Crystal structure and sequence-dependent conformation of the A.G mispaired oligonucleotide d(CGCAAGCTGGCG).

Abstract

The crystal structure of the dodecanucleotide d(CGCAAGCTGGCG) has been determined to a resolution of 2.5 A and refined to an R factor of 19.3% for 1710 reflections.The sequence crystallizes as a B-type double helix, with two G(ant)-A(syn) base pairs. These are stabilized by three-center hydrogen bonds to pyrimidines that induce perturbations in base-pair geometry. The central AGCT region of the helix has a wide (>6 A) minor groove.Mispairing in DNA can occur through genetic recombination events or as errors in replication (1). These mismatches have mutational consequences unless they are corrected by repair processes such as excision repair (2), which in Escherichia coli involves the uvrD gene product DNA helicase II and the dam methylase (3, 4). The A-G mismatch, which results in transversions, appears to have specific excision repair mechanisms associated with it, at least in E. coli (2), with the MutT protein appearing to prevent G-A pairing during replication (5). A-G repairs are less efficiently repaired in some mammalian cells than other heterogeneous mismatches, possibly because of structural differences between them (6).A number of distinct base-pairing possibilities have been suggested for A-G pairing (7,8), including the involvement of imino tautomers for either adenine or guanine. NMR spectroscopy has shown that G(anti)-A(anti) mismatches occur in some oligonucleotides (9, 10) with sequences around the mismatches of 5'-R-A(=G)-G(=A)-Y-3' and 5'-R-A(=G)-R-3', respectively (where = donates a mispair, R is a purine, and Y is a pyrimidine). Alternative G(syn)-A(anti) mispairing has been found at low pH by NMR methods in oligonucleotides with A(=G) flanked at both 5' and 3' sides by either guanine or cytosine (11). X-ray crystallographic studies have revealed both of these possibilities, as well as the less expected G(anti)-A(syn) arrangement (12, 13), in the sequence d(CGC-GAATTAGCG). The G(anti)-A(anti) pairing has been found for the two contiguous A-G base pairs in the crystal structure of the sequence d(CCAAGCTTGG) (14, 15) and G(syn)-A(anti) in the dodecanucleotide d(CGCAAATTG-GCG) (16). The latter structure has by implication protonation at N1 of the adenine to achieve the observed base pairing. Intensity data were collected on an Enraf-Nonius FAST area detector at Birkbeck College for a crystal of size 0.5 x 0.06 x 0.02 mm mounted in a sealed capillary tube. A total of 9842 reflections were collected to a resolution of 2.2 A at 70C. Only the 2495 reflections to 2.5 A (with a merging R factor of 11.9%) were used in the analysis since the merging agreement factor for the (mostly weak) reflections in the range of 2.2-2.5 A was unacceptably high. A total of 1710 unique reflections with F0> 3or (F'0) were obtained. 5' CGCAAGCTGGCGThe structure was solved by molecular replacement using the established structure of the dodecamer d(CGCGAAT-TCGCG) (17). The initial stages ofrefinement were undertaken using the CORELS constrained-restrained refinement package (18). The coordinates of the Dickerson dod...

Crystal Structure of a Mispaired Dodecamer, d(CGAGAATTC(O6Me)GCG)2, Containing a Carcinogenic O6-Methylguanine

“…However, unlike one of the other structures with A(syn) conformations (Webster et al, 1990) thereareno three-center hydrogen bonds nor are there any other non-base-pairing contacts. The base-pair morphology was calculated with a program based on the algorithm developed by Babcock and Olson (1992).…”

Tolerance of DNA Mismatches in Dmc1 Recombinase-mediated DNA Strand Exchange

“…35-37 and citations within). For example, the GA (anti-syn) conformation causes little local or global distortion of the B-DNA helix, whereas the AG (anti-syn) mismatch has poor base stacking within the helix, which perturbs the DNA backbone (35,38). However, for both Dmc1 and RecA, we have observed that mismatches located toward the 5Ј end of the initiating ssDNA have, in general, a stronger inhibitory effect than those located at the 3Ј end of the DNA.…”

"...the tyranny of the lattice...".

“…Nine key representatives are listed in Table 1 (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12). They are instructive because they illustrate sequences with A-tracts and without, with both wide and narrow minor grooves, and in three different crystal packing environments: orthorhombic P212121 and P21212 and monoclinic C2.…”