Experts and Doctors on nucleic acid conformation in United States

Summary

Locale: United States
Topic: nucleic acid conformation

Top Publications

  1. Schumacher M, Choi K, Lu F, Zalkin H, Brennan R. Mechanism of corepressor-mediated specific DNA binding by the purine repressor. Cell. 1995;83:147-55 pubmed
  2. Mougel M, Barklis E. A role for two hairpin structures as a core RNA encapsidation signal in murine leukemia virus virions. J Virol. 1997;71:8061-5 pubmed
    ..These results suggest that C and D stem-and-loop sequences contribute to the M-MuLV cis-acting site for encapsidation. ..
  3. Garzon R, Pichiorri F, Palumbo T, Iuliano R, Cimmino A, Aqeilan R, et al. MicroRNA fingerprints during human megakaryocytopoiesis. Proc Natl Acad Sci U S A. 2006;103:5078-83 pubmed
    ..Our data delineate the expression of microRNAs during megakaryocytopoiesis and suggest a regulatory role of microRNAs in this process by targeting megakaryocytic transcription factors. ..
  4. John S, Wang T, Steffen S, Longhi S, Schmaljohn C, Jonsson C. Ebola virus VP30 is an RNA binding protein. J Virol. 2007;81:8967-76 pubmed publisher
    ..Thus, we show for the first time the direct interaction of EBOV VP30 with RNA and the importance of the N-terminal region for binding RNA...
  5. Roshan U, Chikkagoudar S, Livesay D. Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics. 2008;9:61 pubmed publisher
  6. Tran T, Disney M. Molecular recognition of 6'-N-5-hexynoate kanamycin A and RNA 1x1 internal loops containing CA mismatches. Biochemistry. 2011;50:962-9 pubmed publisher
    ..These studies provide a detailed investigation of factors affecting small molecule recognition of internal loops containing C·A mismatches, which are present in a variety of RNAs that cause disease. ..
  7. Patterson Fortin L, Vakulskas C, Yakhnin H, Babitzke P, Romeo T. Dual posttranscriptional regulation via a cofactor-responsive mRNA leader. J Mol Biol. 2013;425:3662-77 pubmed publisher
    ..While we are not aware of similar dual posttranscriptional regulatory mechanisms, additional examples are likely to emerge. ..
  8. Subsoontorn P, Kim J, Winfree E. Ensemble Bayesian analysis of bistability in a synthetic transcriptional switch. ACS Synth Biol. 2012;1:299-316 pubmed publisher
    ..Our work demonstrates that programmable in vitro biochemical circuits can serve as a testing ground for evaluating methods for the design and analysis of more complex biochemical systems such as living cells. ..
  9. Yin Z, Jayaram M, Pathania S, Harshey R. The Mu transposase interwraps distant DNA sites within a functional transpososome in the absence of DNA supercoiling. J Biol Chem. 2005;280:6149-56 pubmed
    ..We discuss the contribution of both MuA and DNA supercoiling to the 5-noded Mu synapse built at the 3-way junction...

More Information

Publications512 found, 100 shown here

  1. Seetharaman M, Eldho N, Padgett R, Dayie K. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. RNA. 2006;12:235-47 pubmed
  2. Abad M, Rao B, Jackman J. Template-dependent 3'-5' nucleotide addition is a shared feature of tRNAHis guanylyltransferase enzymes from multiple domains of life. Proc Natl Acad Sci U S A. 2010;107:674-9 pubmed publisher
  3. Grierson P, Lillard K, Behbehani G, Combs K, Bhattacharyya S, Acharya S, et al. BLM helicase facilitates RNA polymerase I-mediated ribosomal RNA transcription. Hum Mol Genet. 2012;21:1172-83 pubmed publisher
    ..Given the intricate relationship between rDNA metabolism and growth, our data may help in understanding the etiology of proportional dwarfism in BS. ..
  4. Lin C, Hurley L. Determination of the major tautomeric form of the covalently modified adenine in the (+)-CC-1065-DNA adduct by 1H and 15N NMR studies. Biochemistry. 1990;29:9503-7 pubmed
    ..Parallel 15N NMR experiments on the [6-15N]deoxyadenosine-labeled (+)-CC-1065-12-mer duplex adduct show a triplet-like signal around -276.9 ppm and coupling constants of 91.5 and 85.6 Hz.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  5. Ho P, Eichman B. The crystal structures of DNA Holliday junctions. Curr Opin Struct Biol. 2001;11:302-8 pubmed
    ..Together, these structures provide insight into how local and distant interactions help to define the detailed and general physical features of Holliday junctions at the atomic level. ..
