Jiang, F. & Doudna, J. A. CRISPR–Cas9 structures and mechanisms. Annu. Rev. Biophys. 46, 505–529 (2017).
Google Scholar
Klein, M., Eslami-Mossallam, B., Arroyo, D. G. & Depken, M. Hybridization kinetics explains CRISPR–Cas off-targeting rules. Cell Rep. 22, 1413–1423 (2018).
Google Scholar
Seeman, N. C. & Sleiman, H. F. DNA nanotechnology. Nat. Rev. Mater. 3, 17068 (2017).
Google Scholar
Schneider, F., Möritz, N. & Dietz, H. The sequence of events during folding of a DNA origami. Sci. Adv. 5, eaaw1412 (2019).
Google Scholar
Song, J. et al. Reconfiguration of DNA molecular arrays driven by information relay. Science 357, eaan3377 (2017).
Google Scholar
Cumberworth, A., Frenkel, D. & Reinhardt, A. Simulations of DNA-origami self-assembly reveal design-dependent nucleation barriers. Nano Lett. 22, 6916–6922 (2022).
Google Scholar
Zhan, P. et al. Recent advances in DNA origami-engineered nanomaterials and applications. Chem. Rev. 123, 3976–4050 (2023).
Google Scholar
Wei, X., Nangreave, J. & Liu, Y. Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics. Acc. Chem. Res. 47, 1861–1870 (2014).
Google Scholar
Jungmann, R. et al. Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami. Nano Lett. 10, 4756–4761 (2010).
Google Scholar
Strauss, S. & Jungmann, R. Up to 100-fold speed-up and multiplexing in optimized DNA-PAINT. Nat. Methods 17, 789–791 (2020).
Google Scholar
Gray, D. M. & Tinoco, I. Jr A new approach to the study of sequence‐dependent properties of polynucleotides. Biopolymers 9, 223–244 (1970).
Google Scholar
SantaLucia, J. Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460–1465 (1998).
Google Scholar
SantaLucia, J. Jr & Hicks, D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33, 415–440 (2004).
Google Scholar
Xia, T. et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson–Crick base pairs. Biochemistry 37, 14719–14735 (1998).
Google Scholar
Zuber, J., Schroeder, S. J., Sun, H., Turner, D. H. & Mathews, D. H. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Res. 50, 5251–5262 (2022).
Google Scholar
Markham, N. R. & Zuker, M. in Bioinformatics: Structure, Function, and Applications (ed. Keith, J. M.) 3–31 (Humana, 2008).
Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).
Google Scholar
Rejali, N. A., Ye, F. D., Zuiter, A. M., Keller, C. C. & Wittwer, C. T. Nearest-neighbour transition-state analysis for nucleic acid kinetics. Nucleic Acids Res. 49, 4574–4585 (2021).
Google Scholar
Zhang, J. X. et al. Predicting DNA hybridization kinetics from sequence. Nat. Chem. 10, 91–98 (2018).
Google Scholar
Hertel, S. et al. The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure. Nucleic Acids Res. 50, 7829–7841 (2022).
Google Scholar
Todisco, M. & Szostak, J. W. Hybridization kinetics of out-of-equilibrium mixtures of short RNA oligonucleotides. Nucleic Acids Res. 50, 9647–9662 (2022).
Google Scholar
Phan, T. T., Phan, T. M. & Schmit, J. D. Beneficial and detrimental effects of non-specific binding during DNA hybridization. Biophys. J. 122, 835–848 (2023).
Google Scholar
Untergasser, A. et al. Primer3 — new capabilities and interfaces. Nucleic Acids Res. 40, e115–e115 (2012).
Google Scholar
Wang, J. S. & Zhang, D. Y. Simulation-guided DNA probe design for consistently ultraspecific hybridization. Nat. Chem. 7, 545–553 (2015).
Google Scholar
Haley, N. E. et al. Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement. Nat. Commun. 11, 2562 (2020).
Google Scholar
Ouldridge, T. E., Šulc, P., Romano, F., Doye, J. P. & Louis, A. A. DNA hybridization kinetics: zippering, internal displacement and sequence dependence. Nucleic Acids Res. 41, 8886–8895 (2013).
