Experts and Doctors on nucleic acid conformation in Paris, Île de France, France

Summary

Locale: Paris, Île de France, France
Topic: nucleic acid conformation

Top Publications

  1. Springer M, Graffe M, Dondon J, Grunberg Manago M. tRNA-like structures and gene regulation at the translational level: a case of molecular mimicry in Escherichia coli. EMBO J. 1989;8:2417-24 pubmed
  2. Hoede C, Denamur E, Tenaillon O. Selection acts on DNA secondary structures to decrease transcriptional mutagenesis. PLoS Genet. 2006;2:e176 pubmed
    ..Such selection is stronger in highly expressed genes and suggests a sequence-dependent way to control mutation rates and a novel form of selection affecting the evolution of synonymous mutations. ..
  3. Lionnet T, Spiering M, Benkovic S, Bensimon D, Croquette V. Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proc Natl Acad Sci U S A. 2007;104:19790-5 pubmed
    ..Our results suggest that important regulations occur within the replisome to achieve rapid and processive replication. ..
  4. Gratias A, Lepère G, Garnier O, Rosa S, Duharcourt S, Malinsky S, et al. Developmentally programmed DNA splicing in Paramecium reveals short-distance crosstalk between DNA cleavage sites. Nucleic Acids Res. 2008;36:3244-51 pubmed publisher
  5. Gaillard C, Borde C, Gozlan J, Marechal V, Strauss F. A high-sensitivity method for detection and measurement of HMGB1 protein concentration by high-affinity binding to DNA hemicatenanes. PLoS ONE. 2008;3:e2855 pubmed publisher
  6. Cayrol B, Geinguenaud F, Lacoste J, Busi F, Le Derout J, Piétrement O, et al. Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences. RNA Biol. 2009;6:434-45 pubmed
  7. Bonnefoy E, Rouviere Yaniv J. HU, the major histone-like protein of E. coli, modulates the binding of IHF to oriC. EMBO J. 1992;11:4489-96 pubmed
    ..In addition, we show that HU can modulate the binding of IHF to its specific oriC site. Depending on the relative concentrations of HU and IHF, HU is able either to activate or to inhibit the binding of IHF to oriC. ..
  8. Raibaud O. Nucleoprotein structures at positively regulated bacterial promoters: homology with replication origins and some hypotheses on the quaternary structure of the activator proteins in these complexes. Mol Microbiol. 1989;3:455-8 pubmed
    ..Nucleoprotein structures present at the oriC replication origin and at malB promoters show striking homologies. ..
  9. Libri D, Lemonnier M, Meinnel T, Fiszman M. A single gene codes for the beta subunits of smooth and skeletal muscle tropomyosin in the chicken. J Biol Chem. 1989;264:2935-44 pubmed
    ..Our results indicate that both the smooth and skeletal beta-tropomyosin mRNAs are derived from transcripts of a single gene with a unique promoter by a differential splicing mechanism. ..

More Information

Publications124 found, 100 shown here

  1. Hajnsdorf E, Braun F, Haugel Nielsen J, Le Derout J, Regnier P. Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5' and 3' extremities of the primary transcript. Biochimie. 1996;78:416-24 pubmed
    ..Looping of the rpsO mRNA might explain how RNase E bound at the 5' end can cleave at a site located just upstream the hairpin of the transcription terminator. ..
  2. Mine M, Chen J, Brivet M, Desguerre I, Marchant D, de Lonlay P, et al. A large genomic deletion in the PDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element. Hum Mutat. 2007;28:137-42 pubmed
    ..Our finding not only serves as an important complement to the in vitro approaches to studying L1 retrotransposition, but also reveals a novel mechanism causing human genetic disease...
  3. Dawid A, Cayrol B, Isambert H. RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation. Phys Biol. 2009;6:025007 pubmed publisher
    ..Overall, this suggests that direct coupling among synthesis, folding and regulation of RNAs may have enabled the early emergence of autonomous RNA-based regulation networks in absence of both DNA and protein partners. ..
  4. Sleiman D, Goldschmidt V, Barraud P, Marquet R, Paillart J, Tisne C. Initiation of HIV-1 reverse transcription and functional role of nucleocapsid-mediated tRNA/viral genome interactions. Virus Res. 2012;169:324-39 pubmed publisher
    ..Lastly, we focused on the additional interactions occurring between tRNA(Lys)(3) and the viral RNA and showed that they are dependent on HIV-1 isolates, i.e. the sequence and the structure of the viral RNA. ..
