Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3- d ]pyrimidin-2-one

Abstract

The incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3–4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)]2 and [d(CGCGAAT-X-CGCG)]2 have been determined at 1.9–2.9 Å resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson–Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5′-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization.

Structures of DNA duplexes containing O6-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations

“…They seem to stabilize the duplex structures with no drastic changes in the base pair geometry, as the modified sites are in the major groove. Similar examples are already found in other structures of DNA duplexes crystallized in the presence of this duplex-stabilizing dye (32,33). Only a slight change is found in the groove width; the central shortest P … P distance between the two ODN backbones is 8.9 Å in the absence of Hoechst33258 (23), whereas those of O 6 -CMG5T and O 6 -CMG4C are 9.4 and 9.9 Å, respectively.…”

Complexes of mismatched and complementary DNA with minor groove binders. Structures at nucleotide resolution via an improved hydroxyl radical cleavage methodology

“…Crystal structures of complexes of Hoechst 33258 [41], PDB 296D, and DAPI [40], PDB 3GJH, with DNA are available. The DNAs used for the crystal structures were relatively short palindromes of similar but not the same sequences as used for the cleavage experiments.…”

“…The crystal structures of complexes of DNA in complex with DAPI, [40], structure 3GJH, and Hoechst 33258 [41], structure 296D, were downloaded from the PDB website. Water molecules were deleted and hydrogen atoms added to the structure.…”

Using a Fluorescent Cytosine Analogue tCo To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase

“…The tC° phohphoramidite was purchased from Glenn Research Inc (Sterling, VA). The primer was labeled at the 5'-end with 32 P using T4 polynucleotide kinase and [γ-32P]-ATP and annealed to unlabeled templates as previously described. (42–43) …”

“…Briefly, enzyme and P/T from one syringe were rapidly mixed with Mg 2+ and various [dNTP] from the other syringe for times ranging from 5 ms to 1 min. The final concentrations after mixing were 1 μM enzyme, 90 nM 32 P-labeled P/T, and 10 mM Mg 2+ . In addition, 10×[cold P/T]/[enzyme] was used to ensure that single-turnover conditions were met.…”