  6. Freitas M, Marshall A. Gas phase RNA and DNA ions 2. Conformational dependence of the gas-phase H/D exchange of nucleotide-5'-monophosphates. J Am Soc Mass Spectrom. 2001;12:780-5 pubmed
  7. Tuxworth W, Saghir A, Spruill L, Menick D, McDermott P. Regulation of protein synthesis by eIF4E phosphorylation in adult cardiocytes: the consequence of secondary structure in the 5'-untranslated region of mRNA. Biochem J. 2004;378:73-82 pubmed
    ..These findings indicate that the positive effect of eIF4E phosphorylation on translational efficiency in adult cardiocytes is coupled with the stability of mRNA. ..
  8. Yang Z, Colis L, Basu A, Zou Y. Recognition and incision of gamma-radiation-induced cross-linked guanine-thymine tandem lesion G[8,5-Me]T by UvrABC nuclease. Chem Res Toxicol. 2005;18:1339-46 pubmed
    ..Our result suggests that G[8,5-Me]T intrastrand cross-link is more resistant to excision repair in comparison with the T[6,4]T and AAF adducts and thus will likely persist longer in E. coli cells. ..
  9. Hamilton C, Greco T, Vizthum C, Ginter J, Johnston M, Mueller E. Mechanistic investigations of the pseudouridine synthase RluA using RNA containing 5-fluorouridine. Biochemistry. 2006;45:12029-38 pubmed
    ..These results are interpreted in light of a consistent mechanistic scheme for the handling of f5U by psi synthases. ..
  10. Saikia M, Krokowski D, Guan B, Ivanov P, Parisien M, Hu G, et al. Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. J Biol Chem. 2012;287:42708-25 pubmed publisher
    ..Identification of the stress-specific tRNA cleavage mechanisms and patterns will provide insights into the role of tRNA fragments in signaling pathways and stress-related disorders. ..
  11. Burke J, Kelenis D, Kincaid R, Sullivan C. A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA. RNA. 2014;20:1068-77 pubmed publisher
    ..This study provides mechanistic insight into pri-miRNA processing in cells that has numerous biological implications and will assist in refining Drosha-dependent shRNA design. ..
  12. Yu J, Anchordoquy T. Effects of moisture content on the storage stability of dried lipoplex formulations. J Pharm Sci. 2009;98:3278-89 pubmed publisher
  13. Andronescu M, Pop C, Condon A. Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA. 2010;16:26-42 pubmed publisher
    ..Specifically, the prediction accuracy when using our new parameters improves from 68% to 79% for the DP model, and from 70% to 77% for the CC model. ..
  14. Minca E, Kowalski D. Multiple Rad5 activities mediate sister chromatid recombination to bypass DNA damage at stalled replication forks. Mol Cell. 2010;38:649-61 pubmed publisher
    ..Our results indicate that multiple activities of Rad5 function coordinately with homologous recombination factors to enable replication template switch events that join sister chromatids at stalled forks and bypass DNA damage. ..
  15. Kuo C, Zou A, Jayaram M, Getzoff E, Harshey R. DNA-protein complexes during attachment-site synapsis in Mu DNA transposition. EMBO J. 1991;10:1585-91 pubmed
    ..Three of these sites are loosely held and can be emptied of A upon challenge with heparin. A synaptic complex with only three sites occupied is stable and is fully competent in the subsequent strand-transfer step of transposition...
  16. Rajkovic A, Davis R, Simonsen J, Rottman F. A spliced leader is present on a subset of mRNAs from the human parasite Schistosoma mansoni. Proc Natl Acad Sci U S A. 1990;87:8879-83 pubmed
    ..The presence of a SL sequence in S. mansoni, a member of the phylum Platyhelminthes, suggests that transplicing may be a common feature of other lower invertebrates. ..
  17. Saks M, Sampson J. Variant minihelix RNAs reveal sequence-specific recognition of the helical tRNA(Ser) acceptor stem by E.coli seryl-tRNA synthetase. EMBO J. 1996;15:2843-9 pubmed
    ..The latter effect derives from the organization of the specific contacts that SerRS makes with the neighboring 2--71 and 4--69 acceptor stem base pairs. ..