  5. Durand S, Jahn N, Condon C, Brantl S. Type I toxin-antitoxin systems in Bacillus subtilis. RNA Biol. 2012;9:1491-7 pubmed publisher
    ..Here we review what is known about these confirmed and putative toxin-antitoxin families in B. subtilis, their regulatory mechanisms, their potential roles and how they may link to the physiology of the cell. ..
  6. Yeramian E. Genes and the physics of the DNA double-helix. Gene. 2000;255:139-50 pubmed
    ..There are many evolutionary implications for the results presented and for their proposed interpretations, notably concerning models of mutational dynamics in relation to erasure processes. ..
  7. Miot M, Betton J. Optimization of the inefficient translation initiation region of the cpxP gene from Escherichia coli. Protein Sci. 2007;16:2445-53 pubmed
    ..Our results support the hypothesis that periplasmic expression could be inhibited by sequence elements in the early coding signal sequence region of cpxP. ..
  8. Kamashev D, Balandina A, Rouviere Yaniv J. The binding motif recognized by HU on both nicked and cruciform DNA. EMBO J. 1999;18:5434-44 pubmed
    ..The HU binding motif present in both structures is a pair of inclined DNA helices. ..
  9. Chanfreau G, Buckle M, Jacquier A. Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III. Proc Natl Acad Sci U S A. 2000;97:3142-7 pubmed
    ..These results also indicate that proteins belonging to the same class of RNA endonucleases require different structural elements for RNA cleavage. ..
  10. Moissenet D, Bidet P, Garbarg Chenon A, Arlet G, Vu Thien H. Ralstonia paucula (Formerly CDC group IV c-2): unsuccessful strain differentiation with PCR-based methods, study of the 16S-23S spacer of the rRNA operon, and comparison with other Ralstonia species (R. eutropha, R. pickettii, R. gilardii, and R. sol. J Clin Microbiol. 2001;39:381-4 pubmed
    ..The 16S-23S rDNA intergenic spacer of R. paucula contains the tRNA(Ile) and tRNA(Ala) genes, which are identical to genes described for R. pickettii and R. solanacearum. ..
  11. Gaillard C, Shlyakhtenko L, Lyubchenko Y, Strauss F. Structural analysis of hemicatenated DNA loops. BMC Struct Biol. 2002;2:7 pubmed
    ..The novel possibility to prepare DNA hemicatenanes should be useful to further study this alternative DNA structure and its involvement in replication or recombination. ..
  12. David A, Bleimling N, Beuck C, Lehn J, Weinhold E, Teulade Fichou M. DNA mismatch-specific base flipping by a bisacridine macrocycle. Chembiochem. 2003;4:1326-31 pubmed
    ..Thus, DNA base flipping does not appear to be limited to DNA-modifying enzymes but it is likely to also be induced by a small synthetic molecule binding to a thermodynamically weakened site in DNA. ..
  13. Picard F, Robin S, Lavielle M, Vaisse C, Daudin J. A statistical approach for array CGH data analysis. BMC Bioinformatics. 2005;6:27 pubmed
    ..Adaptive methods for model selection give promising results concerning the estimation of the number of altered regions on the genome. ..
  14. Kamashev D, Balandina A, Mazur A, Arimondo P, Rouviere Yaniv J. HU binds and folds single-stranded DNA. Nucleic Acids Res. 2008;36:1026-36 pubmed
    ..Furthermore HU has a strong preference for poly(dG), while binding to poly(dA) is the weakest. HU binding to ssDNA is probably important for its capacity to cover and protect bacterial DNA both intact and carrying lesions. ..
  15. Fichou Y, Nectoux J, Bahi Buisson N, Rosas Vargas H, Girard B, Chelly J, et al. The first missense mutation causing Rett syndrome specifically affecting the MeCP2_e1 isoform. Neurogenetics. 2009;10:127-33 pubmed publisher
    ..These data suggest the important involvement of the N-terminus in the function of MeCP2 protein, and provide further evidence for the major impact of a specific MeCP2e_1 deficiency in the development of intellectual processing. ..
