Experts and Doctors on nucleic acid conformation in Germany


Locale: Germany
Topic: nucleic acid conformation

Top Publications

  1. Sedlmeier R, Werner T, Kieser H, Hopwood D, Schmieger H. tRNA genes of Streptomyces lividans: new sequences and comparison of structure and organization with those of other bacteria. J Bacteriol. 1994;176:5550-3 pubmed
    ..The structure and organization of tRNA genes of S. lividans and S. coelicolor are compared with those of Escherichia coli and Bacillus subtilis...
  2. Marszalkowski M, Willkomm D, Hartmann R. Structural basis of a ribozyme's thermostability: P1-L9 interdomain interaction in RNase P RNA. RNA. 2008;14:127-33 pubmed
    ..coli P RNA but also increased its maximum turnover rate at 55 degrees C to the highest yet described for a P RNA ribozyme. ..
  3. Will S, Joshi T, Hofacker I, Stadler P, Backofen R. LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA. 2012;18:900-14 pubmed publisher
    ..We provide additional results, a web server for LocARNA/LocARNA-P, and the software package, including documentation and a pipeline for refining screens for structural ncRNA, at ..
  4. Becher P, Orlich M, Thiel H. Mutations in the 5' nontranslated region of bovine viral diarrhea virus result in altered growth characteristics. J Virol. 2000;74:7884-94 pubmed
    ..Restriction of specific infectivity and virus growth of the 5' NTR mutants correlated with reduced amounts of accumulated viral RNAs. ..
  5. Remenyi A, Tomilin A, Pohl E, Lins K, Philippsen A, Reinbold R, et al. Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol Cell. 2001;8:569-80 pubmed
    ..We suggest interface swapping in dimers could be a general mechanism of modulating the activity of transcription factors. ..
  6. Bonin M, Oberstrass J, Vogt U, Wassenegger M, Nellen W. Binding of IRE-BP to its cognate RNA sequence: SFM studies on a universal RNA backbone for the analysis of RNA-protein interaction. Biol Chem. 2001;382:1157-62 pubmed
    ..It thus provides a versatile tool to study specific as well as preferential interaction of other proteins with sequences or structures inserted into a different part of the molecule. ..
  7. Schneider C, Will C, Makarova O, Makarov E, Luhrmann R. Human U4/U6.U5 and U4atac/U6atac.U5 tri-snRNPs exhibit similar protein compositions. Mol Cell Biol. 2002;22:3219-29 pubmed
  8. Randau L, Schauer S, Ambrogelly A, Salazar J, Moser J, Sekine S, et al. tRNA recognition by glutamyl-tRNA reductase. J Biol Chem. 2004;279:34931-7 pubmed
    ..E. coli GluTR showed clear selectivity against mischarged Glu-tRNA(Gln). We concluded that the unique tertiary core structure of E. coli tRNA(Glu) was sufficient for E. coli GluTR to distinguish specifically its glutamyl-tRNA substrate. ..
  9. Cuzic S, Heidemann K, Wöhnert J, Hartmann R. Escherichia coli RNase P RNA: substrate ribose modifications at G+1, but not nucleotide -1/+73 base pairing, affect the transition state for cleavage chemistry. J Mol Biol. 2008;379:1-8 pubmed publisher

More Information

Publications203 found, 100 shown here

  1. Fahrein K, Masta S, Podsiadlowski L. The first complete mitochondrial genome sequences of Amblypygi (Chelicerata: Arachnida) reveal conservation of the ancestral arthropod gene order. Genome. 2009;52:456-66 pubmed publisher
    ..Phylogenetic analysis resulted in weak support for Uropygi being the sister group of Amblypygi...
  2. Rinnenthal J, Klinkert B, Narberhaus F, Schwalbe H. Modulation of the stability of the Salmonella fourU-type RNA thermometer. Nucleic Acids Res. 2011;39:8258-70 pubmed publisher
    ..Binding of the two Mg(2+) ions exhibits a positive cooperativity with a Hill coefficient of 1.47. Free energy values ?G for Mg(2+) binding determined by NMR are in agreement with data determined from CD measurements. ..
