ArticleProceedings of the National Academy of Sciences of the United States of America2023
Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 20 citations in OpenAlex.
- Influence of DNA Mispairing and Abasic Sites on Duplex Dynamics: A Temperature-Jump Infrared Spectroscopy Study.The journal of physical chemistry letters · 2026Article
- Base-pair scale dynamics of a repair helicase on DNA lesions reveal varied damage-sensing mechanisms.bioRxiv : the preprint server for biology · 2026Article
- APE1 Activity is Controlled by Non-G-Quadruplex Conformations in Single- and Double-Stranded G-Quadruplex Constructs.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Evidence of a Three-State Mechanism in DNA Hairpin Folding.Journal of the American Chemical Society · 2025Article
- 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
- Sculpting photoproducts with DNA origami.Chem · 2024Article
- Insights into nucleic acid helix formation from infrared spectroscopy.Biophysical journal · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- Biomolecular infrared spectroscopy: making time for dynamics.Chemical science · 2024Review
- Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.Biophysical journal · 2023Article
- Direct monitoring of the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization from gaps and overhangs.bioRxiv : the preprint server for biology · 2023Article
- Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
DNA duplex stability arises from cooperative interactions between multiple adjacent nucleotides that favor base pairing and stacking when formed as a continuous stretch rather than individually. Lesions and nucleobase modifications alter this stability in complex manners that remain challenging to understand despite their centrality to biology. Here, we investigate how an abasic site destabilizes small DNA duplexes and reshapes base pairing dynamics and hybridization pathways using temperature-jump infrared spectroscopy and coarse-grained molecular dynamics simulations. We show how an abasic site splits the cooperativity in a short duplex into two segments, which destabilizes small duplexes as a whole and enables metastable half-dissociated configurations. Dynamically, it introduces an additional barrier to hybridization by constraining the hybridization mechanism to a step-wise process of nucleating and zipping a stretch on one side of the abasic site and then the other.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.