Genomes and Genes
Experts and Doctors on nucleic acid conformation in United Kingdom
Locale: United Kingdom
Topic: nucleic acid conformation
Publications113 found, 100 shown here
- Tse M, Blatchford C, Oya Alpar H. Evaluation of different buffers on plasmid DNA encapsulation into PLGA microparticles. Int J Pharm. 2009;370:33-40 pubmed publisher..1M NaHCO(3). These results demonstrate that the use of different buffers can aid in retaining the conformation of plasmid DNA, and can also modulate the amount of DNA encapsulated and the release profiles of microparticles. ..
- Cornet F, Hallet B, Sherratt D. Xer recombination in Escherichia coli. Site-specific DNA topoisomerase activity of the XerC and XerD recombinases. J Biol Chem. 1997;272:21927-31 pubmed..XerC or XerD relaxation activities are completely inhibited by the addition of the partner recombinase, providing that the DNA recognition sequence for the inhibiting partner is present. ..
- Cannon W, Gallegos M, Buck M. DNA melting within a binary sigma(54)-promoter DNA complex. J Biol Chem. 2001;276:386-94 pubmed
- Kampmann M. Obstacle bypass in protein motion along DNA by two-dimensional rather than one-dimensional sliding. J Biol Chem. 2004;279:38715-20 pubmed..As illustrated by Monte-Carlo simulation, two-dimensional sliding may not only allow proteins to move around nucleosomes in vivo but also reduce the redundancy of their search for the target site. ..
- Martin C, Ellis T, McGurk C, Jenkins T, Hartley J, Waring M, et al. Sequence-selective interaction of the minor-groove interstrand cross-linking agent SJG-136 with naked and cellular DNA: footprinting and enzyme inhibition studies. Biochemistry. 2005;44:4135-47 pubmed..Finally, SJG-136 efficiently inhibits the action of restriction endonuclease BglII, which has a 5'-A-GATC-T-3' motif at its cleavage site. ..
- Morgan K, Conklin D, Pawson A, Sellar R, Ott T, Millar R. A transcriptionally active human type II gonadotropin-releasing hormone receptor gene homolog overlaps two genes in the antisense orientation on chromosome 1q.12. Endocrinology. 2003;144:423-36 pubmed..A stem-loop motif resembling a selenocysteine insertion sequence and a potential alternative translation initiation site might enable expression of further proteins involved in interactions within the GnRH system. ..
- Russo Krauss I, Ramaswamy S, Neidle S, Haider S, Parkinson G. Structural Insights into the Quadruplex-Duplex 3' Interface Formed from a Telomeric Repeat: A Potential Molecular Target. J Am Chem Soc. 2016;138:1226-33 pubmed publisher..However, with the rearrangement of a single nucleotide, a stable pocket can be produced, thus providing an opportunity for the binding of selective molecules at the interface. ..
- Arnvig K, Pennell S, Gopal B, Colston M. A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2004;101:8325-30 pubmed..Finally, we present evidence that this NusA-RNA interaction affects transcriptional events further downstream. ..
- Tedder P, Zubko E, Westhead D, Meyer P. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA. RNA. 2009;15:1012-20 pubmed publisher..Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. ..
- Moran S, Flanagan J, Namy O, Stuart D, Brierley I, Gilbert R. The mechanics of translocation: a molecular "spring-and-ratchet" system. Structure. 2008;16:664-72 pubmed publisher..The tRNA can thus be considered a molecular spring and EF-2 a Brownian ratchet in a "spring-and-ratchet" system within the translocation process. ..
- Hall J, O Sullivan K, Naseer A, Smith J, Kelly J, Cardin C. Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand. Proc Natl Acad Sci U S A. 2011;108:17610-4 pubmed publisher..The result is noncovalent cross-linking and marked kinking of DNA. ..
- Brackley C, Taylor S, Papantonis A, Cook P, Marenduzzo D. Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization. Proc Natl Acad Sci U S A. 2013;110:E3605-11 pubmed publisher..We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template. ..
