Genomes and Genes
Experts and Doctors on nucleic acid conformation in Switzerland
Topic: nucleic acid conformation
- Bucka A, Stasiak A. RecA-mediated strand exchange traverses substitutional heterologies more easily than deletions or insertions. Nucleic Acids Res. 2001;29:2464-70 pubmed..We discuss evolutionary implications of RecA selectivity against insertions and deletions and propose a molecular mechanism by which RecA can exert this selectivity. ..
- Benarroch Popivker D, Pisano S, Mendez Bermudez A, Lototska L, Kaur P, Bauwens S, et al. TRF2-Mediated Control of Telomere DNA Topology as a Mechanism for Chromosome-End Protection. Mol Cell. 2016;61:274-86 pubmed publisher..The presence of RAP1 at telomeres appears as a backup mechanism to prevent NHEJ when topology-mediated telomere protection is impaired. ..
- Boyko V, Hu Q, Seemanpillai M, Ashby J, Heinlein M. Validation of microtubule-associated Tobacco mosaic virus RNA movement and involvement of microtubule-aligned particle trafficking. Plant J. 2007;51:589-603 pubmed..Our observations confirm a role for microtubules in the spread of TMV infection and associate this role with microtubule-associated trafficking of MP-containing particles in cells engaged in the cell-to-cell movement of the TMV genome. ..
- Manen J. Are both sympatric species Ilex perado and Ilex canariensis secretly hybridizing? Indication from nuclear markers collected in Tenerife. BMC Evol Biol. 2004;4:46 pubmed..At least, this study allows the establishment of precautionary measures when nuclear markers are used in phylogenetic studies of genera having experienced introgression such as the genus Ilex. ..
- Erat M, Kovacs H, Sigel R. Metal ion-N7 coordination in a ribozyme branch domain by NMR. J Inorg Biochem. 2010;104:611-3 pubmed publisher..A second Mg(2+) ion, located in the major groove at the catalytic branch site, coordinates mainly in an outer-sphere fashion to the highly conserved flanking GU wobble pairs but not to N7 of the sandwiched branch adenosine. ..
- Cristofari G, Adolf E, Reichenbach P, Sikora K, Terns R, Terns M, et al. Human telomerase RNA accumulation in Cajal bodies facilitates telomerase recruitment to telomeres and telomere elongation. Mol Cell. 2007;27:882-9 pubmed..Collectively, these data identify subnuclear localization as an important regulatory mechanism for telomere length homeostasis in human cells. ..
- Marín R, Vanicek J. Efficient use of accessibility in microRNA target prediction. Nucleic Acids Res. 2011;39:19-29 pubmed publisher..We also find that 'naïve' global folding sometimes outperforms the local folding approach. ..
- Sauter P, Matthias P. Coactivator OBF-1 makes selective contacts with both the POU-specific domain and the POU homeodomain and acts as a molecular clamp on DNA. Mol Cell Biol. 1998;18:7397-409 pubmed..These data allow us to propose a model of the interaction between OBF-1 and the POU domain, whereby OBF-1 acts as a molecular clamp holding together the two moieties of the POU domain and the DNA. ..
- Barraud P, Heale B, O Connell M, Allain F. Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA. Biochimie. 2012;94:1499-509 pubmed publisher..It also predicts that dADAR dsRBD1 would bind to dsRNA with less sequence specificity than dsRBDs of ADAR2. Altogether, this study gives new insights into dsRNA substrate recognition by Drosophila ADAR. ..
- Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel R. The structural stabilization of the ? three-way junction by Mg(II) represents the first step in the folding of a group II intron. Nucleic Acids Res. 2013;41:2489-504 pubmed publisher..The addition of cobalt(III)hexammine reveals three distinct binding sites. The Mg(II)-promoted structural rearrangement and rigidification of the D1 core can be identified as the first micro-step of D1 folding. ..
