ArticleBiophysical journal2023
Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 19 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
- Article
- Long-Range Allosteric Modulation of DNA Duplex Dynamics Induced by Pyrrole-Imidazole Polyamide Binding.The journal of physical chemistry letters · 2025Article
- A Hybrid Bottom-Up and Data-Driven Machine Learning Approach for Accurate Coarse-Graining of Large Molecular Complexes.Journal of chemical theory and computation · 2025Article
- 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
- Development of DNA Microarray for Indication of Viral Community-Acquired Pneumonia Pathogens.Sovremennye tekhnologii v meditsine · 2025Article
- Modeling Infrared Spectroscopy of Nucleic Acids: Integrating Vibrational Non-Condon Effects with Machine Learning Schemes.Journal of chemical theory and computation · 2024Article
- RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends.Journal of the American Chemical Society · 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
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9 authors at 3 institutions in 1 country.
Funding
Abstract
Hybridization of short nucleic acid segments (<4 nt) to single-strand templates occurs as a critical intermediate in processes such as nonenzymatic nucleic acid replication and toehold-mediated strand displacement. These templates often contain adjacent duplex segments that stabilize base pairing with single-strand gaps or overhangs, but the thermodynamics and kinetics of hybridization in such contexts are poorly understood because of the experimental challenges of probing weak binding and rapid structural dynamics. Here we develop an approach to directly measure the thermodynamics and kinetics of DNA and RNA dinucleotide dehybridization using steady-state and temperature-jump infrared spectroscopy. Our results suggest that dinucleotide binding is stabilized through coaxial stacking interactions with the adjacent duplex segments as well as from potential noncanonical base-pairing configurations and structural dynamics of gap and overhang templates revealed using molecular dynamics simulations. We measure timescales for dissociation ranging from 0.2-40 μs depending on the template and temperature. Dinucleotide hybridization and dehybridization involve a significant free energy barrier with characteristics resembling that of canonical oligonucleotides. Together, our work provides an initial step for predicting the stability and kinetics of hybridization between short nucleic acid segments and various templates.
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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 Socratic graph.