Google Scholar
Hinckley, D. M., Lequieu, J. P. & de Pablo, J. J. Coarse-grained modeling of DNA oligomer hybridization: length, sequence, and salt effects. J. Chem. Phys. 141, 07B613_611 (2014).
Google Scholar
Jones, M. S., Ashwood, B., Tokmakoff, A. & Ferguson, A. L. Determining sequence-dependent DNA oligonucleotide hybridization and dehybridization mechanisms using coarse-grained molecular simulation, Markov state models, and infrared spectroscopy. J. Am. Chem. Soc. 143, 17395–17411 (2021).
Google Scholar
Sanstead, P. J. & Tokmakoff, A. Direct observation of activated kinetics and downhill dynamics in DNA dehybridization. J. Phys. Chem. B 122, 3088–3100 (2018).
Google Scholar
Chen, C., Wang, W., Wang, Z., Wei, F. & Zhao, X. S. Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization. Nucleic Acids Res. 35, 2875–2884 (2007).
Google Scholar
Wang, H., Li, B., Kim, Y.-J., Kwon, O.-H. & Granick, S. Intermediate states of molecular self-assembly from liquid-cell electron microscopy. Proc. Natl Acad. Sci. USA 117, 1283–1292 (2020).
Google Scholar
Neupane, K., Wang, F. & Woodside, M. Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation. Proc. Natl Acad. Sci. USA 114, 1329–1334 (2017).
Google Scholar
Alvey, H. S., Gottardo, F. L., Nikolova, E. N. & Al-Hashimi, H. M. Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics. Nat. Commun. 5, 4786 (2014).
Google Scholar
Dupuis, N. F., Holmstrom, E. D. & Nesbitt, D. J. Single-molecule kinetics reveal cation-promoted DNA duplex formation through ordering of single-stranded helices. Biophys. J. 105, 756–766 (2013).
Google Scholar
Dubini, R. C. et al. 1H NMR chemical exchange techniques reveal local and global effects of oxidized cytosine derivatives. ACS Phys. Chem. Au 2, 237–246 (2022).
Google Scholar
Ashwood, B., Sanstead, P. J., Dai, Q., He, C. & Tokmakoff, A. 5-Carboxylcytosine and cytosine protonation distinctly alter the stability and dehybridization dynamics of the DNA duplex. J. Phys. Chem. B 124, 627–640 (2019).
Google Scholar
Ghosh, S. et al. Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proc. Natl Acad. Sci. USA 117, 14194–14201 (2020).
Google Scholar
Shi, H. et al. NMR chemical exchange measurements reveal that N6-methyladenosine slows RNA annealing. J. Am. Chem. Soc. 141, 19988–19993 (2019).
Google Scholar
Rangadurai, A., Szymaski, E. S., Kimsey, I. J., Shi, H. & Al-Hashimi, H. M. Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion. Prog. Nucl. Mag. Reson. Spectrosc. 112, 55–102 (2019).
Google Scholar
Holmstrom, E. D. & Nesbitt, D. J. Biophysical insights from temperature-dependent single-molecule förster resonance energy transfer. Annu. Rev. Phys. Chem. 67, 441–465 (2016).
Google Scholar
Chung, H. S. Transition path times measured by single-molecule spectroscopy. J. Mol. Biol. 430, 409–423 (2018).
Google Scholar
Hoffer, N. Q. & Woodside, M. T. Probing microscopic conformational dynamics in folding reactions by measuring transition paths. Curr. Opin. Chem. Biol. 53, 68–74 (2019).
Google Scholar
Dans, P. D., Walther, J., Gómez, H. & Orozco, M. Multiscale simulation of DNA. Curr. Opin. Struc. Biol. 37, 29–45 (2016).
Google Scholar
Sponer, J. et al. RNA structural dynamics as captured by molecular simulations: a comprehensive overview. Chem. Rev. 118, 4177–4338 (2018).
Google Scholar
Lipfert, J., Doniach, S., Das, R. & Herschlag, D. Understanding nucleic acid–ion interactions. Annu. Rev. Biochem. 83, 813–841 (2014).
Google Scholar
Abou Assi, H., Garavís, M., González, C. & Damha, M. J. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res. 46, 8038–8056 (2018).
Google Scholar
Grün, J. T. & Schwalbe, H. Folding dynamics of polymorphic G‐quadruplex structures. Biopolymers 113, e23477 (2022).