  18. Gourse R, Gaal T, Bartlett M, Appleman J, Ross W. rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli. Annu Rev Microbiol. 1996;50:645-77 pubmed
    ..The mechanisms contributing to rRNA transcription work together and compensate for one another when individual systems are rendered inoperative. ..
  19. Marx G, Zhou H, Graves D, Osheroff N. Covalent attachment of ethidium to DNA results in enhanced topoisomerase II-mediated DNA cleavage. Biochemistry. 1997;36:15884-91 pubmed
    ..Finally, they provide support for the recently proposed "positional poisoning model" for the actions of DNA lesions and anticancer drugs on the type II enzyme. ..
  20. Chaires J. Drug--DNA interactions. Curr Opin Struct Biol. 1998;8:314-20 pubmed
  21. Dong J, Drohat A, Stivers J, Pankiewicz K, Carey P. Raman spectroscopy of uracil DNA glycosylase-DNA complexes: insights into DNA damage recognition and catalysis. Biochemistry. 2000;39:13241-50 pubmed
    ..These observations are generally not apparent from the high-resolution crystal structures of UDG and its complexes with DNA; thus, Raman spectroscopy can provide unique and valuable insights into the nature of enzyme-DNA interactions. ..
  22. Kern J, Thomas P, Kerwin S. The relationship between ligand aggregation and G-quadruplex DNA selectivity in a series of 3,4,9,10-perylenetetracarboxylic acid diimides. Biochemistry. 2002;41:11379-89 pubmed
    ..The potential impact of these findings on the selectivity of other classes of G-quadruplex DNA ligands is discussed. ..
  23. Ling J, Morley S, Pain V, Marzluff W, Gallie D. The histone 3'-terminal stem-loop-binding protein enhances translation through a functional and physical interaction with eukaryotic initiation factor 4G (eIF4G) and eIF3. Mol Cell Biol. 2002;22:7853-67 pubmed
    ..These data indicate that SLBP stimulates the translation of histone mRNAs through a functional interaction with both the mRNA stem-loop and the 5' cap that is mediated by eIF4G and eIF3. ..
  24. Pogany J, Fabian M, White K, Nagy P. A replication silencer element in a plus-strand RNA virus. EMBO J. 2003;22:5602-11 pubmed
    ..Because similar silencer-promoter interactions are also predicted in other virus genera, this type of RNA-based regulatory mechanism may represent a widely utilized strategy for modulating replication...
  25. Sharkady S, Williams K. A third lineage with two-piece tmRNA. Nucleic Acids Res. 2004;32:4531-8 pubmed
  26. Carrigan M, Ricardo A, Ang D, Benner S. Quantitative analysis of a RNA-cleaving DNA catalyst obtained via in vitro selection. Biochemistry. 2004;43:11446-59 pubmed
    ..This study of a specific catalytically active DNAzyme is an example of studies that will be necessary generally to permit in vitro selection to help us understand the distribution of function in sequence space. ..
  27. Baker D, Youssef O, Chastkofsky M, Dy D, Terns R, Terns M. RNA-guided RNA modification: functional organization of the archaeal H/ACA RNP. Genes Dev. 2005;19:1238-48 pubmed
    ..Cbf5 is the protein that specifically recognizes and binds H/ACA guide RNAs. In addition, Cbf5 recruits the two other essential proteins, Gar1 and Nop10, to the pseudouridylation guide complex...
  28. Guo M, Spitale R, Volpini R, Krucinska J, Cristalli G, Carey P, et al. Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation. J Am Chem Soc. 2009;131:12908-9 pubmed publisher
    ..Overall, the results establish a cogent structure-function paradigm that expands our understanding of how RNA structure can enhance nucleobase reactivity to catalyze biological reactions. ..
  29. Qualley D, STEWART MAYNARD K, Wang F, Mitra M, Gorelick R, Rouzina I, et al. C-terminal domain modulates the nucleic acid chaperone activity of human T-cell leukemia virus type 1 nucleocapsid protein via an electrostatic mechanism. J Biol Chem. 2010;285:295-307 pubmed publisher
    ..The latter inhibits both NA/NC aggregation and rapid protein dissociation from single-stranded DNA. These features make HTLV-1 NC a poor NA chaperone, despite its robust duplex destabilizing capability. ..
  30. Foster E, Simmons D. The SV40 large T-antigen origin binding domain directly participates in DNA unwinding. Biochemistry. 2010;49:2087-96 pubmed publisher
    ..We present a model of DNA threading through the T-ag complex illustrating how single-stranded DNA could pass close to a trough generated by key residues in one monomer of the OBD hexamer. ..