  3. Ritz C, Reiker J, Charles G, Hoxey P, Hunt D, Lowry M, et al. Molecular phylogeny and character evolution in terete-stemmed Andean opuntias (Cactaceae-Opuntioideae). Mol Phylogenet Evol. 2012;65:668-81 pubmed publisher
  4. Gimpel M, Preis H, Barth E, Gramzow L, Brantl S. SR1--a small RNA with two remarkably conserved functions. Nucleic Acids Res. 2012;40:11659-72 pubmed publisher
    ..In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ?1 billion years. ..
  5. Hartmann R, Heinrich J, Schlegl J, Schuster H. Precursor of C4 antisense RNA of bacteriophages P1 and P7 is a substrate for RNase P of Escherichia coli. Proc Natl Acad Sci U S A. 1995;92:5822-6 pubmed
    ..Implications of C4 RNA processing for the lysis/lysogeny decision process of bacteriophages P1 and P7 are discussed. ..
  6. Lerche H, Heine R, Pika U, George A, Mitrovic N, Browatzki M, et al. Human sodium channel myotonia: slowed channel inactivation due to substitutions for a glycine within the III-IV linker. J Physiol. 1993;470:13-22 pubmed
    ..Our electrophysiological and molecular genetic studies strongly suggest that these Na+ channel mutations cause myotonia. The naturally occurring mutants allowed us to gain further insight into the mechanism of Na+ channel inactivation...
  7. Baron C, Heider J, Bock A. Interaction of translation factor SELB with the formate dehydrogenase H selenopolypeptide mRNA. Proc Natl Acad Sci U S A. 1993;90:4181-5 pubmed
    ..SELB complex at the mRNA in the immediate neighborhood of the UGA codon. ..
  8. Achsel T, Brahms H, Kastner B, Bachi A, Wilm M, Luhrmann R. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J. 1999;18:5789-802 pubmed
    ..Finally, we show that the LSm proteins facilitate the formation of U4/U6 RNA duplices in vitro, suggesting that the LSm proteins may play a role in U4/U6 snRNP formation. ..
  9. Blümer N, Schreiter K, Hempel L, Santel A, Hollmann M, Schäfer M, et al. A new translational repression element and unusual transcriptional control regulate expression of don juan during Drosophila spermatogenesis. Mech Dev. 2002;110:97-112 pubmed
    ..This proves that translational activation of dormant mRNAs in spermatogenesis occurs at different time-points which are characteristic for each gene, an essential feature for coordinated sperm morphogenesis. ..
  10. Matassova A, Rodnina M, Wintermeyer W. Elongation factor G-induced structural change in helix 34 of 16S rRNA related to translocation on the ribosome. RNA. 2001;7:1879-85 pubmed
    ..Thus, the present results indicate that EF-G binding to the pretranslocation ribosome induces a structural change of the head of the 30S subunit that is essential for subsequent tRNA-mRNA movement in translocation. ..
  11. Brehm A, Tufteland K, Aasland R, Becker P. The many colours of chromodomains. Bioessays. 2004;26:133-40 pubmed
  12. Ihle Y, Ohlenschläger O, Häfner S, Duchardt E, Zacharias M, Seitz S, et al. A novel cGUUAg tetraloop structure with a conserved yYNMGg-type backbone conformation from cloverleaf 1 of bovine enterovirus 1 RNA. Nucleic Acids Res. 2005;33:2003-11 pubmed
    ..Ohlenschlager, J. Wohnert, E. Bucci, S. Seitz, S. Hafner, R. Ramachandran, R. Zell and M. Gorlach (2004) Structure, 12, 237-248] that the proteinase 3C(pro) recognizes structure rather than sequence. ..
  13. Homann M, Lorger M, Engstler M, Zacharias M, Göringer H. Serum-stable RNA aptamers to an invariant surface domain of live African trypanosomes. Comb Chem High Throughput Screen. 2006;9:491-9 pubmed
    ..We demonstrate that antigen-tagged preparations of the aptamer can bind to live trypanosomes and that they can be used to re-direct immunoglobulins to the parasite surface. ..
