Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 Energetic coupling between DNA bending and base pair opening.

Literature DB >> 3174629

Energetic coupling between DNA bending and base pair opening.

Abstract

The pathway for base pair opening within a B-DNA duplex is investigated by theoretical molecular modeling. The results show that the disruption of a single base pair is energetically compatible with the deductions made from hydrogen exchange measurements. In addition, it is found that the opening process is greatly facilitated by DNA bending and that, conversely, once a base pair is disrupted, DNA can bend very easily. It appears that the energetic coupling between these two processes may play an important role in many biological reactions involving nucleic acid distortion.

Entities: Chemical

Mesh：

Substances：
DNA

Year: 1988 PMID： 3174629 PMCID： PMC282158 DOI： 10.1073/pnas.85.19.7231

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

18 in total

1. Bent helical structure in kinetoplast DNA.

Authors: J C Marini; S D Levene; D M Crothers; P T Englund
Journal: Proc Natl Acad Sci U S A Date: 1982-12 Impact factor: 11.205

2. Sequence selectivity, a test of the nature of the covalent adduct formed between benzo[a]pyrene and DNA.

Authors: K Zakrzewska; B Pullman
Journal: J Biomol Struct Dyn Date: 1987-04

3. Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility.

Authors: R Lavery; K Zakrzewska; B Pullman
Journal: J Biomol Struct Dyn Date: 1986-06

4. A general approach to the optimization of the conformation of ring molecules with an application to valinomycin.

Authors: R Lavery; I Parker; J Kendrick
Journal: J Biomol Struct Dyn Date: 1986-12

5. Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA.

Authors: J Keepers; P A Kollman; T L James
Journal: Biopolymers Date: 1984-11 Impact factor: 2.505

6. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings.

Authors: J W Keepers; P A Kollman; P K Weiner; T L James
Journal: Proc Natl Acad Sci U S A Date: 1982-09 Impact factor: 11.205

7. Base-pair opening and closing reactions in the double helix. A stopped-flow hydrogen exchange study in poly(rA).poly(rU).

Authors: C Mandal; N R Kallenbach; S W Englander
Journal: J Mol Biol Date: 1979-12-05 Impact factor: 5.469

8. Poly(dA-dT).poly(dA-dT) two-pathway proton exchange mechanism. Effect of general and specific base catalysis on deuteration rates.

Authors: B Hartmann; M Leng; J Ramstein
Journal: Biochemistry Date: 1986-06-03 Impact factor: 3.162

9. Determination of the kinetics of deuteration of DNA.RNA hybrids by ultraviolet spectroscopy.

Authors: H Takashima; M Nakanishi; M Tsuboi
Journal: Biochemistry Date: 1985-08-27 Impact factor: 3.162

10. The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.

Authors: R Lavery; H Sklenar; K Zakrzewska; B Pullman
Journal: J Biomol Struct Dyn Date: 1986-04

93 in total

1. DNA bending induced by DNA (cytosine-5) methyltransferases.

Authors: T Raskó; C Finta; A Kiss
Journal: Nucleic Acids Res Date: 2000-08-15 Impact factor: 16.971

2. Structural features of an influenza virus promoter and their implications for viral RNA synthesis.

Authors: S H Bae; H K Cheong; J H Lee; C Cheong; M Kainosho; B S Choi
Journal: Proc Natl Acad Sci U S A Date: 2001-09-11 Impact factor: 11.205

3. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

Authors: M Feig; M Zacharias; B M Pettitt
Journal: Biophys J Date: 2001-07 Impact factor: 4.033

Energetic coupling between DNA bending and base pair opening.

1. Bent helical structure in kinetoplast DNA.

2. Sequence selectivity, a test of the nature of the covalent adduct formed between benzo[a]pyrene and DNA.

3. Binding of non-intercalating antibiotics to B-DNA: a theoretical study taking into account nucleic acid flexibility.

4. A general approach to the optimization of the conformation of ring molecules with an application to valinomycin.

5. Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA.

6. Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings.

7. Base-pair opening and closing reactions in the double helix. A stopped-flow hydrogen exchange study in poly(rA).poly(rU).

8. Poly(dA-dT).poly(dA-dT) two-pathway proton exchange mechanism. Effect of general and specific base catalysis on deuteration rates.

9. Determination of the kinetics of deuteration of DNA.RNA hybrids by ultraviolet spectroscopy.

10. The flexibility of the nucleic acids: (II). The calculation of internal energy and applications to mononucleotide repeat DNA.

1. DNA bending induced by DNA (cytosine-5) methyltransferases.

2. Structural features of an influenza virus promoter and their implications for viral RNA synthesis.

3. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.

4. Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model.

5. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.

6. 1H NMR determination of base-pair lifetimes in oligonucleotides containing single base mismatches.

7. Modeling DNA-bending in the nucleosome: role of AA periodicity.

8. Accurate representation of B-DNA double helical structure with implicit solvent and counterions.

9. Solvation of nucleosides in aqueous mixtures of organic solvents: relevance to DNA open basepairs.

10. NFI and Oct-1 bend the Ad5 origin in the same direction leading to optimal DNA replication.