A Single Carbocyclic Nucleotide Substitution in a 12mer DNA Gives a Hoogsteen Basepaired Duplex (Till 38°C) and a Hairpin (Till 65°C). A 600 MHz NMR Spectroscopic Study

Abstract

The impact of intramolecular stereoelectronic effects has been examined by comparison of the solution structures of natural oligo-DNA duplex, 5′(1C2G3C4G5A6A7T8T9C10G11C12G)2 3′, and its carbocyclic-nucleotide analogues in which the pentose sugar in 2′-dA residue is replaced with its carbocyclic counterpart (i.e. 2′-deoxyaristeromycin). Based on the NMR evidences, it has been shown, that 2′-deoxyaristeromycin analog exists in a dynamic equilibrium between the two forms of duplexes, one with W-C bp and the second with Hoogsteen bp in ca 1:1 ratio at lower temperature (below 35°C) and as hairpin at higher temperature (from ∼40° – 60°C).