  16. Diguet A, Mani N, Geoffroy M, Sollogoub M, Baigl D. Photosensitive surfactants with various hydrophobic tail lengths for the photocontrol of genomic DNA conformation with improved efficiency. Chemistry. 2010;16:11890-6 pubmed publisher
    ..Optimal performance was achieved with AzoC5, which allowed reversible control of DNA conformation with light at a concentration seven times smaller than previously reported. ..
  17. Budkowska A, Kakkanas A, Nerrienet E, Kalinina O, Maillard P, Horm S, et al. Synonymous mutations in the core gene are linked to unusual serological profile in hepatitis C virus infection. PLoS ONE. 2011;6:e15871 pubmed publisher
    ..Such HCV variants may favour core+1/ARFP production during HCV infection. ..
  18. Pellegrini O, Li de la Sierra Gallay I, Piton J, Gilet L, Condon C. Activation of tRNA maturation by downstream uracil residues in B. subtilis. Structure. 2012;20:1769-77 pubmed publisher
    ..We solved the first crystal structure of B. subtilis RNase Z bound to a tRNA(Thr) precursor with U74 and show that the enzyme has a specific binding pocket for this nucleotide. ..
  19. Dozières A, Chapuis J, Thibault S, Baudry E. Genetic structure of the French red squirrel populations: implication for conservation. PLoS ONE. 2012;7:e47607 pubmed publisher
    ..The French red squirrels showed strong signals of population expansion, the opposite to what is observed in most other European populations, making them of particular interest to study the postglacial expansion history of the species. ..
  20. Tiana G, Amitai A, Pollex T, Piolot T, Holcman D, Heard E, et al. Structural Fluctuations of the Chromatin Fiber within Topologically Associating Domains. Biophys J. 2016;110:1234-45 pubmed publisher
  21. Benard L, Philippe C, Dondon L, Grunberg Manago M, Ehresmann B, Ehresmann C, et al. Mutational analysis of the pseudoknot structure of the S15 translational operator from Escherichia coli. Mol Microbiol. 1994;14:31-40 pubmed
    ..It is deduced that a specific pseudoknot conformation is a key element for autoregulation. ..
  22. Plumbridge J, Kolb A. DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo. Mol Microbiol. 1993;10:973-81 pubmed
    ..These observations show that repression is the result of co-operative binding of the repressor to its two sites, resulting in the formation of a loop of DNA. ..
  23. Chiaruttini C, Milet M, Springer M. A long-range RNA-RNA interaction forms a pseudoknot required for translational control of the IF3-L35-L20 ribosomal protein operon in Escherichia coli. EMBO J. 1996;15:4402-13 pubmed
    ..We propose that these two distant sites can base-pair to form a long-range pseudoknot which is required for the control of the expression of the L35 gene. ..
  24. Lopez P, Dreyfus M. The lacZ mRNA can be stabilised by the T7 late mRNA leader in E coli. Biochimie. 1996;78:408-15 pubmed
    ..Yet, the leader replacement did not stabilise the transcript chemically. We propose that this replacement inhibits the initial cleavage step but somehow facilitates the subsequent scavenging process. ..
  25. Gébrane Younès J, Fomproix N, Hernandez Verdun D. When rDNA transcription is arrested during mitosis, UBF is still associated with non-condensed rDNA. J Cell Sci. 1997;110 ( Pt 19):2429-40 pubmed
    ..It is proposed that modifications of the transcription machinery occurring in prometaphase could explain the arrest of transcription, while reverse modifications in late anaphase could explain activation...
  26. Crescenzo Chaigne B, Naffakh N, Van Der Werf S. Comparative analysis of the ability of the polymerase complexes of influenza viruses type A, B and C to assemble into functional RNPs that allow expression and replication of heterotypic model RNA templates in vivo. Virology. 1999;265:342-53 pubmed
    ..Taken together, our results suggest that less strict type-specific interactions are involved for the polymerase complex of influenza A compared with influenza B or C viruses. ..
  27. Kamashev D, Rouviere Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 2000;19:6527-35 pubmed
    ..Both structural motifs are recognized by HU at least 1000-fold more avidly than duplex DNA. ..
  28. Malnou C, Werner A, Borman A, Westhof E, Kean K. Effects of vaccine strain mutations in domain V of the internal ribosome entry segment compared in the wild type poliovirus type 1 context. J Biol Chem. 2004;279:10261-9 pubmed
    ..These data support the previously reported conclusion that the 2A protease has markedly different affinities for the two eIF4G isoforms. ..