  14. Parschat K, Overhage J, Strittmatter A, Henne A, Gottschalk G, Fetzner S. Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Rü61a and transcriptional analysis of genes involved in quinaldine degradation. J Bacteriol. 2007;189:3855-67 pubmed
    ..Even if the putative proteins encoded by ORFs 101 to 103 share motifs with the Tap and terminal proteins involved in telomere patching of Streptomyces linear replicons, their overall sequences and domain structures differ significantly...
  15. Wegscheid B, Hartmann R. In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3'-CCA. Nucleic Acids Res. 2007;35:2060-73 pubmed
    ..We conclude that the observed in vivo defects upon disruption of the CCA interaction are either due to a global deceleration in ptRNA maturation or severe inhibition of 5'-maturation for a ptRNA subset. ..
  16. Matousek J, Orctova L, Ptacek J, Patzak J, Dedic P, Steger G, et al. Experimental transmission of pospiviroid populations to weed species characteristic of potato and hop fields. J Virol. 2007;81:11891-9 pubmed
    ..retroflexus and V. argensis exhibited similarity or identity to the superlethal AS1 viroid variant. All HSVd clones from G. ciliata corresponded to a HSVdg variant, which is strongly pathogenic for European hops...
  17. Fahrein K, Talarico G, Braband A, Podsiadlowski L. The complete mitochondrial genome of Pseudocellus pearsei (Chelicerata: Ricinulei) and a comparison of mitochondrial gene rearrangements in Arachnida. BMC Genomics. 2007;8:386 pubmed publisher
    ..Some gene order changes are valuable characters in phylogenetic analysis of intraordinal relationships, e.g. in Acari...
  18. Bung C, Bochkaeva Z, Terenin I, Zinovkin R, Shatsky I, Niepmann M. Influence of the hepatitis C virus 3'-untranslated region on IRES-dependent and cap-dependent translation initiation. FEBS Lett. 2010;584:837-42 pubmed publisher
  19. Chakraborty P, Grosse F. Human DHX9 helicase preferentially unwinds RNA-containing displacement loops (R-loops) and G-quadruplexes. DNA Repair (Amst). 2011;10:654-65 pubmed publisher
    ..By unwinding these structures, DHX9 may significantly contribute to transcriptional activation and also to the maintenance of genomic stability. ..
  20. Jühling F, Pütz J, Florentz C, Stadler P. Armless mitochondrial tRNAs in Enoplea (Nematoda). RNA Biol. 2012;9:1161-6 pubmed publisher
  21. Ardjomandi N, Niederlaender J, Aicher W, Reinert S, Schweizer E, Wendel H, et al. Identification of an aptamer binding to human osteogenic-induced progenitor cells. Nucleic Acid Ther. 2013;23:44-61 pubmed publisher
    ..Herein, we report the development of an innovative approach for tissue engineering applications. Further studies should be conducted to modify and improve the specificity of the generated aptamer. ..
  22. Grotwinkel J, Wild K, Segnitz B, Sinning I. SRP RNA remodeling by SRP68 explains its role in protein translocation. Science. 2014;344:101-4 pubmed publisher
    ..The ARM opens the conserved 5f RNA loop, which in ribosome-bound SRP establishes a contact to ribosomal RNA. Our data provide the structural basis for eukaryote-specific, SRP68-driven RNA remodeling required for protein translocation. ..
  23. Meißner C, Jahn N, Brantl S. In Vitro Characterization of the Type I Toxin-Antitoxin System bsrE/SR5 from Bacillus subtilis. J Biol Chem. 2016;291:560-71 pubmed publisher
    ..A comparison with the previously well characterized type I TA system from the B. subtilis chromosome, bsrG/SR4, reveals similarities but also significant differences. ..
  24. Wilting R, Schorling S, Persson B, B ck A. Selenoprotein synthesis in archaea: identification of an mRNA element of Methanococcus jannaschii probably directing selenocysteine insertion. J Mol Biol. 1997;266:637-41 pubmed publisher
    ..This element, which is present in the 3' non-translated region of two selenoprotein mRNAs from Methanococcus voltae, is proposed to act in decoding of the UGA with selenocysteine...
  25. Persson T, Cuzic S, Hartmann R. Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. J Biol Chem. 2003;278:43394-401 pubmed
  26. Dühring U, Axmann I, Hess W, Wilde A. An internal antisense RNA regulates expression of the photosynthesis gene isiA. Proc Natl Acad Sci U S A. 2006;103:7054-8 pubmed
    ..The coupled degradation of IsrR/isiA mRNA duplexes appears to be a reversible switch that can respond to environmental changes. IsrR is the only RNA known so far to regulate a photosynthesis component. ..