Google Scholar
Marin-Gonzalez, A., Vilhena, J., Perez, R. & Moreno-Herrero, F. A molecular view of DNA flexibility. Q. Rev. Biophys. 54, e8 (2021).
Google Scholar
Craig, M. E., Crothers, D. M. & Doty, P. Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62, 383–401 (1971).
Google Scholar
Pörschke, D. & Eigen, M. Co-operative non-enzymatic base recognition III. Kinetics of the helix–coil transition of the oligoribouridylic· oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62, 361–381 (1971).
Google Scholar
Jin, R. & Maibaum, L. Mechanisms of DNA hybridization: transition path analysis of a simulation-informed Markov model. J. Chem. Phys. 150, 105103 (2019).
Google Scholar
Ashwood, B., Jones, M. S., Ferguson, A. L. & Tokmakoff, A. Disruption of energetic and dynamic base pairing cooperativity in DNA duplexes by an abasic site. Proc. Natl Acad. Sci. USA 120, e2219124120 (2023).
Google Scholar
Poland, D. & Scheraga, H. A. Theory of Helix–Coil Transitions in Biopolymers (Academic, 1970).
Manning, G. S. On the application of polyelectrolyte limiting laws to the helix–coil transition of DNA. V. Ionic effects on renaturation kinetics. Biopolymers 15, 1333–1343 (1976).
Google Scholar
Hart, D. J., Jeong, J., Gumbart, J. C. & Kim, H. D. Weak tension accelerates hybridization and dehybridization of short oligonucleotides. Nucleic Acids Res. 51, 3030–3040 (2023).
Google Scholar
Whitley, K. D., Comstock, M. J. & Chemla, Y. R. Elasticity of the transition state for oligonucleotide hybridization. Nucleic Acids Res. 45, 547–555 (2017).
Google Scholar
Yakovchuk, P., Protozanova, E. & Frank-Kamenetskii, M. D. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res. 34, 564–574 (2006).
Google Scholar
Zacharias, M. Base-pairing and base-stacking contributions to double-stranded DNA formation. J. Phys. Chem. B 124, 10345–10352 (2020).
Google Scholar
Altun, A., Garcia-Ratés, M., Neese, F. & Bistoni, G. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex. Chem. Sci. 12, 12785–12793 (2021).
Google Scholar
Son, I., Shek, Y. L., Dubins, D. N. & Chalikian, T. V. Hydration changes accompanying helix-to-coil DNA transitions. J. Am. Chem. Soc. 136, 4040–4047 (2014).
Google Scholar
Huguet, J. M., Ribezzi-Crivellari, M., Bizarro, C. V. & Ritort, F. Derivation of nearest-neighbor DNA parameters in magnesium from single molecule experiments. Nucleic Acids Res. 45, 12921–12931 (2017).
Google Scholar
Owczarzy, R., Moreira, B. G., You, Y., Behlke, M. A. & Walder, J. A. Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochem 47, 5336–5353 (2008).
Google Scholar
Rouzina, I. & Bloomfield, V. A. Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. Biophys. J. 77, 3252–3255 (1999).
Google Scholar
Mikulecky, P. J. & Feig, A. L. Heat capacity changes associated with nucleic acid folding. Biopolymers 82, 38–58 (2006).
Google Scholar
Rissone, P., Rico-Pasto, M., Smith, S. & Ritort, F. DNA calorimetric force spectroscopy at single base pair resolution. Prperint at https://arxiv.org/abs/2404.18785 (2024).
Bergonzo, C., Grishaev, A. & Bottaro, S. Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments. RNA 28, 937–946 (2022).
Google Scholar
Plumridge, A., Meisburger, S. P., Andresen, K. & Pollack, L. The impact of base stacking on the conformations and electrostatics of single-stranded DNA. Nucleic Acids Res. 45, 3932–3943 (2017).
Google Scholar
Mondal, B., Chakraborty, D., Hori, N., Nguyen, H. & Thirumalai, D. Competition between stacking and divalent cation mediated electrostatic interactions determines the conformations of short DNA sequences. J. Chem. Theory Comput. 20, 2934–2946 (2024).
Google Scholar
Nüesch, M. F. et al. Nanosecond chain dynamics of single-stranded nucleic acids. Nat. Commun. 15, 6010 (2024).
