ArticleNucleic acids research2017
Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 53 citations in OpenAlex.
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- Kinetics and Activation Strategies in Toehold-Mediated and Toehold-Free DNA Strand Displacement.Biosensors · 2025Review
- Temperature-dependent funnel-like DNA folding landscapes.Nucleic acids research · 2025Article
- Impact of a single 8-oxoguanine lesion on Watson-Crick and Hoogsteen base pair hybridization in telomeric DNA quantified using single-molecule force spectroscopy.Nucleic acids research · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- DNA calorimetric force spectroscopy at single base pair resolution.Nature communications · 2025Article
- Stacking correlation length in single-stranded DNA.Nucleic acids research · 2024Article
- Characterization of human XPD helicase activity with single-molecule magnetic tweezers.Biophysical journal · 2024Article
- Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability.ACS omega · 2024Article
- Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions.Nucleic acids research · 2023Article
- Thermodynamic determination of RNA duplex stability in magnesium solutions.Biophysical journal · 2023Article
- Discrete RNA-DNA hybrid cleavage by the EXD2 exonuclease pinpoints two rate-limiting steps.The EMBO journal · 2023Article
- Nucleic Acid Thermodynamics Derived from Mechanical Unzipping Experiments.Life (Basel, Switzerland) · 2022Review
- Designing highly multiplex PCR primer sets with Simulated Annealing Design using Dimer Likelihood Estimation (SADDLE).Nature communications · 2022Article
- Force-Dependent Folding Kinetics of Single Molecules with Multiple Intermediates and Pathways.The journal of physical chemistry letters · 2022Article
- B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.ChemistryOpen · 2022Article
- Stem-loop formation drives RNA folding in mechanical unzipping experiments.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Mechanical characterization of base analogue modified nucleic acids by force spectroscopy.Physical chemistry chemical physics : PCCP · 2021Article
- Microchemomechanical devices using DNA hybridization.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Sugar-Pucker Force-Induced Transition in Single-Stranded DNA.International journal of molecular sciences · 2021Article
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA hybridization is an essential molecular reaction in biology with many applications. The nearest-neighbor (NN) model for nucleic acids predicts DNA thermodynamics using energy values for the different base pair motifs. These values have been derived from melting experiments in monovalent and divalent salt and applied to predict melting temperatures of oligos within a few degrees. However, an improved determination of the NN energy values and their salt dependencies in magnesium is still needed for current biotechnological applications seeking high selectivity in the hybridization of synthetic DNAs. We developed a methodology based on single molecule unzipping experiments to derive accurate NN energy values and initiation factors for DNA. A new set of values in magnesium is derived, which reproduces unzipping data and improves melting temperature predictions for all available oligo lengths, in a range of temperature and salt conditions where correlation effects between the magnesium bound ions are weak. The NN salt correction parameters are shown to correlate to the GC content of the NN motifs. Our study shows the power of single-molecule force spectroscopy assays to unravel novel features of nucleic acids such as sequence-dependent salt corrections.
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