- Bai X, Martin T, Scheres S, Dietz H. Cryo-EM structure of a 3D DNA-origami object. Proc Natl Acad Sci U S A. 2012;109:20012-7 pubmed publisher..Thereby, our results indicate an attractive route to fabricate nanoscale devices that achieve complex functionalities by DNA-templated design steered by structural feedback. ..
- Hallet B, Arciszewska L, Sherratt D. Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD: an enzymatic switch in site-specific recombination. Mol Cell. 1999;4:949-59 pubmed
- Gadhavi P, Greenwood M, Strom M, King I, Buxton R. The regulatory region of the human desmocollin 3 promoter forms a DNA four-way junction. Biochem Biophys Res Commun. 2001;281:520-8 pubmed
- Pöyry T, Hentze M, Jackson R. Construction of regulatable picornavirus IRESes as a test of current models of the mechanism of internal translation initiation. RNA. 2001;7:647-60 pubmed
- Pöyry T, Kaminski A, Connell E, Fraser C, Jackson R. The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation. Genes Dev. 2007;21:3149-62 pubmed
- Bakhshesh M, Groppelli E, Willcocks M, Royall E, Belsham G, Roberts L. The picornavirus avian encephalomyelitis virus possesses a hepatitis C virus-like internal ribosome entry site element. J Virol. 2008;82:1993-2003 pubmed..AEV is therefore another example of a picornavirus harboring an HCV-like IRES element within its genome, and thus, its classification within the hepatovirus genus may need to be reassessed in light of these findings...
- Kershaw C, Barrass J, Beggs J, O Keefe R. Mutations in the U5 snRNA result in altered splicing of subsets of pre-mRNAs and reduced stability of Prp8. RNA. 2009;15:1292-304 pubmed publisher..Therefore, the integrity of U5 is important for the stability of Prp8 during splicing and provides one possible explanation for why U5 loop 1 and Prp8 are so highly conserved. ..
- Tosch P, Wälti C, Middelberg A, Davies A. Generic technique to generate large branched DNA complexes. Biomacromolecules. 2006;7:677-81 pubmed..The effectiveness of this technique is demonstrated here by the use of Lambda Bacteriophage DNA as a template to generate single- and double-branched DNA structures approximately 120 nm in size. ..
- Wilson T, Li N, Lu J, Frederiksen J, Piccirilli J, Lilley D. Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme. Proc Natl Acad Sci U S A. 2010;107:11751-6 pubmed publisher..We conclude that cleavage of the substrate by the VS ribozyme is catalyzed by deprotonation of the 2'-O nucleophile by G638 and protonation of the 5'-O leaving group by A756. ..
- Liu Z, Laggerbauer B, Luhrmann R, Smith C. Crosslinking of the U5 snRNP-specific 116-kDa protein to RNA hairpins that block step 2 of splicing. RNA. 1997;3:1207-19 pubmed..The crosslinking characteristics of U5 p116 are consistent with it having a role in locating the 3' splice site AG prior to step 2 of splicing. ..
- Baumann P, Benson F, West S. Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro. Cell. 1996;87:757-66 pubmed..It is proposed that hRad51 mediates homology recognition and initiates strand exchange, but that extensive heteroduplex formation in higher organisms requires the actions of additional proteins. ..
- McGlynn P, Al Deib A, Liu J, Marians K, Lloyd R. The DNA replication protein PriA and the recombination protein RecG bind D-loops. J Mol Biol. 1997;270:212-21 pubmed..RecG, like PriA, binds D-loops and unwinds the DNA. However, it prefers branched structures with at least two duplex components. The possibility that it competes with PriA for binding recombination intermediates is discussed. ..
- Cromie G, Millar C, Schmidt K, Leach D. Palindromes as substrates for multiple pathways of recombination in Escherichia coli. Genetics. 2000;154:513-22 pubmed..In the absence of RecA, the RecQ helicase is required for palindrome viability in a sbcC mutant, suggesting that a helicase-dependent pathway exists to allow replicative bypass of secondary structures. ..
- Crellin P, Sewitz S, Chalmers R. DNA looping and catalysis; the IHF-folded arm of Tn10 promotes conformational changes and hairpin resolution. Mol Cell. 2004;13:537-47 pubmed..Further evidence suggests that the molecular mechanism responsible may be mechanical stress in the IHF loop, related to a change in the relative position of the transposase contacts that anchor the loop on either side. ..