- Wälti M, Villalba C, Buser R, Grünler A, Aebi M, Kunzler M. Targeted gene silencing in the model mushroom Coprinopsis cinerea (Coprinus cinereus) by expression of homologous hairpin RNAs. Eukaryot Cell. 2006;5:732-44 pubmed..cinerea and demonstrate the applicability of targeted gene silencing as a powerful reverse genetics approach in this organism...
- Pooggin M, Ryabova L, He X, Fütterer J, Hohn T. Mechanism of ribosome shunting in Rice tungro bacilliform pararetrovirus. RNA. 2006;12:841-50 pubmed..The results suggest that the mechanism of ribosome shunting is evolutionary conserved in plant pararetroviruses...
- Camenisch U, Dip R, Schumacher S, Schuler B, Naegeli H. Recognition of helical kinks by xeroderma pigmentosum group A protein triggers DNA excision repair. Nat Struct Mol Biol. 2006;13:278-84 pubmed..These findings show how an increased deformability of damaged sites, leading to helical kinks recognized by XPA, contributes to target selectivity in DNA repair. ..
- Swarts D, van der Oost J, Jinek M. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Mol Cell. 2017;66:221-233.e4 pubmed publisher..Together, these insights advance our mechanistic understanding of Cas12a enzymes and may contribute to further development of genome editing technologies. ..
- Maris C, Masse J, Chester A, Navaratnam N, Allain F. NMR structure of the apoB mRNA stem-loop and its interaction with the C to U editing APOBEC1 complementary factor. RNA. 2005;11:173-86 pubmed..Thus, the flexibility of the mooring sequence plays a central role in the RNA recognition by ACF. ..
- Strub K, Fornallaz M, Bui N. The Alu domain homolog of the yeast signal recognition particle consists of an Srp14p homodimer and a yeast-specific RNA structure. RNA. 1999;5:1333-47 pubmed..The alignment of the three yeast SRP RNAs known to date suggests a common structure for the putative elongation arrest domain of all three organisms. ..
- Lazarevic V, Soldo B, D sterh ft A, Hilbert H, Mau l C, Karamata D. Introns and intein coding sequence in the ribonucleotide reductase genes of Bacillus subtilis temperate bacteriophage SPbeta. Proc Natl Acad Sci U S A. 1998;95:1692-7 pubmed..Presently, this is the only intein identified in bacteriophages. In addition, bnrdE provides an example of a group I intron and an intein coding sequence within the same gene...
- Soldo B, Lazarevic V, Mauel C, Karamata D. Sequence of the 305 degrees-307 degrees region of the Bacillus subtilis chromosome. Microbiology. 1996;142 ( Pt 11):3079-88 pubmed..The products of the sequenced genes are involved in the regulation of degradative enzymes, competence, flagellar motility and protein secretion. Putative functions of newly identified genes are based on sequence homologies. ..
- Miranda G, Schuppli D, Barrera I, Hausherr C, Sogo J, Weber H. Recognition of bacteriophage Qbeta plus strand RNA as a template by Qbeta replicase: role of RNA interactions mediated by ribosomal proteins S1 and host factor. J Mol Biol. 1997;267:1089-103 pubmed..Qbeta RNA molecules with 3'-truncations formed 3'-terminal loops with similar efficiency as wild-type RNA, indicating that recognition of the 3'-end by host factor is not dependent on a specific 3'-terminal base sequence...
- Muller B, Link J, Smythe C. Assembly of U7 small nuclear ribonucleoprotein particle and histone RNA 3' processing in Xenopus egg extracts. J Biol Chem. 2000;275:24284-93 pubmed..However, this does not depend on the U7 RNA being able to process histone RNA and also occurs with U1 snRNPs; therefore, association of SPH1 cannot be considered as a hallmark of a functional U7 snRNP. ..
