Literature DB >> 8170950

"...the tyranny of the lattice...".

R E Dickerson1, D S Goodsell, S Neidle.   

Abstract

A systematic comparison of crystal structures of nine different B-DNA dodecamers, in three different space groups, with and without A-tracts, shows that crystal packing or lattice forces are of secondary importance for helix axis bending, minor-groove width, and propeller twist. While other local helix parameters may be influenced or even established by crystal packing, the properties just enumerated are determined primarily by base sequence. One and the same crystal packing scheme can accommodate a bend in one of two different directions, or no bend at all. A-tract regions of B-DNA are inherently straight and unbent, with base-pair inclination no different from that of general-sequence B-DNA. Where bends are observed at junctions between G.C and A.T regions, they always involve a roll about base-pair long axes in a direction that compresses the wide major groove and, hence, are 90 degrees away from that necessary for the correctness of the junction model of A-tract bending. The G.C/A.T junction appears to be a flexible hinge, capable of adopting either a straight or a bent conformation under the local influence of weak crystal packing forces. Such forces therefore are a source of information about DNA deformability and not a curse to be deplored. But as an indication of the weakness of crystal packing forces, introduction of a single bromine atom in the major groove is sufficient to eliminate a bend, although brominated and unbrominated crystals are isomorphous.

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Year:  1994        PMID: 8170950      PMCID: PMC43623          DOI: 10.1073/pnas.91.9.3579

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  22 in total

1.  Global features of DNA structure by comparative gel electrophoresis.

Authors:  D M Crothers; J Drak
Journal:  Methods Enzymol       Date:  1992       Impact factor: 1.600

2.  DNA bending, flexibility, and helical repeat by cyclization kinetics.

Authors:  D M Crothers; J Drak; J D Kahn; S D Levene
Journal:  Methods Enzymol       Date:  1992       Impact factor: 1.600

3.  Crystal structure analysis of the B-DNA dodecamer CGTGAATTCACG.

Authors:  T A Larsen; M L Kopka; R E Dickerson
Journal:  Biochemistry       Date:  1991-05-07       Impact factor: 3.162

4.  Analysis of local helix geometry in three B-DNA decamers and eight dodecamers.

Authors:  K Yanagi; G G Privé; R E Dickerson
Journal:  J Mol Biol       Date:  1991-01-05       Impact factor: 5.469

5.  Crystal structure of CATGGCCATG and its implications for A-tract bending models.

Authors:  D S Goodsell; M L Kopka; D Cascio; R E Dickerson
Journal:  Proc Natl Acad Sci U S A       Date:  1993-04-01       Impact factor: 11.205

6.  A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend.

Authors:  A D DiGabriele; T A Steitz
Journal:  J Mol Biol       Date:  1993-06-20       Impact factor: 5.469

7.  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

8.  Crystal structure analysis of a complete turn of B-DNA.

Authors:  R Wing; H Drew; T Takano; C Broka; S Tanaka; K Itakura; R E Dickerson
Journal:  Nature       Date:  1980-10-23       Impact factor: 49.962

9.  Crystal and molecular structure of d(CGTAGATCTACG) at 2.25 A resolution.

Authors:  G A Leonard; W N Hunter
Journal:  J Mol Biol       Date:  1993-11-05       Impact factor: 5.469

10.  Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution.

Authors:  K J Edwards; D G Brown; N Spink; J V Skelly; S Neidle
Journal:  J Mol Biol       Date:  1992-08-20       Impact factor: 5.469

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  54 in total

1.  Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.

Authors:  J Poner; J Florián; H L Ng; J E Poner; N Packová
Journal:  Nucleic Acids Res       Date:  2000-12-15       Impact factor: 16.971

2.  Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

Authors:  D R Bevan; L Li; L G Pedersen; T A Darden
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033

3.  Conformational substates in different crystal forms of the photoactive yellow protein--correlation with theoretical and experimental flexibility.

Authors:  D M van Aalten; W Crielaard; K J Hellingwerf; L Joshua-Tor
Journal:  Protein Sci       Date:  2000-01       Impact factor: 6.725

4.  The structure of a stable intermediate in the A <--> B DNA helix transition.

Authors:  H L Ng; M L Kopka; R E Dickerson
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-29       Impact factor: 11.205

5.  The energetics of structural change in maltose-binding protein.

Authors:  David E Wemmer
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-20       Impact factor: 11.205

6.  DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum.

Authors:  Richard Stefl; Haihong Wu; Sapna Ravindranathan; Vladimír Sklenár; Juli Feigon
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-22       Impact factor: 11.205

7.  Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG.

Authors:  Ho-Leung Ng; Richard E Dickerson
Journal:  Nucleic Acids Res       Date:  2002-09-15       Impact factor: 16.971

8.  Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3'-A-tract junction.

Authors:  N E Mollegaard; C Bailly; M J Waring; P E Nielsen
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

9.  The relative flexibility of B-DNA and A-RNA duplexes: database analysis.

Authors:  Alberto Pérez; Agnes Noy; Filip Lankas; F Javier Luque; Modesto Orozco
Journal:  Nucleic Acids Res       Date:  2004-11-23       Impact factor: 16.971

10.  Changes in DNA bending induced by restricting nucleotide ring pucker studied by weak alignment NMR spectroscopy.

Authors:  Zhengrong Wu; Melissa Maderia; Joseph J Barchi; Victor E Marquez; Ad Bax
Journal:  Proc Natl Acad Sci U S A       Date:  2004-12-23       Impact factor: 11.205

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