Google Scholar
Camunas-Soler, J., Ribezzi-Crivellari, M. & Ritort, F. Elastic properties of nucleic acids by single-molecule force spectroscopy. Annu. Rev. Biophys. 45, 65–84 (2016).
Google Scholar
Dans, P. D. et al. The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules. Nucleic Acids Res. 47, 11090–11102 (2019).
Google Scholar
Nikolova, E. N. et al. Transient Hoogsteen base pairs in canonical duplex DNA. Nature 470, 498–502 (2011).
Google Scholar
Vafabakhsh, R. & Ha, T. Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337, 1097–1101 (2012).
Google Scholar
Da Rosa, G. et al. Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophys. Rev. 13, 995–1005 (2021).
Google Scholar
Sun, T. et al. Bottom-up coarse-grained modeling of DNA. Front. Mol. Biosci. 8, 645527 (2021).
Google Scholar
Printz, M. P. & von Hippel, P. H. Hydrogen exchange studies of DNA structure. Proc. Natl Acad. Sci. USA 53, 363–370 (1965).
Google Scholar
von Hippel, P. H., Johnson, N. P. & Marcus, A. H. Fifty years of DNA ‘breathing’: reflections on old and new approaches. Biopolymers 99, 923–954 (2013).
Google Scholar
Frank-Kamenetskii, M. D. & Prakash, S. Fluctuations in the DNA double helix: a critical review. Phys. Life Rev. 11, 153–170 (2014).
Google Scholar
Manghi, M. & Destainville, N. Physics of base-pairing dynamics in DNA. Phys. Rep. 631, 1–41 (2016).
Google Scholar
McGhee, J. D. & Von Hippel, P. H. Formaldehyde as a probe of DNA structure. 4. Mechanism of the initial reaction of formaldehyde with DNA. Biochemistry 16, 3276–3293 (1977).
Google Scholar
Lukashin, A. V., Vologodskii, A. V., Frank-Kamenetskii, M. D. & Lyubchenko, Y. L. Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde. J. Mol. Biol. 108, 665–682 (1976).
Google Scholar
Guéron, M. & Leroy, J.-L. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261, 383–413 (1995).
Google Scholar
Leroy, J. L., Kochoyan, M., Huynh-Dinh, T. & Guéron, M. Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. J. Mol. Biol. 200, 223–238 (1988).
Google Scholar
Várnai, P., Canalia, M. & Leroy, J.-L. Opening mechanism of G·T/U pairs in DNA and RNA duplexes: a combined study of imino proton exchange and molecular dynamics simulation. J. Am. Chem. Soc. 126, 14659–14667 (2004).
Google Scholar
Giudice, E., Várnai, P. & Lavery, R. Base pair opening within B‐DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res. 31, 1434–1443 (2003).
Google Scholar
Priyakumar, U. D. & MacKerell, A. D. Computational approaches for investigating base flipping in oligonucleotides. Chem. Rev. 106, 489–505 (2006).
Google Scholar
Coman, D. & Russu, I. M. A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys. J. 89, 3285–3292 (2005).
Google Scholar
Hoogsteen, K. The structure of crystals containing a hydrogen-bonded complex of 1-methylthymine and 9-methyladenine. Acta Crystallogr. 12, 822–823 (1959).
Google Scholar
Palmer, A. G. & Massi, F. Characterization of the dynamics of biomacromolecules using rotating-frame spin relaxation NMR spectroscopy. Chem. Rev. 106, 1700–1719 (2006).
Google Scholar
Ray, D. & Andricioaei, I. Free energy landscape and conformational kinetics of hoogsteen base pairing in DNA vs. RNA. Biophys. J. 119, 1568–1579 (2020).
Google Scholar
Vreede, J., Pérez de Alba Ortíz, A., Bolhuis, P. G. & Swenson, D. W. Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA. Nucleic Acids Res. 47, 11069–11076 (2019).
Google Scholar
Krueger, A., Protozanova, E. & Frank-Kamenetskii, M. D. Sequence-dependent basepair opening in DNA double helix. Biophys. J. 90, 3091–3099 (2006).
Google Scholar
Rangadurai, A. et al. Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA? Nucleic Acids Res. 46, 11099–11114 (2018).
Google Scholar
Nonin, S., Leroy, J.-L. & Guéron, M. Terminal base pairs of oligodeoxynucleotides: imino proton exchange and fraying. Biochemistry 34, 10652–10659 (1995).