  27. Marko A, Margraf D, Cekan P, Sigurdsson S, Schiemann O, Prisner T. Analytical method to determine the orientation of rigid spin labels in DNA. Phys Rev E Stat Nonlin Soft Matter Phys. 2010;81:021911 pubmed
    ..The method was applied to the experimental data gathered on ten spin-labeled DNA samples. The angles estimated from the PELDOR data are in excellent agreement with literature values. ..
  28. Schmitz K, Mayer C, Postepska A, Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev. 2010;24:2264-9 pubmed publisher
    ..The results reveal a compelling new mechanism of RNA-dependent DNA methylation, suggesting that recruitment of DNMT3b by DNA:RNA triplexes may be a common and generally used pathway in epigenetic regulation. ..
  29. Jungmann R, Scheible M, Kuzyk A, Pardatscher G, Castro C, Simmel F. DNA origami-based nanoribbons: assembly, length distribution, and twist. Nanotechnology. 2011;22:275301 pubmed publisher
  30. Lapinaite A, Simon B, Skjaerven L, Rakwalska Bange M, Gabel F, Carlomagno T. The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature. 2013;502:519-23 pubmed publisher
    ..This structure provides a means for differential control of methylation levels at the two sites and at the same time offers an unexpected regulatory mechanism for rRNA folding...
  31. Romig H, Ruff J, Fackelmayer F, Patil M, Richter A. Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. Eur J Biochem. 1994;221:411-9 pubmed
  32. Wang X, Tolstonog G, Shoeman R, Traub P. Selective binding of specific mouse genomic DNA fragments by mouse vimentin filaments in vitro. DNA Cell Biol. 1996;15:209-25 pubmed
    ..This includes aspects of global regulation of gene expression such as the position effects associated with translocation of genes to heterochromatic centromere and telomere regions of the chromosomes. ..
  33. Zhang S, Grosse F. Domain structure of human nuclear DNA helicase II (RNA helicase A). J Biol Chem. 1997;272:11487-94 pubmed
    ..A model is suggested in which the flanking domains influence and regulate the unwinding properties of NDH II. ..
  34. Zayed H, Izsvák Z, Khare D, Heinemann U, Ivics Z. The DNA-bending protein HMGB1 is a cellular cofactor of Sleeping Beauty transposition. Nucleic Acids Res. 2003;31:2313-22 pubmed
  35. Reich S, Gössl I, Reuter M, Rabe J, Kruger D. Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I. J Mol Biol. 2004;341:337-43 pubmed
    ..Moreover, our study revealed differences in the DNA-translocation processes mediated by Type I and Type III restriction enzymes. ..
  36. Cherny D, Hoyer W, Subramaniam V, Jovin T. Double-stranded DNA stimulates the fibrillation of alpha-synuclein in vitro and is associated with the mature fibrils: an electron microscopy study. J Mol Biol. 2004;344:929-38 pubmed
    ..Possible mechanisms and implications of dsDNA-alpha-synuclein interactions are discussed. ..
  37. Barthel A, Zacharias M. Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study. Biophys J. 2006;90:2450-62 pubmed
  38. Heidrich N, Moll I, Brantl S. In vitro analysis of the interaction between the small RNA SR1 and its primary target ahrC mRNA. Nucleic Acids Res. 2007;35:4331-46 pubmed
    ..The intracellular concentrations of SR1 were calculated under different growth conditions. ..
  39. Schudoma C, May P, Nikiforova V, Walther D. Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res. 2010;38:970-80 pubmed publisher
    ..The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts. ..
  40. Schlegel M, Essen L, Meggers E. Atomic resolution duplex structure of the simplified nucleic acid GNA. Chem Commun (Camb). 2010;46:1094-6 pubmed publisher
    ..Double helix variations of glycol nucleic acids (GNA) are revealed by the atomic resolution crystal structure of a 6mer GNA duplex containing solely Watson-Crick type hydrogen-bonded base pairs. ..
