Effect of length and netropsin binding on base-pair lifetimes of oligonucleotides with the center core GCGAATTCGC

Abstract

Abstract The imino proton solvent exchange of three self-complementary oligonucleotides with different lengths 5′-d([G[C[GCGAATTCGCG]C]G])-3′ has been studied by 1H NMR selective saturation recovery. From measurements of the solvent exchange rates at different catalysing ammonia base concentrations it is possible to obtain the base pair lifetimes (1, 2). The results at 15°C shows that the base pair lifetime is an individual property dependent on the nature of the base pair and its neighbouring sequence and varies from about 10 to 80 ms for the different base pairs in the core of the oligonucleotides. End effects (“fraying at the ends”) with considerably shorter lifetimes are visible at least two or three base pairs from the ends of the oligonucleotide (see table below).