Google Scholar
Sanstead, P. J., Stevenson, P. & Tokmakoff, A. Sequence-dependent mechanism of DNA oligonucleotide dehybridization resolved through infrared spectroscopy. J. Am. Chem. Soc. 138, 11792–11801 (2016).
Google Scholar
Pörschke, D. A direct measurement of the unzippering rate of a nucleic acid double helix. Biophys. Chem. 2, 97–101 (1974).
Google Scholar
Chen, X., Zhou, Y., Qu, P. & Zhao, X. S. Base-by-base dynamics in DNA hybridization probed by fluorescence correlation spectroscopy. J. Am. Chem. Soc. 130, 16947–16952 (2008).
Google Scholar
Araque, J. & Robert, M. Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity. J. Chem. Phys. 144, 125101 (2016).
Google Scholar
Sanstead, P. J. & Tokmakoff, A. A lattice model for the interpretation of oligonucleotide hybridization experiments. J. Chem. Phys. 150, 185104 (2019).
Google Scholar
Zgarbová, M., Otyepka, M., Sponer, J., Lankas, F. & Jurecka, P. Base pair fraying in molecular dynamics simulations of DNA and RNA. J. Chem. Theory Comput. 10, 3177–3189 (2014).
Google Scholar
Pinamonti, G., Paul, F., Noé, F., Rodriguez, A. & Bussi, G. The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys. 150, 154123 (2019).
Google Scholar
Dabin, A. & Stirnemann, G. Atomistic simulations of RNA duplex thermal denaturation: sequence-and forcefield-dependence. Biophys. Chem. 307, 107167 (2024).
Google Scholar
Patel, D. J. et al. Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution. Biochemistry 21, 428–436 (1982).
Google Scholar
Ashwood, B. et al. Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics. Biophys. J. 123, 118–133 (2024).
Google Scholar
Plumridge, A., Andresen, K. & Pollack, L. Visualizing disordered single-stranded RNA: connecting sequence, structure, and electrostatics. J. Am. Chem. Soc. 142, 109–119 (2019).
Google Scholar
Grotz, K. K. et al. Dispersion correction alleviates dye stacking of single-stranded DNA and RNA in simulations of single-molecule fluorescence experiments. J. Phys. Chem. B 122, 11626–11639 (2018).
Google Scholar
Gao, Y., Wolf, L. K. & Georgiadis, R. M. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Res. 34, 3370–3377 (2006).
Google Scholar
Hata, H., Kitajima, T. & Suyama, A. Influence of thermodynamically unfavorable secondary structures on DNA hybridization kinetics. Nucleic Acids Res. 46, 782–791 (2018).
Google Scholar
Schreck, J. S. et al. DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization. Nucleic Acids Res. 43, 6181–6190 (2015).
Google Scholar
Nakano, M. et al. Local thermodynamics of the water molecules around single-and double-stranded DNA studied by grid inhomogeneous solvation theory. Chem. Phys. Lett. 660, 250–255 (2016).
Google Scholar
Chen, H. et al. Ionic strength-dependent persistence lengths of single-stranded RNA and DNA. Proc. Natl Acad. Sci. USA 109, 799–804 (2012).
Google Scholar
Meisburger, S. P. et al. Polyelectrolyte properties of single stranded DNA measured using SAXS and single‐molecule FRET: beyond the wormlike chain model. Biopolymers 99, 1032–1045 (2013).
Google Scholar
Sim, A. Y., Lipfert, J., Herschlag, D. & Doniach, S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Phys. Rev. E 86, 021901 (2012).
Google Scholar
Viader-Godoy, X., Manosas, M. & Ritort, F. Stacking correlation length in single-stranded DNA. Nucleic Acids Res. 52, 13243–13254 (2024).
Google Scholar
Jacobson, D. R., McIntosh, D. B., Stevens, M. J., Rubinstein, M. & Saleh, O. A. Single-stranded nucleic acid elasticity arises from internal electrostatic tension. Proc. Natl Acad. Sci. USA 114, 5095–5100 (2017).
Google Scholar
McIntosh, D. B., Duggan, G., Gouil, Q. & Saleh, O. A. Sequence-dependent elasticity and electrostatics of single-stranded DNA: signatures of base-stacking. Biophys. J. 106, 659–666 (2014).
