Triple helix-tetraplex equilibrium for G-rich oligonucleotide N30/P50 phosphoramidates: role of molecular concentration and counterions

The formation of a triple helix by a third N30/P50 phosphoramidate GT-rich strand 50-d(T9G5)NP-30 has been studied by FTIR, CD and UV absorbance spectroscopies. We show that in presence of sodium counterions, in conditions of molecular crowding induced by high DNA concentrations, the self-association of the phosphodiester analog into a tetrameric structure is favored and prevents the formation of the triple helix. The use of a phosphoramidate third strand in the same conditions allows to minimize self-association and to form the triple helix with a 50-d(T9G5)NP-30 third strand. Characteristic signatures of T*A$T and G*G$C base triplets have been obtained by FTIR spectroscopy. Formation of a triple helix with the unmodified GT third strand can be observed in dilute solution, in presence of lithium and divalent magnesium ions (1 MLiCl, 50 mMMgCl2). In that case a biphasic UV melting profile (TM at 40 and 60 8C) and a characteristic CD spectrum of a parallel stranded GT triple helix have been obtained. q 2005 Elsevier B.V. All rights reserved.