Triple helix-tetraplex equilibrium for G-rich oligonucleotide N3′ → P5′ phosphoramidates:: role of molecular concentration and counterions

The formation of a triple helix by a third N3' -> P5' phosphoramidate GT-rich strand 5'-d(T(9)G(5))(NP)-3' 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 5'-d(T(9)G(5))(NP)-3' 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 M LiCl, 50 MM MgCl2). In that case a biphasic UV melting profile (T-M at 40 and 60 degrees C) and a characteristic CD spectrum of a parallel stranded GT triple helix have been obtained. (c) 2005 Elsevier B.V. All rights reserved.