- Anderson E, Lever A. Human immunodeficiency virus type 1 Gag polyprotein modulates its own translation. J Virol. 2006;80:10478-86 pubmed..These results suggest that Gag controls the equilibrium between translation and packaging, ensuring production of enough molecules of Gag to make viral particles before encapsidating its genome. ..
- Frazer L, Lovell S, O Keefe R. Analysis of synthetic lethality reveals genetic interactions between the GTPase Snu114p and snRNAs in the catalytic core of the Saccharomyces cerevisiae spliceosome. Genetics. 2009;183:497-515-1SI-4SI pubmed publisher..We propose that the RNA base pairing state is directly or indirectly sensed by the Snu114p G domain allowing the Snu114p C-terminal domain to regulate Brr2p or other proteins to bring about RNA/RNA rearrangements required for splicing...
- Daldrop P, Lilley D. The plasticity of a structural motif in RNA: structural polymorphism of a kink turn as a function of its environment. RNA. 2013;19:357-64 pubmed publisher..While it has the N1 structure in the ribosome, on engineering it into the SAM-I riboswitch, it changes to the N3 structure, resulting in a significant alteration in the trajectory of the helical arms. ..
- West S. The RuvABC proteins and Holliday junction processing in Escherichia coli. J Bacteriol. 1996;178:1237-41 pubmed
- Horn W, Convery M, Stonehouse N, Adams C, Liljas L, Phillips S, et al. The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions. RNA. 2004;10:1776-82 pubmed..Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands. ..
- White M, Lilley D. Characterization of a Holliday junction-resolving enzyme from Schizosaccharomyces pombe. Mol Cell Biol. 1997;17:6465-71 pubmed..cerevisiae and S. pombe suggests that there may be a common pathway for mitochondrial homologous recombination in fungi, plants, protists, and possibly higher eukaryotes. ..
- Dix I, Russell C, O Keefe R, Newman A, Beggs J. Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae. RNA. 1998;4:1239-50 pubmed..This and the close proximity of the spliceosomal translocase, Snu114p, to U5 loop 1 and Prp8p support and extend the proposal that Snu114p mimics U5 loop 1 during a translocation event in the spliceosome. ..
- Vos S, Berrisford D, Avis J. Effect of magnesium ions on the tertiary structure of the hepatitis C virus IRES and its affinity for the cyclic peptide antibiotic viomycin. Biochemistry. 2002;41:5383-96 pubmed..In pseudoknot mutants, Mg(2+) ions have different effects on viomycin binding and thermal stability, suggesting altered tertiary interactions involving subdomain IIId. ..
- Duggin I, Bell S. The chromosome replication machinery of the archaeon Sulfolobus solfataricus. J Biol Chem. 2006;281:15029-32 pubmed..Here, we provide an overview of recent insights into the functioning of the chromosome replication machinery of S. solfataricus, focusing on some of the relatively well characterized core components that act at the DNA replication fork...
- Martinez Senac M, Webb M. Mechanism of translocation and kinetics of DNA unwinding by the helicase RecG. Biochemistry. 2005;44:16967-76 pubmed..The data support the idea that interactions of the duplex template arm with the protein are the major sites of binding and production of translocation...
- Rass U, Ahel I, West S. Molecular mechanism of DNA deadenylation by the neurological disease protein aprataxin. J Biol Chem. 2008;283:33994-4001 pubmed publisher..These results pinpoint APTX as the first protein to adopt canonical histidine triad-type reaction chemistry for the repair of DNA. ..
- Dykeman E, Twarock R. All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein. Phys Rev E Stat Nonlin Soft Matter Phys. 2010;81:031908 pubmed..Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem. ..
- Claeys Bouuaert C, Liu D, Chalmers R. A simple topological filter in a eukaryotic transposon as a mechanism to suppress genome instability. Mol Cell Biol. 2011;31:317-27 pubmed publisher..This provides constraints on the enzymatic mechanism of the double-strand breaks in mariner transposition, excluding the most prevalent of the current models. ..
