Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove

Journal of Molecular Biology

Volumn 317, Issue 3, 2002, Pages 361-374

  Wang, Lei ^a   Kumar, Arvind ^a   Boykin, David W ^a   Bailly, Christian ^b   Wilson, W David ^a  

^a GEORGIA STATE UNIVERSITY   (United States)

^b CENTRE OSCAR LAMBRET   (France)

Author keywords

BIAcore surface plasmon resonance; DNA; Isothermal titration calorimetry; Minor groove; Stacked dimer

Indexed keywords

BENZIMIDAZOLE DERIVATIVE; CATION; DIMER; DNA; MONOMER;

ARTICLE; AT RICH SEQUENCE; BINDING SITE; CALORIMETRY; CORRELATION ANALYSIS; DNA BINDING; DNA SEQUENCE; DNA STRUCTURE; ENTHALPY; ENTROPY; GC RICH SEQUENCE; MOLECULAR MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; SOLVATION; SURFACE PLASMON RESONANCE; TEMPERATURE DEPENDENCE; THERMODYNAMICS; TITRIMETRY;

EID: 0036295082     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2002.5433     Document Type: Article

References (52)

1. Non-intercalating DNA-binding ligands: Specificity of the interaction and their use as tools in biophysical, biochemical and biological investigations of the genetic material
2. Dicationic diarylfurans as anti-Pneumocystis carinii agents
3. Sequence-specific DNA recognition by polyamides
4. Targeting the minor groove of DNA
5. Designed sequence-specific minor groove ligands
6. Chemical approaches to control gene expression
7. Recent developments in sequence selective minor groove DNA effectors
8. Synthetic DNA minor groove-binding drugs
9. Sequence-specific recognition and modification of double helical DNA by minor groove binding conjugates structurally related to netropsin and distamycin
10. Sequence-specific DNA minor groove binders. Design and synthesis of netropsin and distamycin analogues
11. Small molecule-DNA interaction
12. Crystallographic insights into DNA minor groove recognition by drugs
13. Crystal structures of DNA minor groove complexes
14. Structure-activity studies of dicationically substituted bis-benzimidazoles against giardia lamblia: Correlation of antigiardial activity with DNA binding affinity and giardial topoisomerase II inhibition
15. Dicationic furans inhibit development of Cryptosporidium parvum in HSD/CR suckling mice
16. Anti-Pneumocystis activity of bis-amidoximes and bis-O-alkylamidoximes pro-drugs
17. 2,5-bis [4-(N-alkylamidino) phenyl] furans as anti-pneumocystis carinii agents
18. Structural characterization of a 2:1 distamycin A-d(CGCAAATTGGC) complex by two-dimensional NMR
19. Recognition of the four Watson-Crick base-pairs in the DNA minor groove by synthetic ligands
20. A structural basis for recognition of A. T and T. A base-pairs in the minor groove of B-DNA
21. Origins of netropsin binding affinity and specificity: Correlations of thermodynamic and structural data
22. The thermodynamics of polyamide-DNA recognition: Hairpin polyamide binding in minor groove of duplex DNA
23. Interaction of minor groove ligands with an AAATT/AATTT site: Correlation of thermodynamic characterization and solution structure
24. Energetics of drug-DNA interactions
25. Energetics of DNA intercalation reactions
26. 2 duplex: Calorimetric and spectroscopic studies
27. Netropsin binding as a thermodynamic probe of the grooves of parallel DNA
28. Binding of Distamycin A and Netropsin to the 12mer DNA duplexes containing mixed AT·GC sequences with at most five or three successive AT base-pairs
29. A thermodynamic and structural analysis of DNA minor-groove complex formation
30. Contribution to the thermodynamics of protein folding from the reduction in water-accessible non-polar surface area
31. Coupling of local folding to site-specific binding of proteins to DNA
32. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water
33. Drug - DNA interactions
34. Parsing free energies of drug-DNA interactions
35. Specific molecular recognition of mixed nucleic acid sequences: An aromatic dication that binds in the DNA minor groove as a dimer
36. Evaluation of the influence of compound structure on stacked-dimer formation in the DNA minor groove
37. Recognition of ATGA sequences by the unfused aromatic dication DB293 forming stacked dimers in the DNA minor groove
38. Surface plasmon resonance biosensor analysis of RNA-small molecule interactions
39. BIAcore and DNA footprinting for discovery and development of new DNA targeted therapeutics and reagents
40. Determination of the refractive index increments of small molecules for correction of surface plasmon resonance data
41. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
42. Dimerization of coralyne and its propyl analog and their association with DNA
43. 2 and 2,5-bis(4-guanylphenyl)furan, an analogue of berenil. Structural origins of enhanced DNA-binding affinity
44. 2
45. DNA-cation interactions: The major and minor grooves are flexible ionophores
46. Flexible structure of DNA: Ion dependence of minor-groove structure and dynamics
47. Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects
48. Extended aromatic furan amidino derivatives as anti-Pneumocystis carinii agents
49. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
50. A 2nd generation, force field for the simulation of proteins, nucleic acids and organic-molecules