1
|
Del Castillo P, Horobin RW, Blázquez-Castro A, Stockert JC. Binding of cationic dyes to DNA: distinguishing intercalation and groove binding mechanisms using simple experimental and numerical models. Biotech Histochem 2010; 85:247-56. [DOI: 10.3109/10520290903149620] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
3
|
Piehler J, Brecht A, Gauglitz G, Zerlin M, Maul C, Thiericke R, Grabley S. Label-free monitoring of DNA-ligand interactions. Anal Biochem 1997; 249:94-102. [PMID: 9193714 DOI: 10.1006/abio.1997.2160] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We report on the label- and isotope-free monitoring of DNA interactions with low-molecular-weight ligands. An optical technique based on interference at thin layers was used to monitor in real time binding of ligands at DNA which was immobilized by Coulomb interactions at a positively charged surface. Approximately 2 ng DNA/m2 was irreversibly bound to the surface, which remained stable over several days. This result was confirmed by characterization of the layer using spectroscopic ellipsometry. During incubation of immobilized DNA with a variety of intercalators and other DNA-binding compounds in a flow system, interactions were monitored by reflectometric interference spectroscopy. Binding effects between 10 and 400 pg/ mm2 were detected unambiguously. Nonspecific binding effects were excluded by using a negatively charged reference surface. Variation of intercalator concentration allowed the characterization of interaction with respect to kinetics and thermodynamics by the evaluation of binding rate and equilibrium coverage. The affinity constants were determined in the range between 10(5) and 10(6) M-1, in good agreement to those obtained by homogeneous phase assays. Association rate constants between 10(3) and 10(5) M-1 s-1 and dissociation rate constants between 10(-1) and 10(-2) s-1 were determined by evaluation of the binding curves. Both the fast and simple test format and a universal applicability make the new technique described attractive for detecting and characterizing interaction of low-molecular-weight molecules with DNA.
Collapse
Affiliation(s)
- J Piehler
- Institut für Physikalische Chemie, Tübingen, Germany.
| | | | | | | | | | | | | |
Collapse
|
4
|
Alhambra C, Luque FJ, Gago F, Orozco M. Ab Initio Study of Stacking Interactions in A- and B-DNA. J Phys Chem B 1997. [DOI: 10.1021/jp962626a] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristóbal Alhambra
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Francisco J. Luque
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Federico Gago
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| |
Collapse
|
6
|
Zhang H, van der Marel GA, van Boom JH, Wang AH. Conformational perturbation of the anticancer nucleotide arabinosylcytosine on Z-DNA: molecular structure of (araC-dG)3 at 1.3 A resolution. Biopolymers 1992; 32:1559-69. [PMID: 1457732 DOI: 10.1002/bip.360321113] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The left-handed Z-DNA structure of an araC-containing (where araC stands for arabinosylcytosine) hexamer, (araC-dG)3, has been solved by x-ray diffraction analysis at 1.3 A resolution. This hexamer was crystallized in the hexagonal P6(5)22 (a = b = 17.96 A, c = 43.22 A) space group in which the hexamers have statistically disordered packing arrangement along the 6(5) screw axis, yet the crystals diffract x-rays to high resolution. Its structure has been refined by the constrained least square refinement to a final R factor of 0.287 using 737 [> 3.0 sigma(F)] observed reflections. The asymmetric unit of the unit cell contains only a dinucleotide, 5'-p (araC)p(dG). The overall conformation resembles that of the canonical Z-DNA, but with some differences in details. The O2' hydroxyl groups of the araC residues form intramolecular hydrogen bonds with N2 of the 5'-guanine residues. In the deep groove of Z-DNA, these hydroxy groups replace the bridging water molecules that stabilize the guanine in the syn conformation. The results reinforce the earlier observation made by the structural analysis of another hexamer, d(CG[araC]GCG), with a mono-substitution of araC [M.-K. Teng, Y.-C. Liaw, G. A. van der Marel, J. H. van Boom, and A. H.-J. Wang (1989) Biochemistry, vol. 28, pp. 4923-4928]. These two structures show that araC residue can be incorporated readily into the Z structure and probably facilitates the B to Z transition, as supported by uv absorption spectroscopic studies in a number of araC-containing oligonucleotides. The potential biological roles of the araC-modified Z-DNA are discussed.
Collapse
Affiliation(s)
- H Zhang
- Division of Biophysics, University of Illinois, Champaign, Urbana 61801
| | | | | | | |
Collapse
|
8
|
Gao XL, Patel DJ. Antitumour drug-DNA interactions: NMR studies of echinomycin and chromomycin complexes. Q Rev Biophys 1989; 22:93-138. [PMID: 2675172 DOI: 10.1017/s0033583500003814] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The intelligent design of new families of DNA-binding antitumour agents must await an understanding at the molecular level of the structure, dynamics and energetics of drug-DNA interactions on currently available systems. Recent progress in this area has been significant and reflects the interplay between footprinting methods that identify the sequence specificity of drug binding, structural approaches that define conformational features in the crystalline and solution states, hydrogen exchange techniques that monitor transient base pair opening and calorimetric methods that partition the enthalpic and entropic contributions to the binding isotherm.
Collapse
Affiliation(s)
- X L Gao
- Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, New York 10032
| | | |
Collapse
|
9
|
Affiliation(s)
- D J Arndt-Jovin
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Federal Republic of Germany
| | | |
Collapse
|