Protonated pyrimidine-purine-purine triplex

Abstract

We have studied a protonated pyrimidine-purine-purine (Py-Pu-Pu) triplex, which is formed between the d(C)nd(G)n duplex and the d(AG)m oligonucleotide as the third strand and carries the CG*A+ protonated base-triads. We have observed such an intermolecular complex between a plasmid carrying the d(C)18 d(G)18 insert and the d(AG)5 oligonucleotide without bivalent cations in 200 mM of Na+ at pH4.0. Bivalent cations additionally stabilize the complex. We propose the structures for nearly isomorphous base-triads TA*A, CG*G and CG*A+. To identify the H-DNA-like structure, which includes the triplex between d(C)n d(G)n duplex and the AG-strand, we have cloned in a superhelical plasmid the insert: G10TTAA(AG)5. The data on photofootprinting and chemical modification with diethyl pyrocarbonate, potassium permanganate and dimethyl sulfate demonstrate that the H-like structure with triplex carrying CG*G and CG*A+ base triads is actually formed under acid conditions. In the course of this study we have come across unexpected results on probing of Py-Pu-Pu triplexes by dimethyl sulfate (DMS): the protection effect is observed not only for guanines entering the duplex but also for guanines in the third strand lying in the major groove. We have demonstrated this effect not only for the case the novel protonated Py-Pu-Pu triplex but also for the traditional non-protonated Py-Pu-Pu intramolecular triplex (H*-DNA) formed by the d(C)37 d(G)37 insert in supercoiled plasmid in the presence of Mg2+ ions.

Naturally occurring H-DNA-forming sequences are mutagenic in mammalian cells

“…2). We speculate that, under certain conditions in vivo, this sequence might adopt an H-u3 structure (4) where a protonated A pairs to a G (35). Supporting this notion, Rooney and Moore (36) have shown that the GA32 sequence stimulated recombination to similar levels as GG32 on plasmids in mammalian cells, suggesting that cellular conditions can allow for H-DNA formation by this sequence.…”

DNA triple helices: Biological consequences and therapeutic potential

“…Interestingly, protonated base triads such as C-G* A+ can be incorporated into an intermolecular pyrimidine-purine*purine triplex conformation. For example, this triad can be formed between plasmids containing a d(C)n(G)n duplex sequence and a d(AG)n oligonucleotide as the third strand, or intramolecularly on a G 10 TTAA(AG) 5 sequence in a supercoiled plasmid, forming a triplex structure containing C-G*G and C-G*A+ base triads under acid conditions, but without a requirement for bivalent cations [97]. Therefore, the formation of an *H-DNA structure is more versatile and does not require sequences containing perfect mirror symmetry.…”

The duplex DNA is very underwound in the three‐stranded RecA protein‐mediated synaptic complex

“…Chemical modification with potassium permanganate has proved to be an effective approach in the investigation of unusual DNA structures, conformational transitions in DNA and the structure of DNA-protein complexes, both in vitro and in vivo (Lyamichev et al 1989;Zhang & Gralla 1989;McCarthy et al 1990;Jiang et al 1991;Kainz & Roberts 1992;Voloshin et al 1992;Chiu et al 1993;Hsieh et al 1993;Malkov et al 1993;Duncan et al 1994;Gillette et al 1994;Bennett & West 1995). KMnO 4 , like osmium tetroxide, oxidizes the 5-6 double bond of pyridine bases (T q C), leading to the loss of aromaticity.…”