An abasic site induces a bulged conformation in the single‐stranded DNA trimer d(Ap(ab)pA). An NMR and model‐building study

Abstract

Abstract1′,2′‐Dideoxy‐D‐ribofuranose (ab), its 5′‐ and 3′‐phosphorylated analogues (ab5 and ab3), and the DNA trimer d(Ap(ab)pA) have been studied by means of proton NMR spectroscopy. These fragments are of interest as model compounds for abasic lesions occurring in vivo. All abasic sugars exhibit similar S‐type sugar conformations with populations of S‐conformer varying from 75% (in ab and ab5) to 83% (in ab3 and dab(2)), Ps ≈ 144° and Φs in the range from 30 to 33°. Having established the presence of mainly S‐type sugar, we could assign the H1′ and H1″ protons of all abasic residues stereospecifically on the basis of their respective vicinal coupling constants. The trimer exhibits considerable flexibility in the backbone. Moreover, chemical shifts as a function of temperature and chemical‐shift differences between abasic sugar protons in the trimer and in the abasic monomers point to the presence of a structure in which dab(2) is bulged out of the helix and the terminal residues stack on top of each other. Several models which fit the experimental data are presented.