Impact of sugar pucker on base pair and mispair stability

The selection of nucleoside triphosphates by a polymerase is controlled by several energetic and structural features, including base pairing geometry as well as sugar structure and conformation. Whereas base pairing has been considered exhaustively, substantially less is known about the role of sugar modifications for both nucleotide incorporation and primer extension. In this study, we synthesized oligonucleotides containing 2′-fluoro-modified nucleosides with constrained sugar pucker in an internucleotide position and, for the first time, at a primer 3′-end. The thermodynamic stability of these duplexes was examined. The nucleoside 2′-deoxy-2′- fluoroarabinofuranosyluracil [U2′F(ara)] favors the 2′-endo conformation (DNA-like), while 2′-deoxy-2′- fluororibofuranosyluracil [U2′F(ribo)] favors the 3′-endo conformation (RNA-like). Oligonucleotides containing U2′F(ara) have slightly higher melting temperatures (Tm) than those containing U2′F(ribo) when located in internucleotide positions or at the 3′-end and when correctly paired with adenine or mispaired with guanine. However, both modifications decrease the magnitude of ΔH° and ΔS° for duplex formation in all sequence contexts. In examining the thermodynamic properties for this set of oligonucleotides, we find entropy-enthalpy compensation is apparent. Our thermodynamic findings led to a series of experiments with DNA ligase that reveal, contrary to expectation based upon observed Tm values, that the duplex containing the U 2′F(ribo) analogue is more easily ligated. The 2′-fluoro-2′-deoxynucleosides examined here are valuable probes of the impact of sugar constraint and are also members of an important class of antitumor and antiviral agents. The data reported heremay facilitate an understanding of the biological properties of these agents, as well as the contribution of sugar conformation to replication fidelity. © 2009 American Chemical Society.