  29. Guillier M, Allemand F, Dardel F, Royer C, Springer M, Chiaruttini C. Double molecular mimicry in Escherichia coli: binding of ribosomal protein L20 to its two sites in mRNA is similar to its binding to 23S rRNA. Mol Microbiol. 2005;56:1441-56 pubmed
    ..Using a set of genetic, biochemical, biophysical, and structural experiments, we show here that all three sites are recognized similarly by L20. ..
  30. Heddi B, Foloppe N, Oguey C, Hartmann B. Importance of accurate DNA structures in solution: the Jun-Fos model. J Mol Biol. 2008;382:956-70 pubmed publisher
    ..We show how to exploit the relationship between phosphate motions and helicoidal descriptors for structure determination toward an accurate description of DNA structures and dynamics in solution. ..
  31. Hyrien O. Topological analysis of plasmid DNA replication intermediates using two-dimensional agarose gels. Methods Mol Biol. 2009;521:139-67 pubmed publisher
    ..Other applications include the detection of knots that form independently of, or concomitantly with, DNA replication. ..
  32. Moumne R, Pasco M, Prost E, Lecourt T, Micouin L, Tisne C. Fluorinated diaminocyclopentanes as chiral sensitive NMR probes of RNA structure. J Am Chem Soc. 2010;132:13111-3 pubmed publisher
    ..This work provides a proof of concept that small fluorinated moderate binders can act as external probes of RNA structures...
  33. Vekhoff P, Duca M, Guianvarc h D, Benhida R, Arimondo P. Sequence-specific base pair mimics are efficient topoisomerase IB inhibitors. Biochemistry. 2012;51:43-51 pubmed publisher
    ..The three compounds were equally active once conjugated, implying that the intercalation of the nucleobase upon triplex formation is the essential feature for the inhibition activity. ..
  34. Baouendi M, Cognet J, Ferreira C, Missailidis S, Coutant J, Piotto M, et al. Solution structure of a truncated anti-MUC1 DNA aptamer determined by mesoscale modeling and NMR. FEBS J. 2012;279:479-90 pubmed publisher
    ..Database Structural data are available in the Protein Data Bank and BioMagResBank databases under the accession numbers 2L5K and 17129, respectively. ..
  35. Grieb M, Nivina A, Cheeseman B, Hartmann A, Mazel D, Schlierf M. Dynamic stepwise opening of integron attC DNA hairpins by SSB prevents toxicity and ensures functionality. Nucleic Acids Res. 2017;45:10555-10563 pubmed publisher
  36. Curnow K, Pascoe L, Davies E, White P, Corvol P, Clauser E. Alternatively spliced human type 1 angiotensin II receptor mRNAs are translated at different efficiencies and encode two receptor isoforms. Mol Endocrinol. 1995;9:1250-62 pubmed
    ..These transcripts were translated into a larger receptor isoform in vitro and produced a functional receptor with normal ligand binding and signaling properties in transfected cells. ..
  37. Cragnolini T, Derreumaux P, Pasquali S. Coarse-grained simulations of RNA and DNA duplexes. J Phys Chem B. 2013;117:8047-60 pubmed publisher
  38. Huet S, Lavelle C, Ranchon H, Carrivain P, Victor J, Bancaud A. Relevance and limitations of crowding, fractal, and polymer models to describe nuclear architecture. Int Rev Cell Mol Biol. 2014;307:443-79 pubmed publisher
    ..Finally, we identify future challenges in the roadmap to a unified model of the nuclear environment. ..
  39. Plumbridge J, Kolb A. DNA bending and expression of the divergent nagE-B operons. Nucleic Acids Res. 1998;26:1254-60 pubmed
    ..In this case protein-protein contacts between CAP and RNA polymerase are necessary for full activation, but at least a part of the activation is likely due to an effect of CAP binding altering DNA structure. ..
  40. Le Derout J, Folichon M, Briani F, Deh G, R gnier P, Hajnsdorf E. Hfq affects the length and the frequency of short oligo(A) tails at the 3' end of Escherichia coli rpsO mRNAs. Nucleic Acids Res. 2003;31:4017-23 pubmed
    ..Our data led us to the conclusion that Hfq is involved in the recognition of 3' RNA extremities by PAP I...
