Chemical and photochemical probing of DNA complexes

Abstract

An overview of the chemical and photochemical probes which over the past ten years have been used in studies of DNA/ligand complexes and of non-B-form DNA conformations is presented with emphasis on the chemical reactions of the probes with DNA and on their present 'use-profile'. The chemical probes include: dimethyl sulfate, ethyl nitroso urea, diethyl pyrocarbonate, osmium tetroxide, permanganate, aldehydes, methidiumpropyl-EDTA-Fell (MPE), phenanthroline metal complexes and EDTA/FeII. The photochemical probes that have been used include: psoralens, UVB, acridines and uranyl salts. The biological systems analysed by use of these probes are reviewed by tabulation.

Chemical Probing Shows That the Intron-encoded Endonuclease I-SceI Distorts DNA through Binding in Monomeric Form to Its Homing Site

“…16). DNA substrate, uncomplexed or complexed to I-Sce1, was reacted with these reagents and cleaved at the modified bases by reaction with hot piperidine.…”

“…Methylation Protection and Interference-Dimethyl sulfate methylation has been used to probe DNA-protein contacts at the major groove side of G/C base pairs (16). The methylation rate of the guanine residues at positions Ϫ3, Ϫ4, and Ϫ5 and 5, 6, and 7 on the top strand and 3 on the bottom strand is reduced in the complex compared with free DNA (Fig.…”

“…We also employed chemical modification agents of base and sugar residues (for a review, see Ref. 16), diethyl pyrocarbonate (DEPC), which carboxylates purines at the N-7 atom, potassium permanganate (KMnO 4 ), which oxidizes pyrimidine residues at the C 5 ϭC 6 double bond, dimethyl sulfate (DMS), which primarily methylates the N-7 of guanine residues and free hydroxyl radical, generated by Fe-EDTA reduction of hydrogen peroxide, which abstracts C-4Ј hydrogen atoms from deoxyriboses of the DNA backbone. In the scheme that arises from present experiments, I-SceI appears to stabilize, in monomeric form, a constrained helical structure in which the minor groove is widened at the cleavage sites.…”

QuShape: Rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis

“…Chemical probing approaches are widely used to develop secondary and tertiary structure models, to identify molecular and protein ligand interaction sites, to characterize conformational changes, and to examine other functional properties of nucleic acids (Nielsen 1990;Weeks 2010). Chemical probing of RNA structure has become especially important with the realization that much of the information expressed in RNA is encoded in the form of complex higher-order structures.…”

Oxime Esters of 2,6-Diazaanthracene-9,10-dione and 4,5-Diazafluoren-9-one as Photo-induced DNA-Cleaving Agents

“…Photocleavage of nucleic acids (DNA and RNA) can be very useful for molecular biological applications [1]. Organic molecules with DNA-cleaving ability are of great potential in the development of biotechnology and gene therapy [2].…”