Base−Base Recognition of Nonionic Dinucleotide Analogues in an Apolar Environment Studied by Low-Temperature NMR Spectroscopy

Abstract

Two self-complementary dinucleotide analogues T(Si)A and A(Si)T with a nonionic diisopropylsilyl-modified backbone were synthesized, and their association in a nonaqueous aprotic environment was studied by NMR spectroscopy. Using a CDClF(2)/CDF(3) solvent mixture, measurements at temperatures as low as 113 K allowed the observation and structural characterization of individual complexes in the slow exchange regime. The A(Si)T analogue associates to exclusively form a dinucleotide antiparallel duplex with regular Watson-Crick base pairing, but both A and T nucleosides exhibit a predominant C3'-endo sugar pucker reminiscent of an A-type conformation. In contrast to A(Si)T, the T(Si)A dinucleotide is found to exhibit significant variability and flexibility. Thus, different secondary structures with weaker hydrogen bonds for all T(Si)A structures are observed at low temperatures. Although a B-like Watson-Crick antiparallel dinucleotide duplex with a preferred C2'-endo sugar pucker largely predominates at temperatures above 153 K, two additional species, namely a dinucleotide Hoogsteen duplex with a syn glycosidic torsion angle of the adenosine nucleoside and a presumably intramolecularly folded structure, are increasingly populated upon further cooling. By adding typical DNA intercalators like anthracene or benz[c]acridine derivatives to the A(Si)T dinucleotide duplex in the aprotic solvent environment, no binding of the polycyclic aromatic molecules can be detected even at lower temperatures. Obviously, van der Waals and stacking interactions are insufficient to compensate for the other unfavorable contributions to the overall free energy of binding, and only in the presence of additional hydrophobic effects in an aqueous environment does binding occur.

A historical account of hoogsteen base‐pairs in duplex DNA

“…It is worth noting that HG base-pairs have also been observed in DNA containing non-natural modifications in the sugar-phosphate backbone, including the addition of an ethylene bridge between C3 0 and C5 0 in "bicyclo-DNA," which fixes the gamma backbone torsion angle to a noncanonical orientation, 94 a single-residue substitution of sugar O4 0 with a methylene group, 95 or in dinucleotide d(TA) analogs containing a nonionic diisopropylsilyl-modified backbone at very low temperatures. 96…”