ArticleBiophysical journal2013
Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed.
- Thermodynamic and kinetic considerations in DNA triplex formation revealed by ITC.European biophysics journal : EBJ · 2026Article
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- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.Journal of molecular evolution · 2024Article
- Thermodynamic compensation to temperature extremes in B. subtilis vs T. maritima lysine riboswitches.Biophysical journal · 2024Article
- RNA Complexes with Nicks and Gaps: Thermodynamic and Kinetic Effects of Coaxial Stacking and Dangling Ends.Journal of the American Chemical Society · 2024Article
- Transient states during the annealing of mismatched and bulged oligonucleotides.Nucleic acids research · 2024Article
- Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics.Biophysical journal · 2024Article
- The Thermodynamic Fingerprints of Ultra-Tight Nanobody-Antigen Binding Probed via Two-Color Single-Molecule Coincidence Detection.International journal of molecular sciences · 2023Article
- An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA.Journal of the American Chemical Society · 2023Article
- 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
- Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides.Nucleic acids research · 2022Article
- The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.Nucleic acids research · 2022Article
- Pairing statistics and melting of random DNA oligomers: Finding your partner in superdiverse environments.PLoS computational biology · 2022Article
- Triggered Assembly of a DNA-Based Membrane Channel.Journal of the American Chemical Society · 2022Article
- Needles in Haystacks: Understanding the Success of Selective Pairing of Nucleic Acids.International journal of molecular sciences · 2022Article
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3 authors.
Funding
Abstract
In this work, the kinetics of short, fully complementary oligonucleotides are investigated at the single-molecule level. Constructs 6-9 bp in length exhibit single exponential kinetics over 2 orders of magnitude time for both forward (kon, association) and reverse (koff, dissociation) processes. Bimolecular rate constants for association are weakly sensitive to the number of basepairs in the duplex, with a 2.5-fold increase between 9 bp (k'on = 2.1(1) × 10(6) M(-1) s(-1)) and 6 bp (k'on = 5.0(1) × 10(6) M(-1) s(-1)) sequences. In sharp contrast, however, dissociation rate constants prove to be exponentially sensitive to sequence length, varying by nearly 600-fold over the same 9 bp (koff = 0.024 s(-1)) to 6 bp (koff = 14 s(-1)) range. The 8 bp sequence is explored in more detail, and the NaCl dependence of kon and koff is measured. Interestingly, kon increases by >40-fold (kon = 0.10(1) s(-1) to 4.0(4) s(-1) between [NaCl] = 25 mM and 1 M), whereas in contrast, koff decreases by fourfold (0.72(3) s(-1) to 0.17(7) s(-1)) over the same range of conditions. Thus, the equilibrium constant (Keq) increases by ≈160, largely due to changes in the association rate, kon. Finally, temperature-dependent measurements reveal that increased [NaCl] reduces the overall exothermicity (ΔΔH° > 0) of duplex formation, albeit by an amount smaller than the reduction in entropic penalty (-TΔΔS° < 0). This reduced entropic cost is attributed to a cation-facilitated preordering of the two single-stranded species, which lowers the association free-energy barrier and in turn accelerates the rate of duplex formation.
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