Literature DB >> 7737131

Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides.

I Brukner1, R Sánchez, D Suck, S Pongor.   

Abstract

Structural parameters characterizing the bending propensity of trinucleotides were deduced from DNase I digestion data using simple probabilistic models. In contrast to dinucleotide-based models of DNA bending and/or bendability, the trinucleotide parameters are in good agreement with X-ray crystallographic data on bent DNA. This improvement may be due to the fact that the trinucleotide model incorporates more sequence context information than do dinucleotide-based descriptions.

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Year:  1995        PMID： 7737131      PMCID： PMC398274          DOI： 10.1002/j.1460-2075.1995.tb07169.x

Source DB:  PubMed          Journal:  EMBO J        ISSN： 0261-4189            Impact factor:   11.598


  36 in total

1.  1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG.

Authors:  J L Kim; S K Burley
Journal:  Nat Struct Biol       Date:  1994-09

Review 2.  DNA recognition by DNase I.

Authors:  D Suck
Journal:  J Mol Recognit       Date:  1994-06       Impact factor: 2.137

3.  Crystallographic analysis of C-C-A-A-G-C-T-T-G-G and its implications for bending in B-DNA.

Authors:  K Grzeskowiak; D S Goodsell; M Kaczor-Grzeskowiak; D Cascio; R E Dickerson
Journal:  Biochemistry       Date:  1993-08-31       Impact factor: 3.162

4.  DNA recognition by beta-sheets in the Arc repressor-operator crystal structure.

Authors:  B E Raumann; M A Rould; C O Pabo; R T Sauer
Journal:  Nature       Date:  1994-02-24       Impact factor: 49.962

5.  Determinants of repressor/operator recognition from the structure of the trp operator binding site.

Authors:  Z Shakked; G Guzikevich-Guerstein; F Frolow; D Rabinovich; A Joachimiak; P B Sigler
Journal:  Nature       Date:  1994-03-31       Impact factor: 49.962

6.  Sequence-dependent variation in the conformation of DNA.

Authors:  G P Lomonossoff; P J Butler; A Klug
Journal:  J Mol Biol       Date:  1981-07-15       Impact factor: 5.469

7.  DNA structural variations in the E. coli tyrT promoter.

Authors:  H R Drew; A A Travers
Journal:  Cell       Date:  1984-06       Impact factor: 41.582

8.  Sequencing end-labeled DNA with base-specific chemical cleavages.

Authors:  A M Maxam; W Gilbert
Journal:  Methods Enzymol       Date:  1980       Impact factor: 1.600

9.  Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA.

Authors:  I Brukner; S Susic; M Dlakic; A Savic; S Pongor
Journal:  J Mol Biol       Date:  1994-02-11       Impact factor: 5.469

10.  CRP fixes the rotational orientation of covalently closed DNA molecules.

Authors:  M Lavigne; A Kolb; E Yeramian; H Buc
Journal:  EMBO J       Date:  1994-10-17       Impact factor: 11.598
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  101 in total

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Authors:  Kelly M Thayer; D L Beveridge
Journal:  Proc Natl Acad Sci U S A       Date:  2002-06-18       Impact factor: 11.205

Review 2.  Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

Authors:  Stephane Rombauts; Kobe Florquin; Magali Lescot; Kathleen Marchal; Pierre Rouzé; Yves van de Peer
Journal:  Plant Physiol       Date:  2003-07       Impact factor: 8.340

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Journal:  Nucleic Acids Res       Date:  2003-08-01       Impact factor: 16.971

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Authors:  David L Beveridge; Gabriela Barreiro; K Suzie Byun; David A Case; Thomas E Cheatham; Surjit B Dixit; Emmanuel Giudice; Filip Lankas; Richard Lavery; John H Maddocks; Roman Osman; Eleanore Seibert; Heinz Sklenar; Gautier Stoll; Kelly M Thayer; Péter Varnai; Matthew A Young
Journal:  Biophys J       Date:  2004-08-23       Impact factor: 4.033

5.  Intrinsic characteristics of neighboring DNA modulate transposable element activity in Drosophila melanogaster.

Authors:  Caroline Esnault; Azhahianambi Palavesam; Kristina Pilitt; David A O'Brochta
Journal:  Genetics       Date:  2010-10-13       Impact factor: 4.562

6.  Core promoter elements of eukaryotic genes have a highly distinctive mechanical property.

Authors:  Yoshiro Fukue; Noriyuki Sumida; Jun-ichi Nishikawa; Takashi Ohyama
Journal:  Nucleic Acids Res       Date:  2004-11-01       Impact factor: 16.971

7.  Fine mapping of inherent flexibility variation along DNA molecules: validation by atomic force microscopy (AFM) in buffer.

Authors:  Monique Marilley; Albert Sanchez-Sevilla; José Rocca-Serra
Journal:  Mol Genet Genomics       Date:  2005-11-01       Impact factor: 3.291

8.  Agrobacterium T-DNA integration in Arabidopsis is correlated with DNA sequence compositions that occur frequently in gene promoter regions.

Authors:  Richard G Schneeberger; Ke Zhang; Tatiana Tatarinova; Max Troukhan; Shing F Kwok; Josh Drais; Kevin Klinger; Francis Orejudos; Kimberly Macy; Amit Bhakta; James Burns; Gopal Subramanian; Jonathan Donson; Richard Flavell; Kenneth A Feldmann
Journal:  Funct Integr Genomics       Date:  2005-03-03       Impact factor: 3.410

9.  Probing a label-free local bend in DNA by single molecule tethered particle motion.

Authors:  Annaël Brunet; Sébastien Chevalier; Nicolas Destainville; Manoel Manghi; Philippe Rousseau; Maya Salhi; Laurence Salomé; Catherine Tardin
Journal:  Nucleic Acids Res       Date:  2015-03-12       Impact factor: 16.971

10.  An assessment of three dinucleotide parameters to predict DNA curvature by quantitative comparison with experimental data.

Authors:  Aditi Kanhere; Manju Bansal
Journal:  Nucleic Acids Res       Date:  2003-05-15       Impact factor: 16.971
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