  41. Falb M, Amata I, Gabel F, Simon B, Carlomagno T. Structure of the K-turn U4 RNA: a combined NMR and SANS study. Nucleic Acids Res. 2010;38:6274-85 pubmed publisher
    ..Our data suggests that the K-turn consensus sequence does not per se code for the kinked conformation; instead the sharp backbone kink requires to be stabilized by protein binders. ..
  42. Fulle S, Christ N, Kestner E, Gohlke H. HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations. J Chem Inf Model. 2010;50:1489-501 pubmed publisher
  43. Liu S, Ghalei H, Luhrmann R, Wahl M. Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31. RNA. 2011;17:1655-63 pubmed publisher
  44. Kick A, Bönsch M, Mertig M. EGNAS: an exhaustive DNA sequence design algorithm. BMC Bioinformatics. 2012;13:138 pubmed publisher
    ..The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at ..
  45. Jahn N, Brantl S. One antitoxin--two functions: SR4 controls toxin mRNA decay and translation. Nucleic Acids Res. 2013;41:9870-80 pubmed publisher
    ..Therefore, we conclude that SR4 does not only promote degradation of the toxin mRNA but also additionally inhibit its translation. This is the first case of a dual-acting antitoxin RNA. ..
  46. Simos G, Tekotte H, Grosjean H, Segref A, Sharma K, Tollervey D, et al. Nuclear pore proteins are involved in the biogenesis of functional tRNA. EMBO J. 1996;15:2270-84 pubmed
    ..These data suggest that nuclear pore proteins are required for the biogenesis of functional tRNA. ..
  47. Kromayer M, Wilting R, Tormay P, B ck A. Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J Mol Biol. 1996;262:413-20 pubmed publisher
    ..The results indicate that SelB can be considered as an EF-Tu homolog hooked to the mRNA via its C-terminal domain...
  48. Huttenhofer A, Bock A. Selenocysteine inserting RNA elements modulate GTP hydrolysis of elongation factor SelB. Biochemistry. 1998;37:885-90 pubmed
    ..On the basis of these results, we propose that binding of the mRNA hairpin to SelB induces a conformational switch within SelB thereby promoting an increase in ribosome-mediated GTP hydrolysis. ..
  49. Bauernfeind A, Roller C, Meyer D, Jungwirth R, Schneider I. Molecular procedure for rapid detection of Burkholderia mallei and Burkholderia pseudomallei. J Clin Microbiol. 1998;36:2737-41 pubmed
    ..mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel. ..
  50. Volchkov V, Volchkova V, Chepurnov A, Blinov V, Dolnik O, Netesov S, et al. Characterization of the L gene and 5' trailer region of Ebola virus. J Gen Virol. 1999;80 ( Pt 2):355-62 pubmed publisher
    ..The presence of several conserved linear domains commonly found within L proteins of other members of the order Mononegavirales identified this protein as the RNA-dependent RNA polymerase of Ebola virus...
  51. Liu Z, Luyten I, Bottomley M, Messias A, Houngninou Molango S, Sprangers R, et al. Structural basis for recognition of the intron branch site RNA by splicing factor 1. Science. 2001;294:1098-102 pubmed
    ..The branch point adenosine acting as the nucleophile in the first biochemical step of splicing is deeply buried. BPS RNA recognition suggests how SF1 may facilitate subsequent formation of the prespliceosomal complex A. ..
  52. Kundu L, Burgdorf L, Kleiner O, Batschauer A, Carell T. Cleavable substrate containing molecular beacons for the quantification of DNA-photolyase activity. Chembiochem. 2002;3:1053-60 pubmed
    ..The molecular beacon made it possible to measure the activity of purified class I and class II photolyases. Photolyase activity was even detectable in crude cell extracts. ..
  53. Hui J, Reither G, Bindereif A. Novel functional role of CA repeats and hnRNP L in RNA stability. RNA. 2003;9:931-6 pubmed
    ..Based on the wide abundance of CA repetitive sequences in the human genome, this may represent a novel, generally important role of this abundant hnRNP protein. ..
  54. Keiper S, Bebenroth D, Seelig B, Westhof E, Jäschke A. Architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem Biol. 2004;11:1217-27 pubmed
    ..It is proposed that the catalytic pocket is formed by a wedge within one of these helices. ..
