Guanine tetraplex formation by short DNA fragments containing runs of guanine and cytosine.

Using CD spectroscopy, guanine tetraplex formation was studied with short DNA fragments in which cytosine residues were systematically added to runs of guanine either at the 5' or 3' ends. Potassium cations induced the G-tetraplex more easily with fragments having the guanine run at the 5' end, which is just an opposite tendency to what was reported for (G+T) oligonucleotides. However, the present (G+C) fragments simultaneously adopted other conformers that complicated the analysis. We demonstrate that repeated freezing/thawing, performed at low ionic strength, is a suitable method to exclusively stabilize the tetraplex in the (G+C) DNA fragments. In contrast to KCl, the repeated freeze/thaw cycles better stabilized the tetraplex with fragments having the guanine run on the 3' end. The tendency of guanine blocks to generate the tetraplex destabilized the d(G5).d(C5) duplex whose strands dissociated, giving rise to a stable tetraplex of (dG5) and single-stranded (dC5). In contrast to d(G3C3) and d(G5C5), repeated freezing/thawing induced the tetraplex even with the self-complementary d(C3G3) or d(C5G5); hence the latter oligonucleotides preferred the tetraplex to the apparently very stable duplex. The tetraplexes only included guanine blocks while the 5' end cytosines interfered neither with the tetraplex formation nor the tetraplex structure.

UV light-induced crosslinking of the strands of poly(dA-dT) and related alternating purine-pyrimidine DNAs.

Alkaline agarose gel electrophoresis was used to detect UV-induced crosslinking of the strands of poly(dA-dT) and related alternating purine-pyrimidine DNAs in solutions stabilizing various polynucleotide conformations. Strands of the B-form and A-form of poly(dA-dT) were not crosslinked but a UV dose-dependent retarded species appeared in the denaturing gels in parallel with the polynucleotide isomerization into the unusual X-form. Most other polynucleotides adopting the X-form were crosslinked as well. The exceptions include the X-forms of poly(dA-butyl5dU) and poly(dA-pentyl5dU) whose strands do not crosslink because the long exocyclic substituents attached to uracil make the photodimerization impossible. Strands of poly(amino2dA-dT) and poly(dA, amino2dA-dT), the latter polynucleotide containing roughly equal amounts of amino2adenine and adenine, also do not crosslink upon UV irradiation because they isomerize into an A-like conformation which is different from the X-form of poly (dA-dT). In contrast, strands of the mixed copolymers of poly(dA, amino2dA-dT) containing low amino2adenine contents are crosslinked upon UV irradiation, in accordance with the observation that they isomerize into the X-form.

Thymine methyl groups stabilize the putative A-form of the synthetic DNA poly(amino2dA-dT).

Poly(amino2dA-dT) easily isomerizes into a non-B conformer which most authors think is an A-form. We synthesized new DNA analogs poly(amino2dA-ethyl5dU) and poly(amino2dA-dU) to show that they do not prefer this conformer. Hence the putative A-form is, like Z-DNA of poly(dG-dC) but unlike A-DNA, strongly stabilized by the methyl group in position 5 of the pyrimidine base. In addition, the putative A-form is induced by divalent cations while it does not need any alcohol to be stable, both properties being typical for Z-DNA again but quite unusual with A-DNA. Despite these similarities, the putative A-form is also distinct from Z-DNA, as poly(amino2dA-dT) is shown to isomerize into a Z-form in the NaCl + NiCl2 solvent system like poly(dA-dT). The present data indicate that the putative A-form of poly(amino2dA-dT) differs in a significant way from all canonical conformers of DNA. Furthermore, the studies of the poly(amino2dA-dT) family of polydeoxynucleotides reveal a novel type of conformational switch in DNA. We also report the B-Z transitions of poly(amino2dA-ethyl5dU) and poly(amino2dA-dU) and their transitions into the putative A-form in aqueous alcohol solutions.