DNA bending by asymmetrically tethered cations: Influence of tether flexibility

Chemistry and Biology

Volumn 8, Issue 10, 2001, Pages 967-980

  Hardwidge, Philip R ^a   Lee, Dong Kye ^b   Prakash, Thazha P ^b   Iglesias, Beatriz ^b   Den, Robert B ^a   Switzer, Christopher ^b   Maher III, L James ^a  

^a MAYO GRADUATE SCHOOL   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Asymmetric neutralization; Base analogs; Cations; DNA bending; DNA curvature; Electrophoresis; Phosphate

Indexed keywords

CATION; DNA; PHOSPHATE; QUATERNARY AMMONIUM DERIVATIVE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MOLECULAR GENETICS; POLYACRYLAMIDE GEL ELECTROPHORESIS;

CATIONS; DNA; ELECTROPHORESIS, POLYACRYLAMIDE GEL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHOSPHATES; QUATERNARY AMMONIUM COMPOUNDS;

EID: 0034815836     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(01)00065-5     Document Type: Article

References (46)

1. DNA bending in transcription initiation
2. Direct evidence for DNA bending at the lambda replication origin
3. Why should DNA loop?
4. Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
5. Crystal structure of the nucleosome core particle at 2.8 Å resolution
6. Mechanisms of DNA bending
7. Crystal structure of a yeast TBP/TATA-box complex
8. Sex-reversing mutations affect the architecture of SRY-DNA complexes
9. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
10. An estimate of the extent of folding of nucleosomal DNA by laterally asymmetric neutralization of phosphate groups
11. DNA bending by asymmetric phosphate neutralization
12. DNA bending by hexamethylene-tethered ammonium ions
13. DNA bending by a phantom protein
14. Electrostatic mechanisms of DNA deformation
15. DNA structure: Cations in charge?
16. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations
17. Localization of divalent metal ions in the minor groove of DNA A-tracts
18. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending
19. Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G
20. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
21. Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
22. The B-DNA dodecamer at high resolution reveals a spine of water on sodium
23. DNA curvature and phosphate neutralization: An important aspect of specific protein binding
24. The role of DNA-protein salt bridges in molecular recognition: A model study
25. The transcription activation domains of Fos and Jun induce DNA bending through electrostatic interactions
26. Modeling DNA bending induced by phosphate neutralization
27. DNA bending by GCN4 mutants bearing cationic residues
28. Electrostatic effects in DNA bending by GCN4 mutants
29. Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA
30. The role of electrostatics in the sequence selective reaction of charged alkylating agents with DNA
31. Regioselective effect of zwitterionic DNA substitutions on DNA alkylation: Evidence for a strong side chain orientational preference
32. Determination of the extent of DNA bending by an adenine-thymine tract
33. Global features of DNA structure by comparative gel electrophoresis
34. Improved quantitation of DNA curvature using ligation ladders
35. A comparative study of the thermal stability of oligodeoxyribonucleotides containing 5-substituted 2′-deoxyuridines
36. Oligonucleotides derived from 5-(1-propynyl)-2′-O-allyl-uridine and 5-(1-propynyl)-2′-O-allyl-cytidine: Synthesis and RNA duplex formation
37. Solution structure of an intramolecular DNA triplex containing 5-(1-propynyl)-2′-deoxyuridine residues in the third strand
38. Control over the localization of positive charge in DNA: The effect on duplex DNA and RNA stability
39. Antisense gene inhibition by oligonucleotides containing C-5 propyne pyrimidines
40. Conformations of cycloheptadecane. A comparison of methods for conformational searching
41. Possibility of nonkinked packing of DNA in chromatin
42. Formation of chimeric duplexes between zwitterionic and natural DNA
43. Zwitterionic DNA
44. Influence of hairpins on template reannealing at trinucleotide repeat duplexes: A model for slipped DNA
45. An all atom force field for simulations of proteins and nucleic acids
46. Semianalytical treatment of solvation for molecular mechanics and dynamics