Extraordinary Thermal Stability of an Oligodeoxynucleotide Octamer Constructed from Alternating 7-Deaza-7-iodo guanine and 5-Iodocytosine Base Pairs - DNA Duplex Stabilization by Halogen Bonds?

Abstract

A reinvestigation of the published X-ray crystal-structure analyses of 7-halogenated (Br, I) 8-aza-7-deaza-2 `-deoxyguanosines Br(7)c(7)z(8)G(d); 1a and I(7)c(7)z(8)G(d), 1b, as well as of the structurally related 7-deaza-7-iodo-2 `-deoxy-beta-D-ribofuranosyladenine (beta-I(7)c(7)A(d); 2=6e in Table 1) and its alpha-D-anomer (alpha-I(7)c(7)A(d); 3) clearly revealed the existence of halogen bonds between corresponding halogen substituents and the adjacent N(3)-atoms of neighboring nucleoside molecules within the single crystals. These halogen bonds can be rationalized by the presence of a region of positive electrostatic potential, the sigma-hole, on the outermost portion the halogen's surface, while the three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of the halogen substituent. The N(3) atoms of the halogenated nucleosides carry a partial negative charge. This novel type of bonding between nucleosides was tentatively used to explain the extraordinary high stability of oligodeoxynucleotides constructed from halogenated nucleotide building blocks.