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Literature DB >> 3753773

Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure.

Abstract

Programs are presented to plot the gross three-dimensional structure of the DNA double helix with the base sequence as input information. The rules that determine the overall structure of the double helix are those that predict the dependence of local helix parameters (specifically, helix twist angle and relative basepair roll angle) on sequence. For this purpose, the user can select either the Calladine-Dickerson parameters or the Tung-Harvey parameters. These programs can be used as tools to investigate the variation of DNA tertiary structure with sequence, which may play an important role in the sequence-specific recognition of DNA by proteins.

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Substances：
DNA

Year: 1986 PMID： 3753773 PMCID： PMC339421 DOI： 10.1093/nar/14.1.381

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

11 in total

Computer graphics program to reveal the dependence of the gross three-dimensional structure of the B-DNA double helix on primary structure.

1. Bent helical structure in kinetoplast DNA.

2. Evidence for the existence of stable curvature of DNA in solution.

3. DNA bending and kinking.

4. The locus of sequence-directed and protein-induced DNA bending.

5. A molecular mechanical model to predict the helix twist angles of B-DNA.

6. A double helix B-type geometry based on high-resolution proton NMR of single-helical DNA fragments: d(TA)5 x d(TA)5.

7. Base sequence and helix structure variation in B and A DNA.

8. DNA structure and gene regulation.

9. Mechanics of sequence-dependent stacking of bases in B-DNA.

10. Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG.

1. Interdependence of conformational variables in double-helical DNA.

2. A common structural feature in promoter sequences of E. coli.

3. The YYRR box: a conserved dipyrimidine-dipurine sequence element in Drosophila and other eukaryotes.

4. Sequence dependent electrophoretic mobilities and melting temperatures for A-T containing oligodeoxyribonucleotides.

5. Bending and curvature calculations in B-DNA.

6. Long-range organization and sequence-directed curvature of Xenopus laevis satellite 1 DNA.

7. Alterations in the adenine-plus-thymine-rich region of CEN3 affect centromere function in Saccharomyces cerevisiae.

8. Electron microscopy mapping of pBR322 DNA curvature. Comparison with theoretical models.