Google Scholar
Banerjee, A., Anand, M., Kalita, S. & Ganji, M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. Nat. Nanotechnol. 18, 1474–1482 (2023).
Google Scholar
Oweida, T. J., Kim, H. S., Donald, J. M., Singh, A. & Yingling, Y. G. Assessment of AMBER force fields for simulations of ssDNA. J. Chem. Theory Comput. 17, 1208–1217 (2021).
Google Scholar
Bottaro, S., Bussi, G., Kennedy, S. D., Turner, D. H. & Lindorff-Larsen, K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Sci. Adv. 4, eaar8521 (2018).
Google Scholar
Wetmur, J. G. & Davidson, N. Kinetics of renaturation of DNA. J. Mol. Biol. 31, 349–370 (1968).
Google Scholar
Schickinger, M., Zacharias, M. & Dietz, H. Tethered multifluorophore motion reveals equilibrium transition kinetics of single DNA double helices. Proc. Natl Acad. Sci. USA 115, E7512–E7521 (2018).
Google Scholar
Chen, Y.-I. et al. Measuring DNA hybridization kinetics in live cells using a time-resolved 3D single-molecule tracking method. J. Am. Chem. Soc. 141, 15747–15750 (2019).
Google Scholar
Wong, K. L. & Liu, J. Factors and methods to modulate DNA hybridization kinetics. Biotechnol. J. 16, 2000338 (2021).
Google Scholar
Pörschke, D., Uhlenbeck, O. C. & Martin, F. H. Thermodynamics and kinetics of the helix‐coil transition of oligomers containing GC base pairs. Biopolymers 12, 1313–1335 (1973).
Google Scholar
Eigen, M. Methods for investigation of ionic reactions in aqueous solutions with half-times as short as 10–9 sec. Application to neutralization and hydrolysis reactions. Discuss. Faraday Soc. 17, 194–205 (1954).
Google Scholar
Rauzan, B. et al. Kinetics and thermodynamics of DNA, RNA, and hybrid duplex formation. Biochemistry 52, 765–772 (2013).
Google Scholar
Williams, A. P., Longfellow, C. E., Freier, S. M., Kierzek, R. & Turner, D. H. Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28, 4283–4291 (1989).
Google Scholar
Carrillo-Nava, E., Mejía-Radillo, Y. & Hinz, H.-J. Dodecamer DNA duplex formation is characterized by second-order kinetics, positive activation energies, and a dependence on sequence and Mg2+ ion concentration. Biochemistry 47, 13153–13157 (2008).
Google Scholar
Saunders, M. & Ross, P. D. A simple model of the reaction between polyadenylic acid and polyuridylic acid. Biochem. Biophys. Res. Commun. 3, 314–318 (1960).
Google Scholar
Thompson, M. C. et al. Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nat. Chem. 11, 1058–1066 (2019).
Google Scholar
Narayanan, R. et al. Exploring the energy landscape of nucleic acid hairpins using laser temperature-jump and microfluidic mixing. J. Am. Chem. Soc. 134, 18952–18963 (2012).
Google Scholar
Ding, F. et al. Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain. Nucleic Acids Res. 50, 12082–12093 (2022).
Google Scholar
Hoose, A., Vellacott, R., Storch, M., Freemont, P. S. & Ryadnov, M. G. DNA synthesis technologies to close the gene writing gap. Nat. Rev. Chem. 7, 144–161 (2023).
Google Scholar
Schoen, I., Krammer, H. & Braun, D. Hybridization kinetics is different inside cells. Proc. Natl Acad. Sci. USA 106, 21649–21654 (2009).
Google Scholar
Menssen, R. J. & Tokmakoff, A. Length-dependent melting kinetics of short DNA oligonucleotides using temperature-jump IR spectroscopy. J. Phys. Chem. B 123, 756–767 (2019).
Google Scholar
Lukacs, G. L. et al. Size-dependent DNA mobility in cytoplasm and nucleus. J. Biol. Chem. 275, 1625–1629 (2000).
Google Scholar
Ashwood, B. et al. Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs. Biophys. J. 122, 3323–3339 (2023).
Google Scholar
Xiao, S., Sharpe, D. J., Chakraborty, D. & Wales, D. J. Energy landscapes and hybridization pathways for DNA hexamer duplexes. J. Phys. Chem. Lett. 10, 6771–6779 (2019).