- Lankas F, Lavery R, Maddocks J. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure. 2006;14:1527-34 pubmed..The relaxed minicircle is generally associated with a single kink, while two kinks occur with the supercoiled state. No evidence is seen of base unpaired regions. ..
- Akhmedov A, Frei C, Tsai Pflugfelder M, Kemper B, Gasser S, Jessberger R. Structural maintenance of chromosomes protein C-terminal domains bind preferentially to DNA with secondary structure. J Biol Chem. 1998;273:24088-94 pubmed..Consistent with their in vitro DNA binding activity, we show that overexpression of the SMC C termini increases plasmid loss without altering viability or cell cycle progression. ..
- Braguglia D, Heun P, Pasero P, Duncker B, Gasser S. Semi-conservative replication in yeast nuclear extracts requires Dna2 helicase and supercoiled template. J Mol Biol. 1998;281:631-49 pubmed..Using this novel system we demonstrate that semi-conservative replication, but not polymerase activity per se, requires the activity of the DNA helicase encoded by DNA2. ..
- Goldschmidt Clermont M, Rahire M, Rochaix J. Redundant cis-acting determinants of 3' processing and RNA stability in the chloroplast rbcL mRNA of Chlamydomonas. Plant J. 2008;53:566-77 pubmed publisher..This indicated that the two inverted repeats function as redundant mRNA stability determinants in the 3' UTR of rbcL...
- Mudd E, Prentki P, Belin D, Krisch H. Processing of unstable bacteriophage T4 gene 32 mRNAs into a stable species requires Escherichia coli ribonuclease E. EMBO J. 1988;7:3601-7 pubmed..The effects of the processing on the differential stability of the upstream and downstream sequences, and on gene expression, are discussed. ..
- Percival Smith A, Muller M, Affolter M, Gehring W. The interaction with DNA of wild-type and mutant fushi tarazu homeodomains. EMBO J. 1990;9:3967-74 pubmed..These three points of contact allowed us to propose a crude orientation of the ftz HD within the protein-DNA complex. We find that the ftz HD and the Antp HD peptides contact DNA in a similar way. ..
- Bleichenbacher M, Tan S, Richmond T. Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. J Mol Biol. 2003;332:783-93 pubmed..Of particular interest is a previously unobserved region of TFIIA that extends the binding interface with TBP in the yeast, but not in the human complex, and that further elucidates biochemical and genetic results. ..
- Malinovskii V, Nussbaumer A, Haner R. Oligopyrenotides: chiral nanoscale templates for chromophore assembly. Angew Chem Int Ed Engl. 2012;51:4905-8 pubmed publisher..The cationic porphyrin meso-tetrakis(1-methylpyridin-4-yl)porphyrin interacts with the helical polymers in a similar way as with poly(dA:dT). ..
- Wolf J, Gerber A, Keller W. tadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J. 2002;21:3841-51 pubmed..The anticodon is thus a major determinant for tadA substrate specificity. Finally, we show that tadA is an essential gene in E.coli, underscoring the critical function of inosine at the wobble position in prokaryotes. ..
- Samatanga B, Cléry A, Barraud P, Allain F, Jelesarov I. Comparative analyses of the thermodynamic RNA binding signatures of different types of RNA recognition motifs. Nucleic Acids Res. 2017;45:6037-6050 pubmed publisher..Altogether, different modes employed by RRMs to bind cognate ssRNAs utilize various thermodynamics strategies during the association process. ..
- Nocker A, Hausherr T, Balsiger S, Krstulovic N, Hennecke H, Narberhaus F. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. Nucleic Acids Res. 2001;29:4800-7 pubmed..We propose a model in which the temperature-regulated secondary structure of ROSE mRNA influences heat shock gene expression by controlling ribosome access to the ribosome-binding site. ..
