..These studies will provide a new paradigm connecting nucleosome assembly with cell signaling and reveal a novel form of regulation of senescence, a process important for tumor suppression. ..
  33. RNAi-Mediated Heterochromatin Assembly
    Danesh Moazed; Fiscal Year: 2013
    ..silencing) complex uses small interfering RNAs (siRNAs) to target specific chromosome regions by base pairing interactions with nascent noncoding RNAs...
  34. Studies of the Swi1-Swi3 Replication Fork Protection Complex
    Eishi Noguchi; Fiscal Year: 2012
    ..Therefore, elucidating how cells cope with replication arrest is essential for understanding the mechanisms of birth defects and development of cancer, contributing to the development of therapeutic agents. ..
  35. Large-Scale Conformational Changes in Regulation of Transcription Initiation
    M Thomas Record; Fiscal Year: 2011
    ..g. tuberculosis) wreak havoc on public health. Results generated by this proposal will define bacteria-specific aspects of initiation, and thus, reveal novel targets for the next generation of antibiotics. ..
  36. FUNCTIONALLY TETHERED OLIGONUCLEOTIDES
    Gregory L Verdine; Fiscal Year: 2011
    ..Our studies will focus on understanding how DNA cytosine methyltransferases (DCMTases) target particular cytosine residues in DNA for extrusion from the DNA helix and insert them into the extrahelical active site on the enzyme. ..
  37. Interrogation of Androgen Receptor:Forkhead Interaction Using Py-Im Polyamides
    THOMAS FARID MARTINEZ; Fiscal Year: 2013
    ..Biophysical characterization of this novel transcription factor complex combined with genome-wide characterization of genes regulated by AR:Fkhd using polyamides can reveal a new target for prostate cancer drug development. ..
  38. Structural studies of RNase P
    ALFONSO MONDRAGON; Fiscal Year: 2013
    ..structure also shows that RNase P utilizes shape complementarity, specific RNA-RNA contacts, and intermolecular base pairing to recognize its substrate efficiently and that both P RNA and the pre-tRNA help to coordinate two ..
  39. The structural basis of nucleic acid recognition by Toll-like receptors
    Yorgo Modis; Fiscal Year: 2013
    ....
  40. Intramolecular domain movements of PcrA during its helicase function
    Karen R Thickman; Fiscal Year: 2010
    ..Due to its small size, ~700 residues, and likely monomeric state, PcrA is an ideal model for furthering the understanding of helicase functions and malignancies arising from irregular helicase activities. ..
  41. Computational modeling of viral assembly: encapsulation of nucleic acids and env
    Michael F Hagan; Fiscal Year: 2013
    ..A new method to apply Markov state models to assembly reactions is developed. ..
  42. KINETIC DISSECTION OF EUKARYOTIC TRANSLATION INITIATION
    Rachel Green; Fiscal Year: 2013
    ..Our studies will increase our understanding of how translation normally works, which in turn will increase our understanding of how it can break down and result in diseases. ..
  43. Mitochondrial Abnormalities in Schizophrenia and Bipolar Disorder
    MARQUIS PHILIP VAWTER; Fiscal Year: 2013
    ..By understanding the accumulation of mitochondrial DNA defects in brain, it will advance mitochondrial medicine for earlier diagnosis and treatment of brain related disorders. ..
  44. NMR STUDIES OF RETROVIRAL NUCLEIC ACID BINDING PROTEINS
    MICHAEL FINLEY SUMMERS; Fiscal Year: 2013
    ..nucleocapsid (NC - the protein domain responsible for genome selection) binding sites are sequestered by base pairing in the monomeric RNA and become exposed to allow NC binding upon dimerization...
  45. A MACHINE LEARNING APPROACH FOR FINE-SCALE GENOME WIDE DNA METHYLATION ANALYSIS
    John R Edwards; Fiscal Year: 2013
    ..The general framework developed here can be expanded in the future to examine methylation signatures at enhancers and gene bodies, as well as to histone marks or other genomic signals that carry detailed spatial information. ..
  46. Regulation of translation initiation in eukaryotes
    Vincent P Mauro; Fiscal Year: 2010
    ..g. for the production of therapeutic proteins, and new avenues for analyzing the potential contributions of mis-regulation to disease. ..
  47. Testing the Hypothesis of Somatic Cell Retrotransposition in Human Brain
    DOUGLAS FREDERICK LEVINSON; Fiscal Year: 2013
    ..Later in the study we will study cerebellar (hindbrain) tissue from the same subjects to evaluate possible differences between brain regions. ..
  48. Identification of microRNAs as blood-based markers for colorectal cancer
    Wei Zhang; Fiscal Year: 2012
    ..Therefore, the search for plasma markers for colon cancer in this proposal is critically important. ..
  49. Deoxyribozymes for Protein Phosphorylation and Dephosphorylation
    Scott K Silverman; Fiscal Year: 2013
    ..on substrates that are oligonucleotides, for which binding interactions are provided by simple Watson-Crick base pairing. In Aim 1, we will establish a more general, modular approach in which small-molecule substrates are bound by ..