- Hughes T, Brady H. Expression of axin2 is regulated by the alternative 5'-untranslated regions of its mRNA. J Biol Chem. 2005;280:8581-8 pubmed..We discuss this complex regulation in the context of the function of Axin2 as a tumor suppressor. ..
- Elson J, Smith P, Greaves L, Lightowlers R, Chrzanowska Lightowlers Z, Taylor R, et al. The presence of highly disruptive 16S rRNA mutations in clinical samples indicates a wider role for mutations of the mitochondrial ribosome in human disease. Mitochondrion. 2015;25:17-27 pubmed publisher..Thus, our work constitutes an important contribution to an emerging view of the mitoribosome as an important element in human health. ..
- Benson F, West S. Substrate specificity of the Escherichia coli RuvC protein. Resolution of three- and four-stranded recombination intermediates. J Biol Chem. 1994;269:5195-201 pubmed..We interpret these differences in terms of the contiguity of the RecA nucleoprotein filament which may, under certain conditions, limit access to the Holliday junction resolvase. ..
- Pickering T, Garforth S, Sayers J, Grasby J. Variation in the steady state kinetic parameters of wild type and mutant T5 5'-3'-exonuclease with pH. Protonation of Lys-83 is critical for DNA binding. J Biol Chem. 1999;274:17711-7 pubmed..We therefore conclude that protonation of Lys-83 in the wild type protein facilitates DNA binding. The origin of the pH dependence of the kcat parameter of the wild type enzyme is discussed. ..
- Kampranis S, Bates A, Maxwell A. A model for the mechanism of strand passage by DNA gyrase. Proc Natl Acad Sci U S A. 1999;96:8414-9 pubmed..This mechanism is concerted, in that capture of the transported segment by the ATP-operated clamp induces opening of the DNA gate, which in turn stimulates ATP hydrolysis. ..
- Chang K, Varani G, Bhattacharya S, Choi H, McClain W. Correlation of deformability at a tRNA recognition site and aminoacylation specificity. Proc Natl Acad Sci U S A. 1999;96:11764-9 pubmed..Fidelity is ensured because noncognate and inactive mutant tRNAs are bound in the active site in an incorrect conformation that reduces enzymatic activity. ..
- Morrish B, Rumsby M. The 5' untranslated region of protein kinase Cdelta directs translation by an internal ribosome entry segment that is most active in densely growing cells and during apoptosis. Mol Cell Biol. 2002;22:6089-99 pubmed..Our studies suggest a mechanism whereby PKCdelta synthesis can be maintained under these conditions when cap-dependent translation is inhibited. ..
- Beales L, Holzenburg A, Rowlands D. Viral internal ribosome entry site structures segregate into two distinct morphologies. J Virol. 2003;77:6574-9 pubmed
- Bruno M, Flaus A, Stockdale C, Rencurel C, Ferreira H, Owen Hughes T. Histone H2A/H2B dimer exchange by ATP-dependent chromatin remodeling activities. Mol Cell. 2003;12:1599-606 pubmed..This provides eukaryotes with additional means by which they may manipulate chromatin structure. ..
- McGregor N, Ayora S, Sedelnikova S, Carrasco B, Alonso J, Thaw P, et al. The structure of Bacillus subtilis RecU Holliday junction resolvase and its role in substrate selection and sequence-specific cleavage. Structure. 2005;13:1341-51 pubmed publisher..Models for a resolvase-DNA complex address how the enzyme might organize junctions into an approximately 4-fold symmetric form...
- Webster B, Rudolfov J, Hor k P, Littlewood D. The complete mitochondrial genome of the bird schistosome Trichobilharzia regenti (Platyhelminthes: Digenea), causative agent of cercarial dermatitis. J Parasitol. 2007;93:553-61 pubmed publisher..g., T. regenti characterized in this study, but also numerous species within the predominant group of visceral (blood dwelling) bird schistosomes...
- Sabbioneda S, Gourdin A, Green C, Zotter A, Giglia Mari G, Houtsmuller A, et al. Effect of proliferating cell nuclear antigen ubiquitination and chromatin structure on the dynamic properties of the Y-family DNA polymerases. Mol Biol Cell. 2008;19:5193-202 pubmed publisher..When DNA is exposed at replication forks, the polymerase residence times increase, and this is further facilitated by the ubiquitination of PCNA. ..