  31. Brooks K, Hampel K. Rapid steps in the glmS ribozyme catalytic pathway: cation and ligand requirements. Biochemistry. 2011;50:2424-33 pubmed publisher
    ..Folding of the ribozyme is, therefore, relatively independent of cation identity, but the rapid initiation of catalysis upon the addition of ligand is stricter. ..
  32. Stöger R, Genereux D, Hagerman R, Hagerman P, Tassone F, Laird C. Testing the FMR1 promoter for mosaicism in DNA methylation among CpG sites, strands, and cells in FMR1-expressing males with fragile X syndrome. PLoS ONE. 2011;6:e23648 pubmed publisher
    ..Our data indicate that cryptic inter-cell mosaicism in DNA methylation can account for the presence of FMR1 mRNA in some individuals with FXS...
  33. Burke J, Sashital D, Zuo X, Wang Y, Butcher S. Structure of the yeast U2/U6 snRNA complex. RNA. 2012;18:673-83 pubmed publisher
    ..This observation suggests that the U2/U6 structure is well-suited for orienting substrate and cofactors during splicing catalysis. ..
  34. Dhahbi J, Spindler S, Atamna H, Boffelli D, Mote P, Martin D. 5'-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics. 2013;45:990-8 pubmed publisher
    ..The function of the 5'-YRNA fragments is at present unknown, but the processing and secretion of specific YRNAs to produce 5'-end fragments that circulate in stable complexes are consistent with a signaling function. ..
  35. Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov A, Sweeney B, Zirbel C, et al. The Nucleic Acid Database: new features and capabilities. Nucleic Acids Res. 2014;42:D114-22 pubmed publisher
    ..This article describes the recent redesign of the NDB Web site with special emphasis on new RNA-derived data and annotations and their implementation and integration into the search capabilities. ..
  36. Trotta C, Miao F, Arn E, Stevens S, Ho C, Rauhut R, et al. The yeast tRNA splicing endonuclease: a tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell. 1997;89:849-58 pubmed
    ..The presence of endonuclease in Eucarya and Archaea suggests an ancient origin for the tRNA splicing reaction. ..
  37. Heldwein E, Brennan R. Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature. 2001;409:378-82 pubmed
    ..The structure reveals an unexpected mechanism for transcription activation that involves localized base-pair breaking, and base sliding and realignment of the -35 and -10 operator elements. ..
  38. Diamond J, Turner D, Mathews D. Thermodynamics of three-way multibranch loops in RNA. Biochemistry. 2001;40:6971-81 pubmed
    ..Incorporation of the experimental data into the mfold and RNA structure computer programs has contributed to an improvement in prediction of RNA secondary structure from sequence. ..
  39. Igo R, Lawson S, Stuart K. RNA sequence and base pairing effects on insertion editing in Trypanosoma brucei. Mol Cell Biol. 2002;22:1567-76 pubmed
    ..Thus, several aspects of mRNA-gRNA interaction, as well as gRNA base pairing with added U's, optimize editing efficiency, although they are not required for insertion editing. ..
  40. Srinivasan G, James C, Krzycki J. Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science. 2002;296:1459-62 pubmed
    ..Charging a tRNA(CUA) with lysine is a likely first step in translating UAG amber codons as pyrrolysine in certain methanogens. Our results indicate that pyrrolysine is the 22nd genetically encoded natural amino acid...
  41. Ge X, Wu Q, Wang S. SAGE detects microRNA precursors. BMC Genomics. 2006;7:285 pubmed
    ..The observation that some orphan longSAGE tags uniquely match miRNA precursors provides information about the expression of some known and predicted miRNAs. ..
  42. Matsuda D, Dreher T. Cap- and initiator tRNA-dependent initiation of TYMV polyprotein synthesis by ribosomes: evaluation of the Trojan horse model for TYMV RNA translation. RNA. 2007;13:129-37 pubmed
    ..These results favor the initiation coupling model...
  43. Judelson H, Tani S. Transgene-induced silencing of the zoosporogenesis-specific NIFC gene cluster of Phytophthora infestans involves chromatin alterations. Eukaryot Cell. 2007;6:1200-9 pubmed
    ..These data help illuminate the mechanism of silencing in Phytophthora and suggest that caution should be used when interpreting silencing experiments involving closely spaced genes. ..
