Alternate strand recognition of double-helical DNA by (T,G)-containing oligonucleotides in the presence of a triple helix-specific ligand

Abstract

Triple helix formation requires a polypurine- polypyrimidine sequence in the target DNA. Recent works have shown that this constraint can be circumvented by using alternate strand triplex-forming oligonucleotides. We have previously demonstrated that (T,G)-containing triplex- forming oligonucleotides may adopt a parallel or an antiparallel orientation with respect to an oligopurine target, depending upon the sequence and, in particular, upon the number of 5'-GpT-3' and 5'-TpG-3' steps [Sun et al. (1991) C.R. Acad. Sci. Paris Ser III, 313, 585-590]. A single (T,G)-containing oligonucleotide can therefore interact with two oligopurine stretches which alternate on the two strands of the target DNA. The (T,G) switch oligonucleotide contains a 5'-part targeted to one of the oligopurine sequences in a parallel orientation followed by a 3'-part that adopts an antiparallel orientation with respect to the second oligopurine sequence. We show that a limitation to the stability of such a triplex may arise from the instability of the antiparallel part, composed of reverse-Hoogsteen C.GxG and T.AxT base triplets. Using DNase I footprinting and ultraviolet absorption experiments, we report that a benzo[e]pyridoindole derivative [(3-methoxy- 7H-8-methyl-11-[(3'-amino-propyl) amino] benzo[e]pyrido [4,3-b]indole (BePI)], a drug interacting more tightly with a triplex than with a duplex DNA, strongly stabilizes triplexes with reverse-Hoogsteen C.GxG and T.AxT triplets thus allowing a stabilization of the triplex-forming switch (T,G) oligonucleotide on alternating oligopurine- oligopyrimidine 5'-(Pu)14(Py)14-3' duplex sequences. These results lead to an extension of the range of oligonucleotide sequences for alternate strand recognition of duplex DNA.

Potential in vivo roles of nucleic acid triple-helices

“…171 However, TFOs of length greater than 17 nt may exhibit substantial affinity for a secondary (shorter) target site by tolerating mismatches, loops or other structures [172][173][174] or by alternating the target strand in the duplex (as described in the next paragraph). 163 Triplexes in principle tolerate mismatches between the strands, 175,176 however these have a strong destabilizing effect that increases with the number of contiguous mismatches. 177 The destabilizing effect depends furthermore on the nature of the mismatch and its positional location, i.e., a terminal mismatch causes less disruption to the triplex than mismatch in the centre of the triple-helix.…”

“…178 A single TFO can bind to a target duplex in which the polypurine tract switches strands. 163 In this situation, different segments of the TFO bind to different strands in the duplex. The alternating target strand preference is accompanied by a switch in the binding configuration (Hoogsteen/reverse Hoogsteen) of the corresponding binding segment in the TFO.…”

“…The alternating target strand preference is accompanied by a switch in the binding configuration (Hoogsteen/reverse Hoogsteen) of the corresponding binding segment in the TFO. 163 All six possible junctions for combining two short TFO-segments have shown to be functional in vitro. [179][180][181] The cellular environment likely imposes specific constraints on the potential for triple-helix formation.…”

Rational design of a triple helix-specific intercalating ligand

“…Oligonucleotides containing T and G can also form triple helices whose orientation depends on base sequence (see ref. 8 …”

Strong, specific, monodentate G-C base pair recognition by N7-inosine derivatives in the pyrimidine.purine-pyrimidine triple-helical binding motif

“…Because of the restriction of both binding motifs to homopurine and homopyrimidine sequences, much effort has recently been devoted to the search for a more general mode of DNA duplex recognition by oligonucleotides. Approaches involved the use of oligonucleotides that were designed to bind to purine-pyrimidine block sequences either exerting the structural properties of both triplex binding motifs in one strand (7)(8)(9); or by the use of oligonucleotides that were joined in a 3′-3′ or 5′-5′ direction, and that recognize purine tracts on both strands of the corresponding duplex via the Hoogsteen binding mode (10)(11)(12)(13)(14). Other attempts involved the use of oligonucleotides containing modified bases either: (i) to recognize a pyrimidine unit within a purine tract or to span the major groove in order to complex the whole base pair (15)(16)(17); or (ii) to bring about less specific interactions at the site of purine-pyrimidine inversion in the duplex (18,19).…”