- Z ckert W, Meyer J. Circular and linear plasmids of Lyme disease spirochetes have extensive homology: characterization of a repeated DNA element. J Bacteriol. 1996;178:2287-98 pubmed..ORF-C and ORF-E, however, are missing from this region on the Ip21 plasmid. Furthermore, the repeated DNA element as defined by the IRs is present in opposite orientations relative to the flanking sequences on the B31 and Ip21 plasmids...
- Kohler S, Henderson B, Kuhn L. Succinate dehydrogenase b mRNA of Drosophila melanogaster has a functional iron-responsive element in its 5'-untranslated region. J Biol Chem. 1995;270:30781-6 pubmed..Furthermore, Drosophila SDHb represents the second example, after porcine mitochondrial aconitase, of an enzyme of the citric acid cycle whose mRNA possesses all necessary features for translational regulation by cellular iron levels. ..
- Hausser J, Landthaler M, Jaskiewicz L, Gaidatzis D, Zavolan M. Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome Res. 2009;19:2009-20 pubmed publisher..We found that structural features of the target site are only important for Argonaute/EIF2C binding, while sequence features such as the A/U content of the 3' UTR are important for mRNA degradation. ..
- Kressler D, Hurt E, BaÃŸler J. A Puzzle of Life: Crafting Ribosomal Subunits. Trends Biochem Sci. 2017;42:640-654 pubmed publisher..In this review we integrate these first structural insights into an updated overview of the consecutive ribosome assembly steps. ..
- Boehringer D, Ban N. Trapping the ribosome to control gene expression. Cell. 2007;130:983-5 pubmed..These results have implications for our understanding of the mechanism of translation initiation in general. ..
- Ercolini E, Valle F, Adamcik J, Witz G, Metzler R, De Los Rios P, et al. Fractal dimension and localization of DNA knots. Phys Rev Lett. 2007;98:058102 pubmed..60 within error. In (ii), we find nu approximately 0.66, a value between the 3D and 2D (nu=3/4) exponents. Evidence is also presented for the localization of knot crossings in 2D under weak adsorption conditions. ..
- Wenz C, Enenkel B, Amacker M, Kelleher C, Damm K, Lingner J. Human telomerase contains two cooperating telomerase RNA molecules. EMBO J. 2001;20:3526-34 pubmed..We conclude that the telomerase RNA templates in the active enzyme are interdependent and functionally cooperate with each other. We discuss models that may explain the biological and enzymatic roles of telomerase dimerization. ..
- Shimada K, Pasero P, Gasser S. ORC and the intra-S-phase checkpoint: a threshold regulates Rad53p activation in S phase. Genes Dev. 2002;16:3236-52 pubmed..Our data suggest the existence of an S-phase-specific threshold that may be necessary to allow cells to tolerate damage-like DNA structures present at normal replication forks. ..
- Tan T, Bochud Allemann N, Horn E, Schneider A. Eukaryotic-type elongator tRNAMet of Trypanosoma brucei becomes formylated after import into mitochondria. Proc Natl Acad Sci U S A. 2002;99:1152-7 pubmed..Whereas the predicted protein is homologous to prokaryotic and mitochondrial methionyl-tRNA(Met) formyltransferases, it has about twice the mass of any of these proteins. ..
- Zeenko V, Ryabova L, Spirin A, Rothnie H, Hess D, Browning K, et al. Eukaryotic elongation factor 1A interacts with the upstream pseudoknot domain in the 3' untranslated region of tobacco mosaic virus RNA. J Virol. 2002;76:5678-91 pubmed..Its possible role in the regulation of tobamovirus gene expression and replication is discussed. ..
- Heeb S, Blumer C, Haas D. Regulatory RNA as mediator in GacA/RsmA-dependent global control of exoproduct formation in Pseudomonas fluorescens CHA0. J Bacteriol. 2002;184:1046-56 pubmed..By a titration effect, RsmZ may then alleviate the repressing activity of RsmA on the expression of target mRNAs...
