Dual recognition of double-stranded DNA by 2 '-aminoethoxy-modified oligonucleotides: The solution structure of an intramolecular triplex obtained byNMR spectroscopy

The solution structure of an intramolecular triple helical oligonucleotide has been solved by NMR. The third strand of the pyrimidine purine pyrimidin e tripler is composed of 2'-aminoethoxy-modified riboses, whereas the remai ning part of the nucleic acid is DNA, The structure around the aminoethoxy modification was obtained with the help of selective isotope labeling in co njunction with isotope-editing experiments. Dinucleotide steps and interstr and connectivities, as well as the complete backbone conformation of the tr ipler, were derived from J-couplings, NOEs, and P-31 chemical shifts. The s tructure of this tripler, solved by distance geometry, explains the extraor dinary stability and increase in rate of tripler formation induced by 2'-am inoethoxy-modified oligonucleotides: apart from the formation of seven base triples, a well-defined hydrogen-bonding network is formed across the Cric k-Hoogsteen groove involving the amino protons of the aminoethoxy moieties and the phosphates of the purine strand of the DNA. The modified strand ado pts a conformation which is close to an A-type helix, whereas the DNA duple x conformation is best described as an unwound B-type helix. The groove dim ensions and helical parameters of the 2'-aminoethoxy-modified rY.dRdY tripl er are surprisingly well conserved in comparison with DNA triplexes.