  55. Kumar Y, Westram R, Kipfer P, Meier H, Ludwig W. Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package. BMC Bioinformatics. 2006;7:240 pubmed
    ..The extended ARB software package is made freely available for the scientific community via ..
  56. Babinger K, Hallmann A, Schmitt R. Translational control of regA, a key gene controlling cell differentiation in Volvox carteri. Development. 2006;133:4045-51 pubmed
    ..We believe that this is the first report suggesting that translation of an mRNA in a green eukaryote is controlled by ribosome shunting...
  57. Kraunus J, Zychlinski D, Heise T, Galla M, Bohne J, Baum C. Murine leukemia virus regulates alternative splicing through sequences upstream of the 5' splice site. J Biol Chem. 2006;281:37381-90 pubmed
    ..Together, these findings suggest that sequences upstream of the 5' splice site play an important role in splice regulation of simple retroviruses, directly or indirectly attenuating the efficiency of splicing...
  58. Baroth M, Peters Y, Schönbrunner E, Behrens S. Stable recombinants of bovine viral diarrhea virus containing a hepatitis C virus insert. J Gen Virol. 2010;91:1213-7 pubmed publisher
    ..The generation of such BVDV recombinants is relevant for several applications. ..
  59. Sharma C, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464:250-5 pubmed publisher
    ..Our approach establishes a paradigm for mapping and annotating the primary transcriptomes of many living species. ..
  60. Beckmann B, Grünweller A, Weber M, Hartmann R. Northern blot detection of endogenous small RNAs (approximately14 nt) in bacterial total RNA extracts. Nucleic Acids Res. 2010;38:e147 pubmed publisher
  61. Veith T, Martin R, Wurm J, Weis B, Duchardt Ferner E, Safferthal C, et al. Structural and functional analysis of the archaeal endonuclease Nob1. Nucleic Acids Res. 2012;40:3259-74 pubmed publisher
    ..This suggests that the zinc ribbon domain acts as an anchor point for the protein on the nascent subunit positioning it in the proximity of the cleavage site...
  62. Kleineidam R, Pitulle C, Sproat B, Krupp G. Efficient cleavage of pre-tRNAs by E. coli RNAse P RNA requires the 2'-hydroxyl of the ribose at the cleavage site. Nucleic Acids Res. 1993;21:1097-101 pubmed
    ..Based on our data we suggest that the modifications do not interfere with binding of the substrate, whereas they prevent an optimal steric arrangement for the hydrolysis reaction. ..
  63. Achsel T, Ahrens K, Brahms H, Teigelkamp S, Luhrmann R. The human U5-220kD protein (hPrp8) forms a stable RNA-free complex with several U5-specific proteins, including an RNA unwindase, a homologue of ribosomal elongation factor EF-2, and a novel WD-40 protein. Mol Cell Biol. 1998;18:6756-66 pubmed
    ..Since the 220kD protein is also known to contact both the pre-mRNA and the U5 snRNA, it is in a position to relay the functional state of the spliceosome to the other proteins in the complex and thus modulate their activity. ..
  64. Schäfer M, Tastan A, Patzke S, Blaha G, Spahn C, Wilson D, et al. Codon-anticodon interaction at the P site is a prerequisite for tRNA interaction with the small ribosomal subunit. J Biol Chem. 2002;277:19095-105 pubmed
    ..5-A crystal structure of a programmed 70 S ribosome, thus refining which ribosomal components are critical for tRNA fixation at the P site. ..
  65. Beyer S, Simmel F. A modular DNA signal translator for the controlled release of a protein by an aptamer. Nucleic Acids Res. 2006;34:1581-7 pubmed
    ..The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences. ..
  66. Wohlgemuth I, Brenner S, Beringer M, Rodnina M. Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J Biol Chem. 2008;283:32229-35 pubmed publisher
    ..On the other hand, the 50-fold increase in the reaction rate for peptidyl-tRNA ending with Pro suggests that full-length aminoacyl-tRNA in the A site greatly accelerates peptide bond formation. ..