  44. Czyz A, Stillmock K, Hazuda D, Reznikoff W. Dissecting Tn5 transposition using HIV-1 integrase diketoacid inhibitors. Biochemistry. 2007;46:10776-89 pubmed
    ..Thus, DKA inhibitors will provide an important set of tools to investigate the mechanism of action of transposases and integrases. ..
  45. Degtyareva N, Fresia M, Petty J. DNA conformational effects on the interaction of netropsin with A-tract sequences. Biochemistry. 2007;46:15136-43 pubmed
    ..We suggest that these two factors influence the conformation of the minor-groove binding site of DNA. ..
  46. Klein D, Ferré D Amaré A. Crystallization of the glmS ribozyme-riboswitch. Methods Mol Biol. 2009;540:129-39 pubmed publisher
    ..Although their details are specific to the glmS ribozyme, these general strategies may be useful for analyzing and improving crystals of other RNAs. ..
  47. Motea E, Berdis A. Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. Biochim Biophys Acta. 2010;1804:1151-66 pubmed publisher
    ..Finally, the biomedical role of this specialized DNA polymerase is discussed focusing on its involvement in cancer development and its use in biomedical applications such as labeling DNA for detecting apoptosis. ..
  48. Andronescu M, Condon A, Hoos H, Mathews D, Murphy K. Computational approaches for RNA energy parameter estimation. RNA. 2010;16:2304-18 pubmed publisher
    ..Our data, software, results, and parameter sets in various formats are freely available at http://www.cs.ubc.ca/labs/beta/Projects/RNA-Params. ..
  49. Smith A, Fuchs R, Grundy F, Henkin T. The SAM-responsive S(MK) box is a reversible riboswitch. Mol Microbiol. 2010;78:1393-402 pubmed publisher
  50. Pathak K, Pogany J, Xu K, White K, Nagy P. Defining the roles of cis-acting RNA elements in tombusvirus replicase assembly in vitro. J Virol. 2012;86:156-71 pubmed publisher
    ..Collectively, this work has revealed new functions for tombusvirus cis-acting RNA elements and provided insights into the pioneering round of minus-strand synthesis...
  51. Choi S, Seo J, Kwon S, Rao A. Helper virus-independent transcription and multimerization of a satellite RNA associated with cucumber mosaic virus. J Virol. 2012;86:4823-32 pubmed publisher
  52. Gray R, Trent J, Chaires J. Folding and unfolding pathways of the human telomeric G-quadruplex. J Mol Biol. 2014;426:1629-50 pubmed publisher
    ..These experiments reveal a slow, rate-limiting step along the unfolding pathway. ..
  53. Litke J, Li Y, Nocka L, Mukerji I. Probing the Ion Binding Site in a DNA Holliday Junction Using Förster Resonance Energy Transfer (FRET). Int J Mol Sci. 2016;17:366 pubmed publisher
    ..These results support a model in which site-specific binding of two ions in close proximity is required for folding of DNA Holliday junctions into the stacked-X conformation. ..
  54. Lewis N, Williams J, Rekosh D, Hammarskjold M. Identification of a cis-acting element in human immunodeficiency virus type 2 (HIV-2) that is responsive to the HIV-1 rev and human T-cell leukemia virus types I and II rex proteins. J Virol. 1990;64:1690-7 pubmed
    ..The rex proteins worked well in conjunction with either the HIV-1 or the HIV-2 RRE (the 1,042-bp as well as the 272-bp fragment)...
  55. Blinkowa A, Walker J. Programmed ribosomal frameshifting generates the Escherichia coli DNA polymerase III gamma subunit from within the tau subunit reading frame. Nucleic Acids Res. 1990;18:1725-9 pubmed
  56. Marrione P, Cox M. Allosteric effects of RuvA protein, ATP, and DNA on RuvB protein-mediated ATP hydrolysis. Biochemistry. 1996;35:11228-38 pubmed
    ..We propose a model in which individual subunits in a RuvB hexamer are functionally paired, with the three pairs moving sequentially and cooperatively through a multistep ATP hydrolytic cycle. ..
  57. Wang Y, Feng L, Said M, Balderman S, Fayazi Z, Liu Y, et al. Analysis of the 2.0 A crystal structure of the protein-DNA complex of the human PDEF Ets domain bound to the prostate specific antigen regulatory site. Biochemistry. 2005;44:7095-106 pubmed
    ..Collectively, the common and unique interactions with both the DNA bases and the backbone phosphates lead to substrate specificity and individual preference for certain DNA sites. ..
