Literature DB >> 273227

How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations.

M Levitt.   

Abstract

Calculations on a 20-base pair segment of DNA double helix using empirical energy functions show that DNA can be bent smoothly and uniformly into a superhelix with a small enough radius (45 A) to fit the dimensions of chromatin. The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn. This result, which has a simple physical interpretation, explains the pattern of nuclease cuts and the linkage number changes observed for DNA arranged in chromatin.

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Year:  1978        PMID: 273227      PMCID: PMC411311          DOI: 10.1073/pnas.75.2.640

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


  26 in total

1.  Organization of DNA in chromatin.

Authors:  H M Sobell; C C Tsai; S G Gilbert; S C Jain; T D Sakore
Journal:  Proc Natl Acad Sci U S A       Date:  1976-09       Impact factor: 11.205

2.  Sidechain torsional potentials and motion of amino acids in porteins: bovine pancreatic trypsin inhibitor.

Authors:  B R Gelin; M Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  1975-06       Impact factor: 11.205

3.  Structure of nucleosome core particles of chromatin.

Authors:  J T Finch; L C Lutter; D Rhodes; R S Brown; B Rushton; M Levitt; A Klug
Journal:  Nature       Date:  1977-09-01       Impact factor: 49.962

4.  Dynamics of folded proteins.

Authors:  J A McCammon; B R Gelin; M Karplus
Journal:  Nature       Date:  1977-06-16       Impact factor: 49.962

5.  Mechanism of tertiary structural change in hemoglobin.

Authors:  B R Gelin; M Karplus
Journal:  Proc Natl Acad Sci U S A       Date:  1977-03       Impact factor: 11.205

6.  Possibility of nonkinked packing of DNA in chromatin.

Authors:  J L Sussman; E N Trifonov
Journal:  Proc Natl Acad Sci U S A       Date:  1978-01       Impact factor: 11.205

7.  Spheroid chromatin units (v bodies).

Authors:  A L Olins; D E Olins
Journal:  Science       Date:  1974-01-25       Impact factor: 47.728

8.  The secondary structure of DNA in solution and in nucleohistone.

Authors:  S Bram
Journal:  J Mol Biol       Date:  1971-05-28       Impact factor: 5.469

9.  Symmetry and packing in B-DNA.

Authors:  S D Dover
Journal:  J Mol Biol       Date:  1977-03-15       Impact factor: 5.469

10.  Crystallographic refinement of yeast phenylalanine transfer RNA at 2-5A resolution.

Authors:  A Jack; J E Ladner; A Klug
Journal:  J Mol Biol       Date:  1976-12-25       Impact factor: 5.469

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  64 in total

1.  Torsional stress and local denaturation in supercoiled DNA.

Authors:  C J Benham
Journal:  Proc Natl Acad Sci U S A       Date:  1979-08       Impact factor: 11.205

2.  A topological approach to nucleosome structure and dynamics: the linking number paradox and other issues.

Authors:  A Prunell
Journal:  Biophys J       Date:  1998-05       Impact factor: 4.033

3.  Reduced superhelicity of plasmid DNA produced by the rho-15 mutation in Escherichia coli.

Authors:  J S Fassler; G F Arnold; I Tessman
Journal:  Mol Gen Genet       Date:  1986-09

Review 4.  Close encounters with DNA.

Authors:  C Maffeo; J Yoo; J Comer; D B Wells; B Luan; A Aksimentiev
Journal:  J Phys Condens Matter       Date:  2014-09-19       Impact factor: 2.333

5.  Training-free atomistic prediction of nucleosome occupancy.

Authors:  Peter Minary; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-14       Impact factor: 11.205

6.  Histone packing in the nucleosome core particle of chromatin.

Authors:  C W Carter
Journal:  Proc Natl Acad Sci U S A       Date:  1978-08       Impact factor: 11.205

7.  Biomolecular energy calculations using transputer technology.

Authors:  J M Goodfellow; F Vovelle
Journal:  Eur Biophys J       Date:  1989       Impact factor: 1.733

8.  Sequence dependence of base-pair stacking in right-handed DNA in solution: proton nuclear Overhauser effect NMR measurements.

Authors:  D J Patel; S A Kozlowski; R Bhatt
Journal:  Proc Natl Acad Sci U S A       Date:  1983-07       Impact factor: 11.205

9.  A Membrane-Bound Transcription Factor is Proteolytically Regulated by the AAA+ Protease FtsH in Staphylococcus aureus.

Authors:  Won-Sik Yeo; Chiamara Anokwute; Philip Marcadis; Marcus Levitan; Mahmoud Ahmed; Yeun Bae; Kyeongkyu Kim; Tatiana Kostrominova; Qian Liu; Taeok Bae
Journal:  J Bacteriol       Date:  2020-04-09       Impact factor: 3.490

10.  Aromatic N versus aromatic F: bioisosterism discovered in RNA base pairing interactions leads to a novel class of universal base analogs.

Authors:  Alrun N Koller; Jelena Bozilovic; Joachim W Engels; Holger Gohlke
Journal:  Nucleic Acids Res       Date:  2010-01-15       Impact factor: 16.971

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