  67. Vahrenholz C, Riemen G, Pratje E, Dujon B, Michaelis G. Mitochondrial DNA of Chlamydomonas reinhardtii: the structure of the ends of the linear 15.8-kb genome suggests mechanisms for DNA replication. Curr Genet. 1993;24:241-7 pubmed
    ..The unusual structure of the 15.8-kb DNA termini is compared with those of other linear mitochondrial DNAs. Possible mechanisms of 15.8-kb DNA replication are discussed. ..
  68. Chen M, Maerz W, Manfras B, Kuehnl P, Usadel K, Boehm B. Rapid and simple subtyping of the HLA-DRB3 gene in Graves' disease by using temperature-gradient gel electrophoresis. Hum Immunol. 1993;36:199-203 pubmed
    ..The PCR-TGGE technique is a simple, nonisotopic method, which may be useful in rapid screening of large populations for HLA disease markers. ..
  69. Afanasyeva E, Hotz Wagenblatt A, Glatting K, Westermann F. New miRNAs cloned from neuroblastoma. BMC Genomics. 2008;9:52 pubmed publisher
    ..Some of these newly identified sequences reside within frequently altered chromosomal regions in NB tumours and may play a role in NB biology. ..
  70. Thielking V, Selent U, K hler E, Wolfes H, Pieper U, Geiger R, et al. Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis. Biochemistry. 1991;30:6416-22 pubmed
    ..On the basis of these findings we propose that these restriction enzymes and to a certain extent also some of their corresponding modification enzymes interact with DNA in a similar manner...
  71. Praml C, Savelyeva L, Schwab M. Aflatoxin B1 aldehyde reductase (AFAR) genes cluster at 1p35-1p36.1 in a region frequently altered in human tumour cells. Oncogene. 2003;22:4765-73 pubmed
    ..6% identical. Knowledge of the AFAR genes and their structure will be essential in genetic and functional studies, where discrimination of the genes and proteins is a prerequisite for evaluating their individual functions. ..
  72. Voigt O, Erpenbeck D, Worheide G. Molecular evolution of rDNA in early diverging Metazoa: first comparative analysis and phylogenetic application of complete SSU rRNA secondary structures in Porifera. BMC Evol Biol. 2008;8:69 pubmed publisher
  73. Batisse J, Batisse C, Budd A, Bottcher B, Hurt E. Purification of nuclear poly(A)-binding protein Nab2 reveals association with the yeast transcriptome and a messenger ribonucleoprotein core structure. J Biol Chem. 2009;284:34911-7 pubmed publisher
    ..Electron microscopy revealed that many of the mRNPs have a characteristic elongated structure. Our data suggest that mRNPs, although associated with different mRNAs, have a unifying core structure. ..
  74. Kemmerich F, Swoboda M, Kauert D, Grieb M, Hahn S, Schwarz F, et al. Simultaneous Single-Molecule Force and Fluorescence Sampling of DNA Nanostructure Conformations Using Magnetic Tweezers. Nano Lett. 2016;16:381-6 pubmed publisher
    ..The synchronized orthogonal readout in different observation channels will facilitate deciphering the complex mechanisms of biomolecular machines. ..
  75. Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, et al. Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. elife. 2016;5: pubmed publisher
    ..By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases. ..
  76. Schmitz M, Steger G. Description of RNA folding by "simulated annealing". J Mol Biol. 1996;255:254-66 pubmed
    ..The computed results are in accordance with experimental data and biological functions known for PSTVd. ..
  77. Li D, Willkomm D, Schön A, Hartmann R. RNase P of the Cyanophora paradoxa cyanelle: a plastid ribozyme. Biochimie. 2007;89:1528-38 pubmed
    ..Likely related to this low robustness, extensive structural changes towards an E. coli-type P5-7/P15-17 subdomain as a canonical interaction site for tRNA 3'-CCA termini could not be coaxed into increased ribozyme activity. ..
  78. Azizi H, Romão T, Santos Charret K, Padmanabhan P, de Melo Neto O, Müller McNicoll M, et al. RNA secondary structure and nucleotide composition of the conserved hallmark sequence of Leishmania SIDER2 retroposons are essential for endonucleolytic cleavage and mRNA degradation. PLoS ONE. 2017;12:e0180678 pubmed publisher
  79. Overmann J, Tuschak C. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch Microbiol. 1997;167:302-9 pubmed
    ..The latter technique is, therefore, well suited for the rapid screening of isolated pure cultures of green sulfur bacteria...
