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

The solution structure of an intramolecular triple helical oligonucleotide has been solved by NMR. The third strand of the pyrimidine purine pyrimidine tripler is composed of 2'-aminoethoxy-modified riboses, whereas the remaining part of the nucleic acid is DNA, The structure around the aminoethoxy modification was obtained with the help of selective isotope labeling in conjunction with isotope-editing experiments. Dinucleotide steps and interstrand connectivities, as well as the complete backbone conformation of the tripler, were derived from J-couplings, NOEs, and P-31 chemical shifts. The structure of this tripler, solved by distance geometry, explains the extraordinary stability and increase in rate of tripler formation induced by 2'-aminoethoxy-modified oligonucleotides: apart from the formation of seven base triples, a well-defined hydrogen-bonding network is formed across the Crick-Hoogsteen groove involving the amino protons of the aminoethoxy moieties and the phosphates of the purine strand of the DNA. The modified strand adopts a conformation which is close to an A-type helix, whereas the DNA duplex conformation is best described as an unwound B-type helix. The groove dimensions and helical parameters of the 2'-aminoethoxy-modified rY.dRdY tripler are surprisingly well conserved in comparison with DNA triplexes.