- Pickard B, Knight H, Hamilton R, Soares D, Walker R, Boyd J, et al. A common variant in the 3'UTR of the GRIK4 glutamate receptor gene affects transcript abundance and protects against bipolar disorder. Proc Natl Acad Sci U S A. 2008;105:14940-5 pubmed publisher..These data suggest a mechanism whereby the genetic protective effect is mediated through increased kainate receptor expression. ..
- Gardiner T, Christov C, Langley A, Krude T. A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication. RNA. 2009;15:1375-85 pubmed publisher..Therefore, we have identified a new RNA motif that is conserved in vertebrate Y RNA evolution, and essential and sufficient for Y RNA function in human chromosomal DNA replication. ..
- Zawadzki P, May P, Baker R, Pinkney J, Kapanidis A, Sherratt D, et al. Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes. Proc Natl Acad Sci U S A. 2013;110:17302-7 pubmed publisher..These observations, along with the calculated intermediate lifetimes, inform the reaction mechanism, which plays a key role in chromosome unlinking in most bacteria with circular chromosomes. ..
- Murchie A, Thomson J, Walter F, Lilley D. Folding of the hairpin ribozyme in its natural conformation achieves close physical proximity of the loops. Mol Cell. 1998;1:873-81 pubmed..The ribozyme is active as a four-way junction, and the rate of cleavage may be modulated by the conformation of the four-way junction. ..
- Dix I, Russell C, O Keefe R, Newman A, Beggs J. Protein-RNA interactions in the U5 snRNP of Saccharomyces cerevisiae. RNA. 1998;4:1675-86 pubmed..This and the close proximity of the spliceosomal translocase, Snu114p, to U5 loop 1 and Prp8p support and extend the proposal that Snu114p mimics U5 loop 1 during a translocation event in the spliceosome. ..
- Zhao Z, Wilson T, Maxwell K, Lilley D. The folding of the hairpin ribozyme: dependence on the loops and the junction. RNA. 2000;6:1833-46 pubmed..The four-way junction thus provides a scaffold in the natural RNA that facilitates the folding of the ribozyme into the active form...
- Rodriguez A. Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional "latch" in the mechanism of reverse gyrase. J Biol Chem. 2002;277:29865-73 pubmed publisher..This suggests that the mechanism of reverse gyrase is best described by a combination of recently proposed models...
- Rodr guez A. Investigating the role of the latch in the positive supercoiling mechanism of reverse gyrase. Biochemistry. 2003;42:5993-6004 pubmed publisher..The latch therefore plays an important role in the communication between the two domains of reverse gyrase...
- Punginelli C, Ize B, Stanley N, Stewart V, Sawers G, Berks B, et al. mRNA secondary structure modulates translation of Tat-dependent formate dehydrogenase N. J Bacteriol. 2004;186:6311-5 pubmed..A detailed mutational analysis has demonstrated the importance of this mRNA stem-loop in modulating FDH-N translation. ..
- Leo E, Gould K, Pan X, Capranico G, Sanderson M, Palumbo M, et al. Novel symmetric and asymmetric DNA scission determinants for Streptococcus pneumoniae topoisomerase IV and gyrase are clustered at the DNA breakage site. J Biol Chem. 2005;280:14252-63 pubmed..However, both pneumococcal enzymes cleaved an E. coli gyrase site suggesting overlap in gyrase determinants. We propose a model for the cleavage complex of topo IV/gyrase that accommodates the unique -2A/+6T and other preferences. ..
- Van de Bor V, Hartswood E, Jones C, Finnegan D, Davis I. gurken and the I factor retrotransposon RNAs share common localization signals and machinery. Dev Cell. 2005;9:51-62 pubmed..We propose that the transposition of other elements may exploit the host's RNA transport signals and machinery. ..
- Hoogenkamp M, Krysinska H, Ingram R, Huang G, Barlow R, Clarke D, et al. The Pu.1 locus is differentially regulated at the level of chromatin structure and noncoding transcription by alternate mechanisms at distinct developmental stages of hematopoiesis. Mol Cell Biol. 2007;27:7425-38 pubmed..Our results provide important insights into how overlapping, but different, sets of transcription factors program tissue-specific chromatin structures in the hematopoietic system. ..