- Ekundayo B, Richmond T, Schalch T. Capturing Structural Heterogeneity in Chromatin Fibers. J Mol Biol. 2017;429:3031-3042 pubmed publisher..The chromatin fiber architectures observed here provide a basis for understanding heterogeneous chromatin higher-order structures as they occur in a genomic context. ..
- Pooggin M, Futterer J, Skryabin K, Hohn T. Ribosome shunt is essential for infectivity of cauliflower mosaic virus. Proc Natl Acad Sci U S A. 2001;98:886-91 pubmed..Finally, by using an artificial stem structure that blocks scanning, we obtained direct evidence that ribosome shunt operates during CaMV infection...
- Gutmann S, Haebel P, Metzinger L, Sutter M, Felden B, Ban N. Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature. 2003;424:699-703 pubmed publisher..On the basis of this structure, we propose a model for the binding of tmRNA on the ribosome...
- Amzallag A, Vaillant C, Jacob M, Unser M, Bednar J, Kahn J, et al. 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res. 2006;34:e125 pubmed..We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes. ..
- Tan S, Richmond T. Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature. 1998;391:660-6 pubmed..This 'chameleon' sequence of MATalpha2 may be important for recognizing natural operator sites. ..
- Oberstrass F, Lee A, Stefl R, Janis M, Chanfreau G, Allain F. Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol. 2006;13:160-7 pubmed..Using microarray gene profiling, we identified several genes in S. cerevisiae that seem to be regulated by Vts1p and contain one or more copies of the SRE. ..
- Kutter C, Schöb H, Stadler M, Meins F, Si Ammour A. MicroRNA-mediated regulation of stomatal development in Arabidopsis. Plant Cell. 2007;19:2417-29 pubmed..These findings and the nonoverlapping patterns of AGL16 mRNA and miR824 localization led us to propose that the miR824/AGL16 pathway functions in the satellite meristemoid lineage of stomatal development. ..
- Kramer A, Grüter P, Gröning K, Kastner B. Combined biochemical and electron microscopic analyses reveal the architecture of the mammalian U2 snRNP. J Cell Biol. 1999;145:1355-68 pubmed..Comparison to the two-domain structure of the 17S U2 snRNP corroborates the biochemical results in that binding of SF3a contributes to an increase in size of the 12S U2 domain and possibly induces a structural change in the SF3b domain. ..
- Christen T, Bischoff M, Hobi R, Kuenzle C. High mobility group proteins 1 and 2 bind preferentially to brominated poly(dG-dC).poly(dG-dC) in the Z-DNA conformation but not to other types of Z-DNA. FEBS Lett. 1990;267:139-41 pubmed..In contrast, the 58 kDa protein remained unidentified for lack of any significant homology with known protein sequences. ..
- Arnold Schulz Gahmen B, Salti Montesanto V, Nguyen J, Hirschbein L, Le Hegarat F. The Bacillus subtilis nucleoid-associated protein HPB12 strongly compacts DNA. J Bacteriol. 1994;176:50-60 pubmed..Acta 1009:161-167, 1989), and gives rise to a tightly compacted DNA-protein complex. N-terminal sequencing of purified HPB12 showed that all but one of the first 26 amino acids were identical to those of the L24 ribosomal protein. ..
- Jinek M, Jiang F, Taylor D, Sternberg S, Kaya E, Ma E, et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science. 2014;343:1247997 pubmed publisher..The observation that extensive structural rearrangements occur before target DNA duplex binding implicates guide RNA loading as a key step in Cas9 activation. ..
- Hassler M, Richmond T. The B-box dominates SAP-1-SRF interactions in the structure of the ternary complex. EMBO J. 2001;20:3018-28 pubmed..Comparison with a similar region from the yeast MATalpha2-MCM1-DNA complex suggests a common binding motif through which MADS-box proteins may interact with additional factors such as Fli-1. ..
