DNA base flipping by a base pair-mimic nucleoside

Abstract

On the basis of non-covalent bond interactions in nucleic acids, we synthesized the deoxyadenosine derivatives tethering a phenyl group (X) and a naphthyl group (Z) by an amide linker, which mimic a Watson–Crick base pair. Circular dichroism spectra indicated that the duplexes containing X and Z formed a similar conformation regardless of the opposite nucleotide species (A, G, C, T and an abasic site analogue F), which was not observed for the natural duplexes. The ΔG370 values among the natural duplexes containing the A/A, A/G, A/C, A/T and A/F pairs differed by 5.2 kcal mol−1 while that among the duplexes containing X or Z in place of the adenine differed by only 1.9 or 2.8 kcal mol−1, respectively. Fluorescence quenching experiments confirmed that 2-amino purine opposite X adopted an unstacked conformation. The structural and thermodynamic analyses suggest that the aromatic hydrocarbon group of X and Z intercalates into a double helix, resulting in the opposite nucleotide base flipping into an unstacked position regardless of the nucleotide species. This observation implies that modifications at the aromatic hydrocarbon group and the amide linker may expand the application of the base pair-mimic nucleosides for molecular biology and biotechnology.

A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding

“…Relationship Between PCA Eigenvectors and Base Flipping mentions simulations where, after inducing extreme helical bending (.80°) using a flooding potential, occurrences of spontaneous base flipping were seen. This is obviously related to the reduction of the p-stacking interactions that stabilize the closed helix (61). Inducing a less drastic helical bend using a milder flooding potential could possibly reduce the timescale of flipping to computationally tractable values, although this has not been investigated further here.…”

Conformational changes of the phenyl and naphthyl isocyanate-DNA adducts during DNA replication and by minor groove binding molecules

“…Our previous studies using the UV thermal melting curves and fluorescence spectra suggested that dA phe and dA naph introduced into a DNA sequence do not form a base pair with thymine in a complementary strand but induce base flipping (6,7). These spectroscopic measurements, however, only provide suggestive evidence for the base conformation.…”

“…The 2′-deoxyadenosine and 2′-deoxycytidine derivatives shown in Figure 1A were synthesized and identified as previously described (6,7). DNA oligonucleotides containing the nucleotide derivatives and those labeled with Cyanine 3 (Cy3) at their 5′-ends were synthesized on a solid support using conventional phosphoramidite chemistry with an automated DNA synthesizer (Model 391, Applied Biosystems).…”

“…The melting temperature ( T m ) at which half of a duplex structure was denatured was determined from the melting curve. The thermodynamic parameters Δ H °, Δ S ° and the free energy change at 37°C (Δ G °) for DNA duplex formations were determined from the T m obtained at different total strand concentrations ( C t ) using a plot of T m − 1 versus log ( C t /4) and from the melting curves fit to a theoretical equation assuming a two-state transition (6,9). …”

Design and Synthesis of Triazolyl‐Donor/Acceptor Unnatural Nucleosides and Oligonucleotide Probes Containing Triazolyl‐Phenanthrene Nucleoside

“…The design of such molecules to stabilize or recognize the abasic lesion continues to be a fundamental and challenging task. In an effort to unfold the mechanism by which DNA‐repair enzymes recognize and distinguish abasic from normal DNA, several strategies have been put forth to recognize/stabilize abasic DNA via the design of small‐molecule intercalators (Yoshimoto et al, ), oligodeoxynucleotide (ODN) probes containing non‐nucleosidic building blocks (Langenegger and Haner et al, , ; Malinovskii et al, ), and/or modified nucleosides (Matray and Kool, ; Kool et al, ; Smirnov et al, ; Brotschi et al, ; Nakano et al, ; Verhagen et al, ; Wojciechowski et al, ) as nucleobase surrogates. While all the reported non‐nucleoside base surrogates and/or modified nucleosides are found to stabilize abasic sites better than natural adenine, they fail to stabilize an abasic duplex to an extent comparable to the stability of a natural A‐T pair.…”