- Joly N, Burrows P, Buck M. An intramolecular route for coupling ATPase activity in AAA+ proteins for transcription activation. J Biol Chem. 2008;283:13725-35 pubmed publisher..Such functional organization most likely applies to other AAA+ proteins, including Ltag (simian virus 40), Rep40 (Adeno-associated virus-2), and p97 (Mus musculus) in which the asparagine to Walker B motif relationship is conserved. ..
- Tan Wong S, French J, Proudfoot N, Brown M. Dynamic interactions between the promoter and terminator regions of the mammalian BRCA1 gene. Proc Natl Acad Sci U S A. 2008;105:5160-5 pubmed publisher..Significantly, BRCA1 promoter and terminator interactions vary in different breast cancer cell lines, indicating that defects in BRCA1 chromatin structure may contribute to dysregulated expression of BRCA1 seen in breast tumors. ..
- Manzano D, Marquardt S, Jones A, Bäurle I, Liu F, Dean C. Altered interactions within FY/AtCPSF complexes required for Arabidopsis FCA-mediated chromatin silencing. Proc Natl Acad Sci U S A. 2009;106:8772-7 pubmed publisher..These altered interactions would appear to be a necessary step in this RNA-mediated chromatin silencing. ..
- Kafasla P, Lin H, Curry S, Jackson R. Activation of picornaviral IRESs by PTB shows differential dependence on each PTB RNA-binding domain. RNA. 2011;17:1120-31 pubmed publisher..Surprisingly, therefore, the binding of PTB in its normal orientation does not guarantee IRES activation; three native RBDs are sufficient for correct binding but not for activation if the missing RBD-IRES interaction is critical. ..
- Kudla G, Granneman S, Hahn D, Beggs J, Tollervey D. Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA interactions in yeast. Proc Natl Acad Sci U S A. 2011;108:10010-5 pubmed publisher..CLASH should allow transcriptome-wide analyses of RNA-RNA interactions in many organisms...
- Ouldridge T, Hoare R, Louis A, Doye J, Bath J, Turberfield A. Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker. ACS Nano. 2013;7:2479-90 pubmed publisher..Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation. ..
- Krook A, Kumar S, Laing I, Boulton A, Wass J, O Rahilly S. Molecular scanning of the insulin receptor gene in syndromes of insulin resistance. Diabetes. 1994;43:357-68 pubmed
- Nicol S, Fuller Pace F. The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA. Proc Natl Acad Sci U S A. 1995;92:11681-5 pubmed
- Gregg A, McGlynn P, Jaktaji R, Lloyd R. Direct rescue of stalled DNA replication forks via the combined action of PriA and RecG helicase activities. Mol Cell. 2002;9:241-51 pubmed..The combined action of PriA and RecG helicase activities may thus avoid the potential dangers of rescue pathways involving fork breakage and recombination. ..
- Winkler G, Kristjuhan A, Erdjument Bromage H, Tempst P, Svejstrup J. Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo. Proc Natl Acad Sci U S A. 2002;99:3517-22 pubmed..By using chromatin immunoprecipitation, we show that the levels of multiply acetylated histone H3 and H4 in chromatin are decreased in vivo in yeast cells lacking ELP3. ..
- Gallego J, Greatorex J, Zhang H, Yang B, Arunachalam S, Fang J, et al. Rev binds specifically to a purine loop in the SL1 region of the HIV-1 leader RNA. J Biol Chem. 2003;278:40385-91 pubmed..HIV-1 appears to have a second Rev-binding site close to the major splice donor site that may have an additional role in the viral life cycle. ..
- Pickering B, Mitchell S, Spriggs K, Stoneley M, Willis A. Bag-1 internal ribosome entry segment activity is promoted by structural changes mediated by poly(rC) binding protein 1 and recruitment of polypyrimidine tract binding protein 1. Mol Cell Biol. 2004;24:5595-605 pubmed..Mutational analysis of the PTB-1 and PCBP1 binding sites suggests that PCBP1 acts as an RNA chaperone to open the RNA in the vicinity of the ribosome entry window while PTB-1 is probably an essential part of the preinitiation complex. ..
