Solution Structure of a Duplex DNA with an Abasic Site in a dA Tract

Abstract

The presence of dA tracts in DNA can lead to stable curvature of the DNA, and this curvature can be important in gene regulation, DNA packaging, and other processes. Since damage to DNA may eliminate this stable curvature, the solution state structure of the duplex of d(CGCAAAAATGCG) paired with d(CGCATTDTTCCG), with D indicating an abasic site, has been determined. The undamaged DNA bends into the major groove both in solution and in the crystal state. The presence of the abasic site in the dA tract region induces changes in the DNA structure up to four base pairs away from the damaged site. The structure of the DNA is dependent on whether the abasic site is in the alpha or beta hemiacetal form. These consequences are quite different from the more localized effects that have been observed for "normal" DNAs containing abasic sites. Thus, there appears to be a strong sequence dependence of the structural effects of abasic sites just as there is for undamaged DNA. Furthermore, these results indicate that the presence of an abasic site can alter DNA bending and hence is likely to have significant long range effects on gene regulation and other properties that are dependent on the stable curvature of DNA.

Sloppy Bypass of an Abasic Lesion Catalyzed by a Y-family DNA Polymerase

“…Although almost exclusively true for a replicative polymerase that replicates undamaged DNA with high fidelity, bypass of a DNA lesion by Dpo4, a low fidelity enzyme, has been shown by us here and others previously (18 -22) to generate a variety of deletion and addition mutations in the vicinity of the lesion, indicating an equilibrium between several conformationally distinct DNA species exploited for bypass. This equilibrium is particularly relevant at structurally flexible AP sites (23,24) and thus invalidates the assumption of "one dNTP for each template base" for lesion bypass. As such, the definition of fidelity, although suitable for studies with undamaged DNA, cannot be strictly applied to these incorporation events.…”

Structures of Apurinic and Apyrimidinic Sites in Duplex DNAs

“…NMR Procedures-NMR data were acquired at 500 MHz on a Varian Inova and at 400 MHz on a Varian Unityplus spectrometer, at Wesleyan, and at 500 MHz on a Bruker 500 MHz DMX spectrometer at the University of Wisconsin, Madison, using methods described previously (11,(57)(58)(59) and modified as discussed below. All 31 P experiments were obtained at 161 MHz using the 400-MHz Varian Unityplus.…”

“…Quantitation and Assignment of NOE Cross-peaks-The spectra were assigned using the procedures described previously for abasic site-containing DNAs (11,58,62). The standard sequential connectivities of B-form DNA could be used except at the site of the damage.…”

“…Also, it now appears that some polymerases may place all four bases opposite an abasic site and not only dA residues (10) leading to both apurinic and apyrimidinic sites. The structure of damaged DNA is sequence-dependent as is the structure of undamaged DNA, and the presence of an abasic site within a curved DNA sequence can have large, long range structural effects (11). Results on the structures of repair enzymes have led to the suggestion that the abasic site can be recognized directly (12).…”

“…The structural features of AD can be compared with those of a damaged DNA with thymine glycol (57) in the same position as the abasic site. The structural features of AD can also be compared with a DNA in which the abasic site is in the middle of a curved DNA stretch (11). These comparisons indicate what may be some of the common and distinct features of damaged DNAs.…”