- Huck L, Scherrer A, Terzi L, Johnson A, Bernstein H, Cusack S, et al. Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain. Nucleic Acids Res. 2004;32:4915-24 pubmed..Our results suggest a model in which the loop-loop interaction and binding of the protein SRP9/14 play an important role in the early steps of SRP RNA folding and assembly. ..
- Martin F, Schaller A, Eglite S, Schumperli D, Muller B. The gene for histone RNA hairpin binding protein is located on human chromosome 4 and encodes a novel type of RNA binding protein. EMBO J. 1997;16:769-78 pubmed..In addition, recombinant HBP expressed in S. cerevisiae was functional in histone pre-mRNA processing, confirming that we have indeed identified the human HBP gene. ..
- Garcia P, Bradley G, Hayes C, Krintel S, Soultanas P, Janscak P. RPA alleviates the inhibitory effect of vinylphosphonate internucleotide linkages on DNA unwinding by BLM and WRN helicases. Nucleic Acids Res. 2004;32:3771-8 pubmed
- Barekati Z, Radpour R, Kohler C, Zhang B, Toniolo P, Lenner P, et al. Methylation profile of TP53 regulatory pathway and mtDNA alterations in breast cancer patients lacking TP53 mutations. Hum Mol Genet. 2010;19:2936-46 pubmed publisher..Additionally, release of significant aberrant methylated PTEN in matched serum samples might represent a promising biomarker for breast cancer. ..
- Kasas S, Alonso L, Jacquet P, Adamcik J, Haeberli C, Dietler G. Microcontroller-driven fluid-injection system for atomic force microscopy. Rev Sci Instrum. 2010;81:013704 pubmed publisher..This latter circumstance was exemplified by the online imaging of conformational changes in DNA molecules during the injection of anticancer drug into the fluid chamber. ..
- Pfister P, Corti N, Hobbie S, Bruell C, Zarivach R, Yonath A, et al. 23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G. Proc Natl Acad Sci U S A. 2005;102:5180-5 pubmed
- Tan S, Richmond T. Eukaryotic transcription factors. Curr Opin Struct Biol. 1998;8:41-8 pubmed..In addition, recent studies of proximal/distal promoter complexes demonstrate that DNA-binding motifs may be modified in nature by adding secondary structure elements to diversify DNA-binding specificities and affinities. ..
- Spingler B. Anions or cations: who is in charge of inhibiting the nickel(II) promoted B- to Z-DNA transition?. Inorg Chem. 2005;44:831-3 pubmed..We believe that this is the first reported example of the role of chloride anions, which appear to modulate the interaction of nickel(II) ions with the polyanionic DNA. ..
- Grüter P, Tabernero C, von Kobbe C, Schmitt C, Saavedra C, Bachi A, et al. TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus. Mol Cell. 1998;1:649-59 pubmed..Thus, TAP, like its yeast homolog Mex67p, is a bona fide mRNA nuclear export mediator. TAP is the second cellular RNA binding protein shown to be directly involved in the export of its target RNA...
- Baechtold H, Kuroda M, Sok J, Ron D, Lopez B, Akhmedov A. Human 75-kDa DNA-pairing protein is identical to the pro-oncoprotein TLS/FUS and is able to promote D-loop formation. J Biol Chem. 1999;274:34337-42 pubmed..Interestingly, the oncogenic fusion form TLS-CHOP is not able to promote DNA pairing. These data suggest a possible role for hPOMp75/TLS in maintenance of genomic integrity. ..
- Rudolph C, Kunz C, Parisi S, Lehmann E, Hartsuiker E, Fartmann B, et al. The msh2 gene of Schizosaccharomyces pombe is involved in mismatch repair, mating-type switching, and meiotic chromosome organization. Mol Cell Biol. 1999;19:241-50 pubmed..Our data show that besides having a function in mismatch repair, S. pombe msh2 is required for correct termination of copy synthesis during mating-type switching as well as for proper organization of chromosomes during meiosis. ..