  41. Plassart E, Reboul J, Rime C, Recan D, Millasseau P, Eymard B, et al. Mutations in the muscle sodium channel gene (SCN4A) in 13 French families with hyperkalemic periodic paralysis and paramyotonia congenita: phenotype to genotype correlations and demonstration of the predominance of two mutations. Eur J Hum Genet. 1994;2:110-24 pubmed
    ..Recurrent mutations of SCN4A may contribute to the predominance of these two mutations in the French population. ..
  42. Guillier M, Allemand F, Raibaud S, Dardel F, Springer M, Chiaruttini C. Translational feedback regulation of the gene for L35 in Escherichia coli requires binding of ribosomal protein L20 to two sites in its leader mRNA: a possible case of ribosomal RNA-messenger RNA molecular mimicry. RNA. 2002;8:878-89 pubmed
    ..However L20 can bind to each site independently in vitro. One site is similar to the L20-binding site on 23S rRNA. Here we propose that L20 recognizes its mRNA and its rRNA in similar way. ..
  43. Cocquet J, Chong A, Zhang G, Veitia R. Reverse transcriptase template switching and false alternative transcripts. Genomics. 2006;88:127-31 pubmed
    ..However, care should be taken in the annotation of alternative transcripts, especially when the RT used is poorly thermostable and when the putative intron is flanked by direct repeats, which are the substrate for template switching. ..
  44. 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. ..
  45. Pichon C, Felden B. Small RNA gene identification and mRNA target predictions in bacteria. Bioinformatics. 2008;24:2807-13 pubmed publisher
    ..Here we review the computational studies that have contributed to detecting the sRNA gene and mRNA targets in bacteria and the methods for their experimental testing. In addition, the remaining challenges are discussed. ..
  46. van der Maarel J, Guttula D, Arluison V, Egelhaaf S, Grillo I, Forsyth V. Structure of the H-NS-DNA nucleoprotein complex. Soft Matter. 2016;12:3636-42 pubmed publisher
    ..The two observed binding modes and their modulation by magnesium ions provide a structural basis for H-NS-mediated genome organisation and expression regulation. ..
  47. Regnier P, Grunberg Manago M. Cleavage by RNase III in the transcripts of the met Y-nus-A-infB operon of Escherichia coli releases the tRNA and initiates the decay of the downstream mRNA. J Mol Biol. 1989;210:293-302 pubmed
  48. Chiaruttini C, Milet M, Hayes D, Expert Bezançon A. Crosslinking of ribosomal proteins S4, S5, S7, S8, S11, S12 and S18 to domains 1 and 2 of 16S rRNA in the Escherichia coli 30S particle. Biochimie. 1989;71:839-52 pubmed
    ..These results are discussed in the light of current knowledge of the tertiary structure of 16S rRNA in the E. coli 30S ribosomal subunit. ..
  49. Bonnefoy E. The ribosomal S16 protein of Escherichia coli displaying a DNA-nicking activity binds to cruciform DNA. Eur J Biochem. 1997;247:852-9 pubmed
    ..Overall these experiments indicate that S16 requires a cruciform-like DNA structure to bind DNA and the presence of a particular sequence in order to introduce specific single-stranded cuts into a DNA molecule. ..
  50. Uzan M. RNA processing and decay in bacteriophage T4. Prog Mol Biol Transl Sci. 2009;85:43-89 pubmed publisher
    ..The tRNA gene cluster also codes for a homing DNA endonuclease, SegB, responsible for spreading the tRNA genes to other T4-related phage. ..
  51. Luo D, Condon C, Grunberg Manago M, Putzer H. In vitro and in vivo secondary structure probing of the thrS leader in Bacillus subtilis. Nucleic Acids Res. 1998;26:5379-87 pubmed
    ..The leader sequences, and in particular the specifier domains, of the other genes of this family can be folded similarly to the experimentally solved thrS structure. ..
  52. Piro B, Reisberg S, Noel V, Pham M. Investigations of the steric effect on electrochemical transduction in a quinone-based DNA sensor. Biosens Bioelectron. 2007;22:3126-31 pubmed
    ..The results indicate that the current depends on the length of the double strand. A model which can explain the electrochemical behavior takes into account the steric hindrance of the ODN strands. ..
