A-tract DNA disfavours triplex formation

Journal of Molecular Biology

Volumn 315, Issue 4, 2002, Pages 737-748

  Sandström, Karin ^a   Wärmländer, Sebastian ^a   Gräslund, Astrid ^a   Leijon, Mikael ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

A tract; Anti gene strategy; NMR; Thermal denaturation; Triplex DNA

Indexed keywords

DNA; PROTON;

ACIDITY; ARTICLE; BASE PAIRING; DENATURATION; DNA DETERMINATION; DNA STRUCTURE; GENE INSERTION; GENE SEQUENCE; GENE TARGETING; IN VIVO STUDY; ION EXCHANGE; ISOLATION PROCEDURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PH; PRIORITY JOURNAL; RIGIDITY; STRUCTURE ANALYSIS; ULTRAVIOLET SPECTROPHOTOMETRY;

INSERTION SEQUENCES;

EID: 0036307662     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5249     Document Type: Article

References (56)

1. Formation of a three-stranded polynucleotide molecule
2. H-DNA and related structures
3. Stability and structure of model DNA triplexes and quadruplexes and their interactions with small ligands
4. DNA H form requires a homopurine-homopyrimidine mirror repeat
5. Sequence-specific recognition and modification of double-helical DNA by oligonucleotides
6. An oligopurine sequence bias occurs in eukaryotic viruses
7. An overabundance of long oligopurine tracts occurs in the genome of simple and complex eukaryotes
8. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences
9. Poly(pyrimidine).poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH
10. Electrostatic effects in DNA triple helices
11. Prediction of the stability of DNA triplexes
12. Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays
13. High base-pair opening rates in tracts of GC base-pairs
14. The structure of a stable intermediate in the A → B DNA helix transition
15. Sequence-dependent elastic properties of DNA
16. The structure of an oligo(dA). oligo(dT) tract and its biological implications
17. The unusual conformation adopted by the adenine tracts in kine-toplast DNA
18. A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations
19. Evidence from base-pair kinetics for two types of adenine tract structures in solution: Their relation to DNA curvature
20. Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: Evidence for a secondary long-lived open state of the base-pair
21. Sequence elements responsible for DNA curvature
22. Crystallographic study of one turn of G/C-rich B-DNA
23. Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA
24. C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G
25. Poly(dA). poly(dT) exists in an unusual conformation under physiological conditions: Propidium binding to poly(dA). poly(dT) and poly[d(A-T)]. poly[d(A-T)]
26. Sequence-dependent cooperative interactions in A/T-containing oligo-and polydeoxyribonucleotides
27. A premelting conformational transition in poly(dA)-poly(dT) coupled to daunomycin binding
28. Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: Correlations with DNA bending
29. Hydrophobicities of the nucleic acid bases: Distribution coefficients from water to cyclohexane
30. Structural analysis of the (dA)10.2(dT)10 triple helix
31. Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution
32. Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences
33. 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Application to a lac operator fragment
34. Studies of base-pair kinetics by NMR measurement of proton exchange
35. Structural basis for DNA bending
36. Triple-strand formation in the homopurine:homopyrimidine DNA oligonucleotides d(G-A)4 and d(T-C)4
37. Structure of a G.T.A triplet in an intramolecular DNA triplex
38. Base-pair opening in double-stranded nucleic acids
39. Sequence and structural selectivity of nucleic acid binding ligands
40. Selectivity of polyamines in triplex DNA stabilization
41. Comb-type polycations effectively stabilize DNA triplex
42. Binding of RecA to anti-parallel poly(dA).2poly(dT) triple helix DNA
43. DNA bending at adenine.thymine tracts
44. Mechanics of sequence-dependent stacking of bases in B-DNA
45. Effects of diaminopurine and inosine substitutions on A-tract induced DNA curvature. Importance of the 3′-A-tract junction
46. The contribution of cytosine protonation to the stability of parallel DNA triple helices
47. Stability and properties of double and triple helices - Dramatic effects of rna or dna backbone composition
48. The effect of amino groups on the stability of DNA duplexes and triplexes based on purines derived from inosine
49. Duplex and triple-helix formation with da19 and dt19-thermodynamic parameters from calorimetric, nmr, and circular-dichroism studies
50. Structure and stability of a DNA triple helix in solution: NMR studies on d(T)6.d(A)6.d(T)6 and its complex with a minor groove binding drug
51. Structural constraints regulating triple helix formation by A-tracts
52. Effects of sequence and length on imino proton exchange and base-pair opening kinetics in DNA oligonucleotide duplexes
53. Thermodynamics of DNA triplex formation in oligomers with and without cytosine bases - Influence of buffer species, pH, and sequence
54. Absorbance melting curves of RNA