Integrity of duplex structures without hydrogen bonding: DNA with pyrene paired at abasic sites

Abstract

DNA polymerases specifically insert the hydrophobic pyrene deoxynucleotide (P) opposite tetrahydrofuran (F), an stable abasic site analog, and DNA duplexes containing this non-hydrogen-bonded pair possess a high degree of thermodynamic stability. These observations support the hypothesis that steric complementarity and stacking interactions may be sufficient for maintaining stability of DNA structure and specificity of DNA replication, even in the absence of hydrogen bonds across the base pair. Here we report the NMR characterization and structure determination of two DNA molecules containing pyrene residues. The first is a 13mer duplex with a pyrene.tetrahydrofuran pair (P.F pair) at the ninth position and the second mimics a replication intermediate right after incorporation of a pyrene nucleoside opposite an abasic site. Our data indicate that both molecules adopt right-handed helical conformations with Watson- Crick alignments for all canonical base pairs. The pyrene ring stays inside the helix close to its baseless partner in both molecules. The single-stranded region of the replication intermediate folds back over the opposing strand, sheltering the hydrophobic pyrene moiety from water exposure. The results support the idea that the stability and replication of a P.F pair is due to its ability to mimic Watson-Crick structure.

Fluorinated DNA Bases as Probes of Electrostatic Effects in DNA Base Stacking

“…The effects of sterics, stacking, hydrogen bonding, and minor-groove solvation have been considered as contributing factors. [1][2][3][4] Probably the dominant stabilizing factor in helical DNA is base stacking. [5,6] In order to probe the physical factors that contribute to the stability of this stacking in water, measured melting data of short DNA oligomers, both naturally and nonnaturally substituted, has been studied.…”

Designable DNA Functions toward New Nanobiotechnology

“…Planar aromatic molecules are often examined because the compounds have high potential for the stacking interaction and may intercalate between base pairs in a duplex. 25,26 Notably, it is reported that even a very large aromatic group such as pyrene 27 and porphyrin 28 increases the duplex stability.…”

Use of Multiple Fluorescent Labels in Biological Sensing

“…Examples of scaffolds for bringing together multiple light-absorbing and -emitting species include dendrimers, [1] peptide backbones, [2] hydrocarbon frameworks, [3] organic polymer backbones, [4] and DNA. [5] In the last category, we have prepared DNA-like oligomers in which DNA bases are replaced by fluorescent chromophores.…”