  53. Postic G, Frapy E, Dupuis M, Dubail I, Livny J, Charbit A, et al. Identification of small RNAs in Francisella tularensis. BMC Genomics. 2010;11:625 pubmed publisher
    ..tularensis deal with the unique and diverse set of environments with which it must contend. ..
  54. Rougee M, Faucon B, Mergny J, Barcelo F, Giovannangeli C, Garestier T, et al. Kinetics and thermodynamics of triple-helix formation: effects of ionic strength and mismatches. Biochemistry. 1992;31:9269-78 pubmed
    ..E., Crothers, D. M., & Doty, P. (1971) J. Mol. Biol. 62, 383-401; Pörschke, D., Eigen, M. (1971) J. Mol. Biol. 62, 361-381]. ..
  55. Bonnefoy E, Takahashi M, Yaniv J. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J Mol Biol. 1994;242:116-29 pubmed
    ..These results support a model where two HU-protein dimers specifically bind to two equivalent angles present opposite each other in the four-way-junction-DNA structure with almost no dimer-dimer interactions. ..
  56. Delarbre C, Rasmussen A, Arnason U, Gachelin G. The complete mitochondrial genome of the hagfish Myxine glutinosa: unique features of the control region. J Mol Evol. 2001;53:634-41 pubmed publisher
    ..The comparison of the mtDNAs of two M. glutinosa specimens, excluding the control region, shows a 0.6% divergence at the nucleotide level as a sample of intraspecies polymorphism...
  57. Marujo P, Braun F, Haugel Nielsen J, Le Derout J, Arraiano C, Regnier P. Inactivation of the decay pathway initiated at an internal site by RNase E promotes poly(A)-dependent degradation of the rpsO mRNA in Escherichia coli. Mol Microbiol. 2003;50:1283-94 pubmed
    ..We also discuss the role of poly(A)-dependent decay in mRNA metabolism. ..
  58. Dazza M, Ekwalanga M, Nende M, Shamamba K, Bitshi P, Paraskevis D, et al. Characterization of a novel vpu-harboring simian immunodeficiency virus from a Dent's Mona monkey (Cercopithecus mona denti). J Virol. 2005;79:8560-71 pubmed
    ..Although it harbors a vpu gene, SIVden is phylogenetically closer to SIVdeb isolated from De Brazza's monkeys (Cercopithecus neglectus), which lacks a vpu gene, than to Cercopithecus monkey viruses, which harbor a vpu sequence...
  59. Ranaei Siadat E, Fabret C, Seijo B, Dardel F, Grosjean H, Nonin Lecomte S. RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C5-methylation of uridine in both tmRNA and tRNA. RNA Biol. 2013;10:572-8 pubmed publisher
    ..The evidence comes from the lack of m (5)U in purified tmRNA or TLD variants recovered from an Escherichia coli mutant strain deleted of the trmA gene. Detection of m (5)U in RNA was performed by NMR analysis...
  60. Sacerdot C, Chiaruttini C, Engst K, Graffe M, Milet M, Mathy N, et al. The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli. Mol Microbiol. 1996;21:331-46 pubmed
    ..On the basis of our in vivo results we propose, as suspected from earlier in vitro results, that IF3 regulates the expression of its own gene by using its ability to differentiate between 'normal' and 'abnormal' initiation codons. ..
  61. Martin M, Fargion S, Brissot P, Pellat B, Beaumont C. A point mutation in the bulge of the iron-responsive element of the L ferritin gene in two families with the hereditary hyperferritinemia-cataract syndrome. Blood. 1998;91:319-23 pubmed
    ..Further studies will be necessary to elucidate the mechanism responsible for the onset of cataract. ..
  62. Duband Goulet I, Courvalin J. Inner nuclear membrane protein LBR preferentially interacts with DNA secondary structures and nucleosomal linker. Biochemistry. 2000;39:6483-8 pubmed
  63. Duarte M, Graham K, Daher A, Battisti P, Bannwarth S, Segeral E, et al. Characterization of TRBP1 and TRBP2. Stable stem-loop structure at the 5' end of TRBP2 mRNA resembles HIV-1 TAR and is not found in its processed pseudogene. J Biomed Sci. 2000;7:494-506 pubmed
    ..Our data indicate that TRBP proteins act at a level prior to Tat function. TRBP could contribute to improved HIV expression in murine models. ..
