Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH

Abstract

The equimolar mixture of d(CTCTTCTTTCTTTTCTTTCTTCTC) (dY24) and d(GAGAAGAAAGA) (dR11) [designated (dY24).(dR11)], forms at pH = 5 a DNA triplex, which mimicks the H-DNA structure. The DNA triplex was identified by the following criteria: (i) dY24 and dR11 co-migrate in a poly-acrylamide gel, with a mobility and a retardation coefficient comparable to those observed for an 11-triad DNA triplex, previously characterized in our laboratories (1); (ii) the intercalator ethidium bromide shows a poor affinity for (dR11).(dY24) at pH = 5, and a high affinity at pH = 8; (iii) the (dR11).(dY24) mixture is not a substrate for DNase I at pH = 5; (iv) the CD spectrum of (dR11).(dY24), at pH = 5, is consistent with those previously reported for triple-stranded DNA. The (dR11).(dY24) mixture exhibits a thermally induced co-operative transition, which appears to be monophasic, reversible and concentration dependent. This transition is attributed to the disruption of the DNA triplex into single strands. The enthalpy change of the triplex-coil transition was measured by DSC (delta Hcal = 129 +/- 6 kcal/mol) and, assuming a two-state model, by analysis of UV-denaturation curves (average of two methods delta HUV = 137 +/- 13 kcal/mol). Subtracting from delta Hcal of triplex formation the contributions due to the Watson-Crick helix and to the protonation of the C-residues, we found that each pyrimidine binding into the major groove of the duplex, through a Hoogsteen base pair, is accompanied by an average delta H = -5.8 +/- 0.6 kcal/mol. The effect on the stability of the (dR11).(dY24) triplex due to the substitution of a T:A:T triad with a T:T:T one was also investigated.

Single strand targeted triplex-formation. Destabilization of guanine quadruplex structures by foldback triplex-forming oligonucleotides

“…The appearance of a slow moving band in the presence ofpotassium or sodium ions on native gels could be the result of the formation of a tetraplex structure (14). The tetraplex band formation was dependent on the nature and concentration of the cation present in the solution (23)(24)(25) (Fig. 2A).…”

“…* To whom correspondence should be addressed New designs of antisense oligonucleotides have recently been reported, including circular (21,22), linear (22)(23)(24)(25) and ligandconjugated linear oligonucleotides (26,27), all of which target single-stranded nucleic acid structures through triplex formation. These oligonucleotides contain three distinct domains.…”

Characterization of the DNA triplex formed by d(TGGGTGGGTGGTTGGGTGGG) and a critical R · Y sequence located in the promoter of the murine Ki‐ras proto‐oncogene

“…Such DNA structures have been studied with different methods including eletrophoresis [2~], UV-spectroscopy [5][6][7][8][9][10][11][12][13] and NMR [14,15].…”

Oligonucleotide clamps arrest DNA synthesis on a single-stranded DNA target.

“…A 24-mer pyrimidine oligonucleotide was also shown to bind an 11-mer purine oligonucleotide by forming a triplex structure (4). Circular oligonucleotides can also form triple-helical structures when…”