GUANINE TETRAPLEX FORMATION BY SHORT DNA FRAGMENTS CONTAINING RUNS OFGUANINE AND CYTOSINE

Using CD spectroscopy, guanine tetraplex formation was studied with sh ort DNA fragments in which cytosine residues were systematically added to runs of guanine either at the 5' or 3' ends. Potassium cations ind uced the G-tetraplex more easily with fragments having the guanine run at the 5' end, which is just an opposite tendency to what was reporte d for (G+T) oligonucleotides. However, the present (G+C) fragments sim ultaneously adopted other conformers that complicated the analysis. We demonstrate that repeated freezing/thawing, performed at low ionic st rength, is a suitable method to exclusively stabilize the tetraplex in the (G+C) DNA fragments. In contrast to KCI, the repeated freeze/thaw cycles better stabilized the tetraplex with fragments having the guan ine run on the 3' end. The tendency of guanine blocks to generate the tetraplex destabilized the d(G(5)).d(C-5) duplex whose strands dissoci ated, giving rise to a stable tetraplex of (dG(5)) and single-stranded (dC(5)). in contrast to d(G(5)C(5)) and d(G(5)C(5)), repeated freezin g/thawing induced the tetraplex even with the self-complementary d(C(3 )G(3)) or d(C(5)G(5)); 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.