  58. Roy H, Ling J, Alfonzo J, Ibba M. Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem. 2005;280:38186-92 pubmed
  59. Adkins N, McBryant S, Johnson C, Leidy J, Woodcock C, Robert C, et al. Role of nucleic acid binding in Sir3p-dependent interactions with chromatin fibers. Biochemistry. 2009;48:276-88 pubmed publisher
    ..The initial step appears to be rapidly followed by the spreading of silencing using linker DNA as a track. ..
  60. Valadkhan S, Mohammadi A, Jaladat Y, Geisler S. Protein-free small nuclear RNAs catalyze a two-step splicing reaction. Proc Natl Acad Sci U S A. 2009;106:11901-6 pubmed publisher
    ..These results prove that the complex formed by U6 and U2 RNAs is a ribozyme and can potentially carry out RNA-based catalysis in the spliceosome. ..
  61. Hou C, Chan N, Gu L, Li G. Incision-dependent and error-free repair of (CAG)(n)/(CTG)(n) hairpins in human cell extracts. Nat Struct Mol Biol. 2009;16:869-75 pubmed publisher
    ..We discuss the implications of these data for understanding the etiology of neurological diseases and trinucleotide repeat instability. ..
  62. Zhao H, Finch C, Sequeira R, Johnson B, Johnson J, Casjens S, et al. Crystal structure of the DNA-recognition component of the bacterial virus Sf6 genome-packaging machine. Proc Natl Acad Sci U S A. 2010;107:1971-6 pubmed publisher
  63. Aker M, Bomsztyk K, Emery D. Poly(ADP-ribose) polymerase-1 (PARP-1) contributes to the barrier function of a vertebrate chromatin insulator. J Biol Chem. 2010;285:37589-97 pubmed publisher
    ..Taken together, this study demonstrates that binding of PARP-1 plays a key functional role in the barrier activity of the extended cHS4 insulator core element. ..
  64. Koh Y, Wang Y, Qiu C, Opperman L, Gross L, Tanaka Hall T, et al. Stacking interactions in PUF-RNA complexes. RNA. 2011;17:718-27 pubmed publisher
  65. Kirmizialtin S, Silalahi A, Elber R, Fenley M. The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophys J. 2012;102:829-38 pubmed publisher
    ..However, Mg(2+) distributions are still at significant variances for shorter distances. ..
  66. Mitchell D, Jarmoskaite I, Seval N, Seifert S, Russell R. The long-range P3 helix of the Tetrahymena ribozyme is disrupted during folding between the native and misfolded conformations. J Mol Biol. 2013;425:2670-86 pubmed publisher
    ..Further, the results strongly suggest that misfolding arises from a topological error within the ribozyme core, and a specific topology is proposed. ..
  67. Gracia B, Russell R. RNA catalytic activity as a probe of chaperone-mediated RNA folding. Methods Mol Biol. 2014;1086:225-37 pubmed publisher
    ..This protocol allows folding to be followed under a broad range of solution conditions, including those that do not support catalytic activity, and facilitates studies of chaperone proteins. ..
  68. Mutisya D, Hardcastle T, Cheruiyot S, Pallan P, Kennedy S, Egli M, et al. Amide linkages mimic phosphates in RNA interactions with proteins and are well tolerated in the guide strand of short interfering RNAs. Nucleic Acids Res. 2017;45:8142-8155 pubmed publisher
    ..Our results suggest that an amide can mimic important hydrogen bonding interactions with proteins required for RNAi activity and may be a promising modification for optimization of biological properties of siRNAs. ..
  69. Shan Q, Cox M, Inman R. DNA strand exchange promoted by RecA K72R. Two reaction phases with different Mg2+ requirements. J Biol Chem. 1996;271:5712-24 pubmed
    ..The mutant protein also facilitates the autocatalytic cleavage of the LexA repressor, but at a reduced rate. ..
  70. Bull J, Jacobson A, Badgett M, Molineux I. Viral escape from antisense RNA. Mol Microbiol. 1998;28:835-46 pubmed
    ..Thus, at least in this system, a population of viruses that evolved to escape from a single antisense RNA would require a cocktail of several antisense RNAs for inhibition. ..
