ArticleProceedings of the National Academy of Sciences of the United States of America2022
Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Thermodynamic prediction of RNA cellular activity from sequence via conformational ensembles.Cell · 2026Article
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Nature communications · 2026Article
- Assessing the contribution of rare DNA states to cancer mutational signatures using sequence-specific conformational fingerprinting.Research square · 2025Article
- Kinetic Dissection of Proton-Coupled Conformational Transitions in Nucleic Acids by Integrating pH-Dependent NMR and Chemical Modifications.Journal of the American Chemical Society · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Quantitative and systematic NMR measurements of sequence-dependent A-T Hoogsteen dynamics uncovers unique conformational specificity in the DNA double helix.bioRxiv : the preprint server for biology · 2024Article
- Direct Measurement of 8OG Syn-Anti Flips in Mutagenic 8OG·A and Long-Range Damage-Dependent Hoogsteen Breathing Dynamics UsingThe journal of physical chemistry. B · 2024Article
- Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA.Nucleic acids research · 2024Article
- Direct Measurement of 8OGbioRxiv : the preprint server for biology · 2024Article
- Conformational dynamics of RNA G4C2 and G2C4 repeat expansions causing ALS/FTD using NMR and molecular dynamics studies.Nucleic acids research · 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
- Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Why are G-quadruplexes good at preventing protein aggregation?RNA biology · 2023Article
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9 authors.
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Abstract
Thermodynamic preferences to form non-native conformations are crucial for understanding how nucleic acids fold and function. However, they are difficult to measure experimentally because this requires accurately determining the population of minor low-abundance (<10%) conformations in a sea of other conformations. Here, we show that melting experiments enable facile measurements of thermodynamic preferences to adopt nonnative conformations in DNA and RNA. The key to this "delta-melt" approach is to use chemical modifications to render specific minor non-native conformations the major state. The validity and robustness of delta-melt is established for four different non-native conformations under various physiological conditions and sequence contexts through independent measurements of thermodynamic preferences using NMR. Delta-melt is faster relative to NMR, simple, and cost-effective and enables thermodynamic preferences to be measured for exceptionally low-populated conformations. Using delta-melt, we obtained rare insights into conformational cooperativity, obtaining evidence for significant cooperativity (1.0 to 2.5 kcal/mol) when simultaneously forming two adjacent Hoogsteen base pairs. We also measured the thermodynamic preferences to form G-C
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