- Briggs G, Mahdi A, Wen Q, Lloyd R. DNA binding by the substrate specificity (wedge) domain of RecG helicase suggests a role in processivity. J Biol Chem. 2005;280:13921-7 pubmed..This keeps the helicase motor in contact with the substrate, enabling it to drive dsDNA translocation with high efficiency. ..
- Tan Wong S, Wijayatilake H, Proudfoot N. Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex. Genes Dev. 2009;23:2610-24 pubmed publisher..We predict that gene loop conformations enhance gene expression by facilitating rapid transcriptional response to changing environmental conditions. ..
- Jin H, Kelley A, Ramakrishnan V. Crystal structure of the hybrid state of ribosome in complex with the guanosine triphosphatase release factor 3. Proc Natl Acad Sci U S A. 2011;108:15798-803 pubmed publisher..The substantial conformational rearrangements in the complex are described and suggest how RF3, by stabilizing the hybrid state of the ribosome, facilitates the dissociation of class I release factors. ..
- Williams R, Rhodius V, Bell A, Kolb A, Busby S. Orientation of functional activating regions in the Escherichia coli CRP protein during transcription activation at class II promoters. Nucleic Acids Res. 1996;24:1112-8 pubmed..Using the method of 'oriented heterodimers' we show that these alternative activating regions are functional in the downstream subunit of the bound CRP dimer. ..
- Pan X, Fisher L. Cloning and characterization of the parC and parE genes of Streptococcus pneumoniae encoding DNA topoisomerase IV: role in fluoroquinolone resistance. J Bacteriol. 1996;178:4060-9 pubmed..These results suggest that DNA topoisomerase IV is an important target for fluoroquinolones in S. pneumoniae and establish this organism as a useful gram-positive system for resistance studies...
- Bennett R, West S. Resolution of Holliday junctions in genetic recombination: RuvC protein nicks DNA at the point of strand exchange. Proc Natl Acad Sci U S A. 1996;93:12217-22 pubmed..In these studies, junction targeting was achieved by incorporating uncharged methyl phosphonates into the DNA backbone, providing further evidence for the importance of charge-charge repulsions in determining DNA structure. ..
- Whitby M, Dixon J. Substrate specificity of the SpCCE1 holliday junction resolvase of Schizosaccharomyces pombe. J Biol Chem. 1998;273:35063-73 pubmed..This mechanism has the drawback of limiting dissociation from noncleavable junctions. We discuss why this might not be a problem in vivo. ..
- Redko Y, Tock M, Adams C, Kaberdin V, Grasby J, McDowall K. Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates. J Biol Chem. 2003;278:44001-8 pubmed..Combined, these observations establish a foundation for the functional interpretation of a three-dimensional structure of the catalytic domain of RNaseE when solved. ..
- Rafferty J, Bolt E, Muranova T, Sedelnikova S, Leonard P, Pasquo A, et al. The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold. Structure. 2003;11:1557-67 pubmed..Key residues identified by mutagenesis experiments are well positioned to interact with the DNA. ..
- Crow M, Deng T, Addley M, Brownlee G. Mutational analysis of the influenza virus cRNA promoter and identification of nucleotides critical for replication. J Virol. 2004;78:6263-70 pubmed..Overall, our results suggest that the corkscrew secondary-structure model is required for authentic cRNA promoter activity in vivo, although the precise role of the 3' hairpin loop remains unknown. ..
- Zachos G, Rainey M, Gillespie D. Chk1-dependent S-M checkpoint delay in vertebrate cells is linked to maintenance of viable replication structures. Mol Cell Biol. 2005;25:563-74 pubmed
- Massey T, Mercogliano C, Yates J, Sherratt D, L we J. Double-stranded DNA translocation: structure and mechanism of hexameric FtsK. Mol Cell. 2006;23:457-69 pubmed publisher..Comparison of FtsK monomer structures from two different crystal forms highlights a conformational change that we propose is the structural basis for a rotary inchworm mechanism of DNA translocation...