  64. Charvin G, Strick T, Bensimon D, Croquette V. Topoisomerase IV bends and overtwists DNA upon binding. Biophys J. 2005;89:384-92 pubmed
    ..89 and a strongly bound state (with probability p = 0.11). The methodology introduced here to characterize the Topo IV/DNA complex is very general and could be used to study other DNA/protein complexes. ..
  65. Li Y, Vergne J, Torchet C, Maurel M. In vitro selection of adenine-dependent ribozyme against Tpl2/Cot oncogene. FEBS J. 2009;276:303-14 pubmed publisher
    ..The selected 'Tpl2/Cot-YL ribozyme' efficiently cleaves its target sequence in cis and in trans; furthermore, the ribozyme efficiently cleaves a longer target sequence of 54 nucleotides in trans, as well as the full-length mRNA. ..
  66. Kupiec J, Kay A, Hayat M, Ravier R, P ri s J, Galibert F. Sequence analysis of the simian foamy virus type 1 genome. Gene. 1991;101:185-94 pubmed
    ..The homology between SFV1 and HFV reaches 89% in the reverse transcriptase domain of the pol gene. but is much smaller in other parts of the genome...
  67. Sikorav J, Church G. Complementary recognition in condensed DNA: accelerated DNA renaturation. J Mol Biol. 1991;222:1085-108 pubmed
    ..These may model a mechanism of recombinational protein function. ..
  68. Portier C, Philippe C, Dondon L, Grunberg Manago M, Ebel J, Ehresmann B, et al. Translational control of ribosomal protein S15. Biochim Biophys Acta. 1990;1050:328-36 pubmed
    ..Binding of S15 to these two domains suggests that the pseudoknot could be stabilized by S15. A model is presented in which two alternative structures would explain the molecular basis of the S15 autocontrol. ..
  69. Brunel C, Romby P, Sacerdot C, de Smit M, Graffe M, Dondon J, et al. Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli. J Mol Biol. 1995;253:277-90 pubmed
    ..This molecular amplification device might be an essential component of translational control considering the low free repressor/ribosome ratio of the low affinity of translational repressors for their target operators. ..
  70. Li de la Sierra Gallay I, Mathy N, Pellegrini O, Condon C. Structure of the ubiquitous 3' processing enzyme RNase Z bound to transfer RNA. Nat Struct Mol Biol. 2006;13:376-7 pubmed publisher
    ..Binding of tRNA to RNase Z causes conformational changes in both partners to promote reorganization of the catalytic site and tRNA cleavage...
  71. Condon C. Maturation and degradation of RNA in bacteria. Curr Opin Microbiol. 2007;10:271-8 pubmed
    ..coli and the identification of an enzyme in B. subtilis that appears to fit the bill as a major player in RNA decay in this organism. ..
  72. Ribeyre C, Lopes J, Boulé J, Piazza A, Guédin A, Zakian V, et al. The yeast Pif1 helicase prevents genomic instability caused by G-quadruplex-forming CEB1 sequences in vivo. PLoS Genet. 2009;5:e1000475 pubmed publisher
    ..Hence, we conclude that CEB1 instability in pif1Delta cells depends on the potential to form G-quadruplex structures, suggesting that Pif1 could play a role in the metabolism of G4-forming sequences. ..
  73. Balandina A, Kamashev D, Rouviere Yaniv J. The bacterial histone-like protein HU specifically recognizes similar structures in all nucleic acids. DNA, RNA, and their hybrids. J Biol Chem. 2002;277:27622-8 pubmed
  74. Choonee N, Even S, Zig L, Putzer H. Ribosomal protein L20 controls expression of the Bacillus subtilis infC operon via a transcription attenuation mechanism. Nucleic Acids Res. 2007;35:1578-88 pubmed publisher
    ..Our data suggest that Nomura's model of ribosomal protein biosynthesis based on autogenous control and molecular mimicry is also valid in Gram-positive organisms...
  75. Haentjens Sitri J, Allemand F, Springer M, Chiaruttini C. A competition mechanism regulates the translation of the Escherichia coli operon encoding ribosomal proteins L35 and L20. J Mol Biol. 2008;375:612-25 pubmed
    ..We show that the pseudoknot, which is known to be essential for L20 binding and regulation, also enhances 30S binding to mRNA as if this structure is specifically recognised by the ribosome. ..
  76. Lavigne M, Herbert M, Kolb A, Buc H. Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J Mol Biol. 1992;224:293-306 pubmed
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