ArticleBiophysical journal2024
Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.
Article in Biophysical journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Influence of DNA Mispairing and Abasic Sites on Duplex Dynamics: A Temperature-Jump Infrared Spectroscopy Study.The journal of physical chemistry letters · 2026Article
- Singlet oxygen-mediated photocatalytic generation of abasic sites in DNA.Communications chemistry · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- NAIRDB: a database of Fourier transform infrared (FTIR) data for nucleic acids.Nucleic acids research · 2025Article
- Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes.Journal of chemical theory and computation · 2024Article
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Insights into nucleic acid helix formation from infrared spectroscopy.Biophysical journal · 2024Article
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6 authors.
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Abstract
Local perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolved spectroscopy and molecular dynamics simulations, we unravel an interplay between AP-site position and nucleobase sequence that controls energetic and dynamic disruption to the duplex. The duplex is disrupted into two segments by an entropic barrier for base-pairing on each side of the AP site. The barrier induces fraying of the short segment when an AP site is near the termini. Shifting the AP site inward promotes a transition from short-segment fraying to fully encompassing the barrier into the thermodynamics of hybridization, leading to further destabilization of the duplex. Nucleobase sequence determines the length scale for this transition by tuning the barrier height and base-pair stability of the short segment, and certain sequences enable out-of-register base-pairing to minimize the barrier height.
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