  80. Zaychikov E, Denissova L, Guckenberger R, Heumann H. Escherichia coli RNA polymerase translocation is accompanied by periodic bending of the DNA. Nucleic Acids Res. 1999;27:3645-52 pubmed
    ..We suggest that the periodicity of the bending angle reflects periodic changes of the conformation of the halted complexes that might have relevance for the translocation mechanism. ..
  81. Willkomm D, Gruegelsiepe H, Goudinakis O, Kretschmer Kazemi Far R, Bald R, Erdmann V, et al. Evaluation of bacterial RNase P RNA as a drug target. Chembiochem. 2003;4:1041-8 pubmed
  82. Wild K, Bange G, Bozkurt G, Segnitz B, Hendricks A, Sinning I. Structural insights into the assembly of the human and archaeal signal recognition particles. Acta Crystallogr D Biol Crystallogr. 2010;66:295-303 pubmed publisher
    ..Differences in SRP assembly between mammalia and archaea are therefore independent of SRP19 and are based on differences in SRP RNA itself. A new SRP-assembly scheme is presented. ..
  83. Ilik I, Quinn J, Georgiev P, Tavares Cadete F, Maticzka D, Toscano S, et al. Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell. 2013;51:156-73 pubmed publisher
    ..We propose that repetitive structural motifs in lncRNAs could provide plasticity during multiprotein complex assemblies to ensure efficient targeting in cis or in trans along chromosomes...
  84. Schiffer S, R sch S, Marchfelder A. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 2002;21:2769-77 pubmed publisher
    ..thaliana and M.janaschii are the first members of these families to which a function can now be assigned. Proteins with high sequence similarity to the RNase Z enzymes from A.thaliana and M.janaschii are present in all three kingdoms...
  85. Lizano E, Scheibe M, Rammelt C, Betat H, Mörl M. A comparative analysis of CCA-adding enzymes from human and E. coli: differences in CCA addition and tRNA 3'-end repair. Biochimie. 2008;90:762-72 pubmed publisher
  86. Liu C, Hühne R, Tu J, Lorbach E, Droge P. The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases. Genes Cells. 1998;3:221-33 pubmed
  87. Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W. Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol. 2000;7:215-9 pubmed publisher
    ..This forces a pendulum-like motion of helix a4, which increases the separation of the attached DNA binding domains by 3 A, abolishing the affinity of TetR for its operator DNA...
  88. Pul U, Wurm R, Wagner R. The role of LRP and H-NS in transcription regulation: involvement of synergism, allostery and macromolecular crowding. J Mol Biol. 2007;366:900-15 pubmed
    ..The formation of this regulatory structure appears to be directly affected by environmental changes. ..
  89. Mourão A, Varrot A, Mackereth C, Cusack S, Sattler M. Structure and RNA recognition by the snRNA and snoRNA transport factor PHAX. RNA. 2010;16:1205-16 pubmed publisher
    ..Our data suggest that the PHAX-RBD mediates auxiliary RNA contacts with the snRNA and snoRNA substrates that are required for transport and/or substrate release. ..
  90. Wang Z, Droge P. Long-range effects in a supercoiled DNA domain generated by transcription in vitro. J Mol Biol. 1997;271:499-510 pubmed
    ..coli is bound to multiple sites within the phage lambda attachment region. We discuss implications of our in vitro findings with respect to possible in vivo functions of the dynamic nature of transcription-induced supercoiling. ..
  91. Wilting R, Vamvakidou K, Bock A. Functional expression in Escherichia coli of the Haemophilus influenzae gene coding for selenocysteine-containing selenophosphate synthetase. Arch Microbiol. 1998;169:71-5 pubmed
    ..We also show that the selenocysteine synthesis and the insertion systems of the two organisms are fully compatible despite conspicuous differences in the mRNA recognition motif. ..
  92. Klinkert B, Elles I, Nickelsen J. Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon. Nucleic Acids Res. 2006;34:386-94 pubmed
    ..In conclusion, the data suggest that these new element serves as a negative regulator which mediates a rapid shut-down of D2 synthesis. ..