Hydrogen bonding, base stacking, and steric effects in DNA replication

Annual Review of Biophysics and Biomolecular Structure

Volumn 30, Issue , 2001, Pages 1-22

  Kool, E T ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

DNA polymerase; Replication fidelity; Watson Crick hydrogen bonding

Indexed keywords

DNA POLYMERASE;

BIOTECHNOLOGY; DNA REPLICATION; DNA STRUCTURE; ENZYME ACTIVITY; HYDROGEN BOND; MOLECULAR STABILITY; POLYMERIZATION; PRIORITY JOURNAL; REVIEW; STEREOCHEMISTRY;

DNA; HYDROGEN BONDING; MODELS, CHEMICAL; NUCLEOTIDES;

EID: 0034979126     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.30.1.1     Document Type: Review

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12. Structure of taq polymerase with DNA at the polymerase active site
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14. Nucleotide insertion and primer extension at basic template sites in different sequence contexts
15. Biochemical basis of DNA replication fidelity
16. Highly precise shape mimicry by difluorotoluene deoxynucleoside, a replication-competent substitute for thymidine
17. Solution structure of a duplex DNA containing a replicable difluorotoluene-adenine pair
18. Solution structure of a nonpolar, non-hydrogen bonded base pair surrogate in DNA
19. Factors contributing to aromatic stacking in water: Evaluation in the context of DNA
20. Experimental measurement of aromatic stacking in the context of duplex DNA
21. Recognition by viral and cellular DNA polymerases of nucleosides bearing bases with nonstandard hydrogen bonding patterns
22. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance
23. Sequence dependent DNA structure: The role of base stacking interactions
24. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal
25. Molecular recognition by circular oligonucleotides. Increasing the selectivity of DNA binding
26. Preorganization strategies for improving the recognition properties of DNA
27. A mechanism for shape selection during DNA synthesis
28. Modified DNAs as substrates for polymerases
29. Mimicking the structures and functions of DNA: Insights into DNA stability and replication
30. Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity
31. Bistranded, multisite replication of an unconventional difluorotoluene-adenine base pair and confirmation by "inverse" sequencing
32. Mutagenesis by apurinic/apyrimidinic sites
33. Selective and stable DNA base pairing without hydrogen bonds
34. A specific partner for abasic damage in DNA
35. Efforts toward expansion of the genetic alphabet: DNA polymerase recognition of a highly stable, self-pairing hydrophobic base
36. Nearest neighbor influences on DNA polymerase insertion fidelity
37. Structure and base pairing properties of a replication-competent nonpolar isostere for deoxyadenosine
38. Efficient replication of a DNA base pair between nonhydrogen-bonded nucleoside analogues
39. Minor groove interactions between polymerase and DNA: More essential than Watson-Crick bonds?
40. A functional H-bonding map of the minor groove binding tracks of six DNA polymerases
41. Varied molecular interactions in the active sites of several several DNA polymerases: Nonpolar nucleoside isosteres as probes
42. A thymidine triphosphate shape mimic lacking Watson-Crick pairing ability is replicated with high specificity
43. Difluorotoluene, a nonpolar isostere of thymine, codes specifically and efficiently for adenine in DNA replication
44. Efforts toward the expansion of the genetic alphabet: Information storage and replication with unnatural hydrophobic base pairs
45. Structures of ternary complexes of rat DNA polymerase beta, a DNA template-primer, and ddCTP
46. Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
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48. The proofreading pathway of bacteriophage T4 DNA polymerase
49. Naphthalene, phenanthrene, and pyrene as DNA base analogues: Synthesis, structure, and fluorescence in DNA
50. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
51. Improved nearest-neighbor parameters for predicting DNA duplex stability
52. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin
53. Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
54. Nonpolar aromatic nucleosides as hydrophobic isosteres of DNA nucleosides
55. Corrigendum
56. Hydrophobic, non-hydrogen-bonding bases and base pairs in DNA
57. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid
58. Free energy increments for hydrogen-bonds in nucleic acid base pairs
59. Difluorotoluene, a thymine isostere, does not hydrogen bond after all