interactions of 4′, 6-diamidine-2-phenylindole with synthetic polynucleotides (original) (raw)

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Department of Biochemistry, New York University School of Medicine

550 First Avenue, New York, NY 10016, USA

* Present Address: Memorial Sloan-Kettering Cancer Center New York, New York 10021

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Department of Biochemistry, New York University School of Medicine

550 First Avenue, New York, NY 10016, USA

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* Present Address: Memorial Sloan-Kettering Cancer Center New York, New York 10021

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Published:

10 August 1979

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Jan Kapuściński, Wlodzimierz Szer, interactions of 4′, 6-diamidine-2-phenylindole with synthetic polynucleotides, Nucleic Acids Research, Volume 6, Issue 11, 10 August 1979, Pages 3519–3534, https://doi.org/10.1093/nar/6.11.3519
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Abstract

4′, 6-Diamidine-2-phenylindole forms fluorescent complexes with synthetic DNA duplexes containing AT, AU and IC base pairs; no fluorescent complexes were observed with duplexes containing GC base pairs or with duplexes containing a single AT base pair sandwiched between GC pairs. The binding site size is one molecule of dye per 3 base pairs. The intrinsic binding constants are higher for alternating sequence duplexes than for the corresponding homopolymer pairs. With the exception of the four-stranded helical poly rI which exhibits considerable fluorescence enhancement upon binding of the ligand, none of the single- or multi-stranded polyribonucleotides and ribo-deoxydbonucieotide hybrid structures form fluorescent complexes with the dye. Poly rI is the only RNA which forms a DNA B-like structure (Arnott et al . (1974) Biochem. J. 141 537). The B conformation of the helix and the absence of guanine appear to be the major determinants of the specificity of the fluorescent binding mode of the dye. Nonfluorescent interactions of the dye with polynucleotides are nonspecific; IN absorption and circular dichroic spectra demonstrate binding to synthetic single- and double-stranded DNA and RNA analogs, including those containing GC base pairs.

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Author notes

* Present Address: Memorial Sloan-Kettering Cancer Center New York, New York 10021

© 1979 Information Retrieval Limited

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