  71. Frank J, Sengupta J, Gao H, Li W, Valle M, Zavialov A, et al. The role of tRNA as a molecular spring in decoding, accommodation, and peptidyl transfer. FEBS Lett. 2005;579:959-62 pubmed
    ..Recent findings show that the tRNA structure itself undergoes large conformational changes as well, and that the decoding process must be seen as a complex dynamic interplay between tRNA and the ribosome. ..
  72. Santangelo T, Reeve J. Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol. 2006;355:196-210 pubmed
  73. Gong B, Chen J, Chase E, Chadalavada D, Yajima R, Golden B, et al. Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. J Am Chem Soc. 2007;129:13335-42 pubmed
  74. Chen Y, Potratz J, Tijerina P, Del Campo M, Lambowitz A, Russell R. DEAD-box proteins can completely separate an RNA duplex using a single ATP. Proc Natl Acad Sci U S A. 2008;105:20203-8 pubmed publisher
    ..This mechanism may underlie the functions of DEAD-box proteins by allowing them to generate local rearrangements without disrupting the global structures of their targets. ..
  75. Kulshina N, Baird N, Ferré D Amaré A. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nat Struct Mol Biol. 2009;16:1212-7 pubmed publisher
  76. Yu Q, Kuzmiak H, Olsen L, Kulkarni A, Fink E, Zou Y, et al. Saccharomyces cerevisiae Esc2p interacts with Sir2p through a small ubiquitin-like modifier (SUMO)-binding motif and regulates transcriptionally silent chromatin in a locus-dependent manner. J Biol Chem. 2010;285:7525-36 pubmed publisher
    ..Moreover, we dissect Esc2p and identify a putative SUMO-binding motif that is necessary and sufficient for interacting with Sir2p and SUMO and is required for the function of Esc2p in transcriptional silencing. ..
  77. Jagadeeswaran G, Zheng Y, Sumathipala N, Jiang H, Arrese E, Soulages J, et al. Deep sequencing of small RNA libraries reveals dynamic regulation of conserved and novel microRNAs and microRNA-stars during silkworm development. BMC Genomics. 2010;11:52 pubmed publisher
    ..We identified 101 homologs of conserved miRNAs, 14 species-specific and two antisense miRNAs in the silkworm. Our results provided deeper insights into changes in conserved and novel miRNA and miRNA* accumulation during development. ..
  78. Zadeh J, Wolfe B, Pierce N. Nucleic acid sequence design via efficient ensemble defect optimization. J Comput Chem. 2011;32:439-52 pubmed publisher
    ..Empirically, the sequence design algorithm exhibits asymptotic optimality and the exponent in the time complexity bound is sharp. ..
  79. Degtyareva N, Petty J. Non-B conformations of CAG repeats using 2-aminopurine. Methods Enzymol. 2011;492:213-31 pubmed publisher
    ..Because 2-aminopurine provides both structural and energetic information via fluorescence and also is an innocuous substitution for adenine, significant progress in elucidating the secondary structures of (CAG) repeats will be achieved. ..
  80. Seth P, Yu J, Jazayeri A, Pallan P, Allerson C, Østergaard M, et al. Synthesis and antisense properties of fluoro cyclohexenyl nucleic acid (F-CeNA), a nuclease stable mimic of 2'-fluoro RNA. J Org Chem. 2012;77:5074-85 pubmed publisher
  81. Chen A, Garcia A. Mechanism of enhanced mechanical stability of a minimal RNA kissing complex elucidated by nonequilibrium molecular dynamics simulations. Proc Natl Acad Sci U S A. 2012;109:E1530-9 pubmed publisher
    ..We propose that these stabilizing features explain the unusual stability of other retroviral kissing-loop complexes such as the HIV dimerization site. ..
  82. Kranawetter C, Brady S, Sun L, Schroeder M, Chen S, Heng X. Nuclear Magnetic Resonance Study of RNA Structures at the 3'-End of the Hepatitis C Virus Genome. Biochemistry. 2017;56:4972-4984 pubmed publisher
    ..Our NMR detection of these RNA conformations and the structural equilibrium in the 3'-end of the HCV genome support its roles in coordinating various steps of HCV replication...
  83. LeBlanc R, Longhini A, Le Grice S, Johnson B, Dayie T. Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment. Nucleic Acids Res. 2017;45:e146 pubmed publisher
    ..The method was further extended to assigning a 6 nt bulge from a 61 nt viral RNA element justifying its use for a wide range RNA chemical shift resonance assignment problems...
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