  50. Clinical sequencing in cancer: Clinical ethical and technological studies
    GAIL PAIRITZ JARVIK; Fiscal Year: 2013
    ..Finally, we will perform CRCP gene discovery studies for families without identifiable CRCP mutations;such novel gene discovery can impact prevention and treatment. ..
  51. RNA IN VIRAL DNA PACKAGING
    Shelley Grimes; Fiscal Year: 2012
    ..pRNA forms a novel cyclic hexamer by intermolecular base pairing of identical molecules...
  52. Uracil Damage Recognition by Uracil DNA Glycosylase
    James T Stivers; Fiscal Year: 2013
    ..The characterization of the molecular interactions in this pathway provides the basis for identifying new targets for biomedical intervention in the immune response, cancer therapy and viral pathogenesis. ..
  53. Regulation of Retinal Physiology by micro-RNAs
    KRZYSZTOF NMI PALCZEWSKI; Fiscal Year: 2013
    ..They act by base pairing to partially complementary sequences on target messenger RNAs to inhibit protein synthesis, primarily through ..
  54. Synthesis, Structure and Repair of DNA Interstrand Crosslinks
    ORLANDO D SCHARER; Fiscal Year: 2013
    ..Since our studies involve ICLs formed by antitumor agents as well as ones with novel structures, they could lead to the development of antitumor agents with improved properties. ..
  55. Regulation of erythropoiesis by the miR-144/451 microRNA locus
    Mitchell J Weiss; Fiscal Year: 2013
    ..by inhibiting the translation and stability of specific target mRNAs that are recognized via Watson-Crick base pairing. This proposal investigates the role of miRs 144 and 451, which are encoded on a single gene locus that is ..
  56. Mitochondrial Deletions in Mood Disorders
    MARQUIS PHILIP VAWTER; Fiscal Year: 2013
    ..These results could lead to novel treatments that target mitochondrial functional deficits and reduce the accumulation of somatic deletions, thereby improving therapy of mood disorders. ..
  57. Identifying Conserved Genetic Networks for Eukaryotic MMR Genes
    Winfried Edelmann; Fiscal Year: 2012
    ..The goal of our studies is not only to determine novel interactions and/or functions of essential MMR genes, but also to identify highly effective chemotherapeutic strategies for a prevalent human cancer syndrome. ..
  58. Ribosomal scanning and initiation codon selection
    Tatyana V Pestova; Fiscal Year: 2013
    ..These studies will determine the molecular basis for key events in translation initiation, and its regulation by trans-acting factors, which is a prerequisite for the development of rational therapies to treat such diseases. ) ..
  59. The role of non-canonical base pairs in RNA editing
    Blaine H M Mooers; Fiscal Year: 2013
    ..No one has effectively why non-canonical base pairing is a conserved feature of the binary mRNA-gRNA complex that is central to RNA editing in trypanosomes...
  60. DNA sequence imaging using a Low Energy Electron Microscope
    Marian Mankos; Fiscal Year: 2012
    ..The proposed research will develop a new approach to low cost, high quality genome sequencing needed to enable the use of genomic information in individual health care. ..
  61. Misregulation of the TDP-43 RNA target, Sortilin, in neurodegeneration
    Leonard Petrucelli; Fiscal Year: 2013
    ....
  62. CSHL Course on Advanced Sequencing Technologies &Applications
    David J Stewart; Fiscal Year: 2013
    ....
  63. A SARS-CoV Spike Protein Vaccine
    B Sim; Fiscal Year: 2005
    ..abstract_text> ..
  64. Mechanisms of Sequence-Based Resistance to Viruses and Plasmids in Eubacteria
    Erik J Sontheimer; Fiscal Year: 2010
    ..The proposed studies will clarify the mechanisms of CRISPR function, and will therefore contribute to our ability to exploit this natural pathway to prevent and treat infectious disease. ..
  65. MOLECULAR MECHANISM OF REGULATION OF THE LUX REGULON
    Thomas Baldwin; Fiscal Year: 1991
    ..Knowledge of the molecular mechanism of the remarkable regulation of the lux system would comprise a major addition to our understanding of this of this most fundamental aspect of living systems, control of expression...
  66. MUTATION IDENTIFICATION IN HERITABLE CHONDRODYSTROPHIES
    Deborah Redford Badwal; Fiscal Year: 1993
    ..The strategy should be applicable to defining mutations of any gene that is expressed in cartilage and provide an avenue for understanding the molecular basis of this extremely heterogeneous group of heritable disorders...
  67. Comprehensive Mutational Analysis of the Cancer Genome
    Dennis Ballinger; Fiscal Year: 2004
    ..abstract_text> ..
  68. DNA Sequencing at a Stretch
    Di Gao; Fiscal Year: 2009
    ....
  69. APPLYING GENOME MISMATCH SCANNING TO THE HUMAN GENOME
    Patrick Brown; Fiscal Year: 1999
    ..2. Further developing the enzymatic and hybridization steps in the procedure. 3. Developing PCR- based variations on GMS for affected relative pair and linkage disequilibrium mapping in the human genome. ..
  70. GENETIC ANALYSIS OF RIBOSOMAL RNA FUNCTION
    Philip Cunningham; Fiscal Year: 2000
    ..Phylogenetic analyses and our previous results suggest that base pairing at specific residues between two of these highly conserved sequences is required for ribosome function...