DNA Unwinding Induced by Photoaddition of Psoralen Derivatives and Determination of Dark-binding Equilibrium Constants by Gel Electrophoresis

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1978 Jun 1

PMID 275838

Citations 15

Authors

G Wiesehahn

J E Hearst

Affiliations

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Abstract

Derivatives of furo[3,2-g]coumarin (psoralen) can bind to the DNA double helix and, in the presence of long-wavelength UV light, the bound psoralen may react covalently with pyrimidine residues on one or both strands of the helix. By using agarose gel electrophoresis, we have determined the unwinding angle associated with each of four different psoralen derivatives to be 28 degrees +/- 4 degrees . For 4,5',8-trimethylpsoralen (trioxsalen) the unwinding angle was found to be independent of the initial DNA superhelix density in the range that is accessible to agarose gel electrophoresis. Also by using agarose gel electrophoresis, we have determined the unwinding angle for ethidium intercalation. This was done by the total relaxation of supercoiled DNA in the presence of a series of ethidium concentrations. By using published values for the association constant for ethidium binding to DNA and evaluating the final superhelix density (after removal of ethidium) of the DNA on gels, we calculated an unwinding angle of 29 degrees +/- 3 degrees . Assuming an unwinding angle of 28 degrees for the noncovalent intercalation of psoralen derivatives, we used the same procedure to determine intercalation binding constants. The association constants for 4'-aminomethyltrioxsalen were 300-1400 M(-1) in NaCl at 0.2-0.05 M and 300-2500 M(-1) in Mg(2+) at 4-0.5 mM. The association constant for 4'-hydroxymethyltrioxsalen in 0.5 mM Mg(2+) was determined to be 70 M(-1).

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References

Musajo L, Rodighiero G, Colombo G, TORLONE V, DallAcqua F . PHOTOSENSITIZING FUROCOUMARINS: INTERACTION WITH DNA AND PHOTO-INACTIVATION OF DNA CONTAINING VIRUSES. Experientia. 1965; 21:22-4. DOI: 10.1007/BF02136362. View

LEPECQ J, Paoletti C . A fluorescent complex between ethidium bromide and nucleic acids. Physical-chemical characterization. J Mol Biol. 1967; 27(1):87-106. DOI: 10.1016/0022-2836(67)90353-1. View

Hearst J, THIRY L . The photoinactivation of an RNA animal virus, vesicular stomatitis virus, with the aid of newly synthesized psoralen derivatives. Nucleic Acids Res. 1977; 4(5):1339-47. PMC: 343759. DOI: 10.1093/nar/4.5.1339. View

Shure M, Pulleyblank D, Vinograd J . The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity. Nucleic Acids Res. 1977; 4(5):1183-205. PMC: 343749. DOI: 10.1093/nar/4.5.1183. View

Hyde J, Hearst J . Binding of psoralen derivatives to DNA and chromatin: influence of the ionic environment on dark binding and photoreactivity. Biochemistry. 1978; 17(7):1251-7. DOI: 10.1021/bi00600a019. View

Wieshahn G, Hyde J, Hearst J . The photoaddition of trimethylpsoralen to Drosophila melanogaster nuclei: a probe for chromatin substructure. Biochemistry. 1977; 16(5):925-32. DOI: 10.1021/bi00624a018. View

Shen C, Hearst J . Detection of long-range sequence order in Drosophila melanogaster satellite DNA IV by a photochemical crosslinking reaction and denaturation microscopy. J Mol Biol. 1977; 112(3):495-507. DOI: 10.1016/s0022-2836(77)80195-2. View

Mickel S, Arena Jr V, BAUER W . Physical properties and gel electrophoresis behavior of R12-derived plasmid DNAs. Nucleic Acids Res. 1977; 4(5):1465-82. PMC: 343768. DOI: 10.1093/nar/4.5.1465. View

Cech T, Pardue M . Cross-linking of DNA with trimethylpsoralen is a probe for chromatin structure. Cell. 1977; 11(3):631-40. DOI: 10.1016/0092-8674(77)90080-0. View

10.

Isaacs S, Shen C, Hearst J, Rapoport H . Synthesis and characterization of new psoralen derivatives with superior photoreactivity with DNA and RNA. Biochemistry. 1977; 16(6):1058-64. DOI: 10.1021/bi00625a005. View

11.

Modrich P, Zabel D . EcoRI endonuclease. Physical and catalytic properties of the homogenous enzyme. J Biol Chem. 1976; 251(19):5866-74. View

12.

DallAcqua F, Marciani S, Ciavatta L, Rodighiero G . Formation of inter-strand cross-linkings in the photoreactions between furocoumarins and DNA. Z Naturforsch B. 1971; 26(6):561-9. DOI: 10.1515/znb-1971-0613. View

13.

Wang J . Interactions between twisted DNAs and enzymes: the effects of superhelical turns. J Mol Biol. 1974; 87(4):797-816. DOI: 10.1016/0022-2836(74)90085-0. View

14.

Bordin F, Baccichetti F . The furocoumarin photosensitizing effect on the virus-producing Graffi leukaemia cells. Z Naturforsch C Biosci. 1974; 29C(9-10):630-2. DOI: 10.1515/znc-1974-9-1029. View

15.

Clewell D, Helinski D . Effect of growth conditions on the formation of the relaxation complex of supercoiled ColE1 deoxyribonucleic acid and protein in Escherichia coli. J Bacteriol. 1972; 110(3):1135-46. PMC: 247537. DOI: 10.1128/jb.110.3.1135-1146.1972. View

16.

Wang J . The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol. 1974; 89(4):783-801. DOI: 10.1016/0022-2836(74)90053-9. View

17.

Keller W, Wendel I . Stepwise relaxation of supercoiled SV40 DNA. Cold Spring Harb Symp Quant Biol. 1975; 39 Pt 1:199-208. DOI: 10.1101/sqb.1974.039.01.026. View

18.

Depew D, Wang J . Conformational fluctuations of DNA helix. Proc Natl Acad Sci U S A. 1975; 72(11):4275-9. PMC: 388703. DOI: 10.1073/pnas.72.11.4275. View

19.

Parrish J, Fitzpatrick T, Tanenbaum L, Pathak M . Photochemotherapy of psoriasis with oral methoxsalen and longwave ultraviolet light. N Engl J Med. 1974; 291(23):1207-11. DOI: 10.1056/NEJM197412052912301. View

20.

Bazaral M, Helinski D . Circular DNA forms of colicinogenic factors E1, E2 and E3 from Escherichia coli. J Mol Biol. 1968; 36(2):185-94. DOI: 10.1016/0022-2836(68)90374-4. View