Google Scholar
Murugan, R. Lattice model on the rate of DNA hybridization. Phys. Rev. E 105, 064410 (2022).
Google Scholar
Grabenhorst, L., Sturzenegger, F., Hasler, M., Schuler, B. & Tinnefeld, P. Single-molecule FRET at 10 MHz count rates. J. Am. Chem. Soc. 146, 3539–3544 (2024).
Google Scholar
Bastos, M., Castro, V., Mrevlishvili, G. & Teixeira, J. Hydration of ds-DNA and ss-DNA by neutron quasielastic scattering. Biophys. J. 86, 3822–3827 (2004).
Google Scholar
Kuchuk, K. & Sivan, U. Hydration structure of a single DNA molecule revealed by frequency-modulation atomic force microscopy. Nano Lett. 18, 2733–2737 (2018).
Google Scholar
Tripathi, P., Firouzbakht, A., Gruebele, M. & Wanunu, M. Direct observation of single-protein transition state passage by nanopore ionic current jumps. J. Phys. Chem. Lett. 13, 5918–5924 (2022).
Google Scholar
Sturzenegger, F. et al. Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nat. Commun. 9, 4708 (2018).
Google Scholar
Kim, J.-Y. & Chung, H. S. Disordered proteins follow diverse transition paths as they fold and bind to a partner. Science 368, 1253–1257 (2020).
Google Scholar
Wilson, H. & Wang, Q. ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling. Nat. Methods 18, 816–820 (2021).
Google Scholar
Jang, S. S. et al. Characterizing the conformational free-energy landscape of RNA stem-loops using single-molecule field-effect transistors. J. Am. Chem. Soc. 145, 402–412 (2022).
Google Scholar
Needham, L.-M. et al. Label-free detection and profiling of individual solution-phase molecules. Nature 629, 1062–1068 (2024).
Google Scholar
Zerze, Gl. H., Stillinger, F. H. & Debenedetti, P. G. Thermodynamics of DNA hybridization from atomistic simulations. J. Phys. Chem. B 125, 771–779 (2021).
Google Scholar
Love, O. et al. Assessing the current state of amber force field modifications for DNA — 2023 edition. J. Chem. Theory Comput. 19, 4299–4307 (2023).
Google Scholar
Liebl, K. & Zacharias, M. Tumuc1: a new accurate DNA force field consistent with high-level quantum chemistry. J. Chem. Theory Comput. 17, 7096–7105 (2021).
Google Scholar
Liebl, K. & Zacharias, M. Toward force fields with improved base stacking descriptions. J. Chem. Theory Comput. 19, 1529–1536 (2023).
Google Scholar
Liebl, K. & Zacharias, M. The development of nucleic acids force fields: from an unchallenged past to a competitive future. Biophys. J. 122, 2841–2851 (2022).
Google Scholar
Yoo, J., Winogradoff, D. & Aksimentiev, A. Molecular dynamics simulations of DNA–DNA and DNA–protein interactions. Curr. Opin. Struct. Biol. 64, 88–96 (2020).
Google Scholar
Kuhrova, P. et al. Improving the performance of the amber RNA force field by tuning the hydrogen-bonding interactions. J. Chem. Theory Comput. 15, 3288–3305 (2019).
Google Scholar
Pan, A. C. et al. Atomic-level characterization of protein–protein association. Proc. Natl Acad. Sci. USA 116, 4244–4249 (2019).
Google Scholar
Maciejczyk, M., Spasic, A., Liwo, A. & Scheraga, H. A. DNA duplex formation with a coarse-grained model. J. Chem. Theory Comput. 10, 5020–5035 (2014).
Google Scholar
Markegard, C. B., Fu, I. W., Reddy, K. A. & Nguyen, H. D. Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment. J. Phys. Chem. B 119, 1823–1834 (2015).
Google Scholar
Fritz, D., Koschke, K., Harmandaris, V. A., van der Vegt, N. F. & Kremer, K. Multiscale modeling of soft matter: scaling of dynamics. Phys. Chem. Chem. Phys. 13, 10412–10420 (2011).
Google Scholar
Ingólfsson, H. I. et al. The power of coarse graining in biomolecular simulations. Wiley Interdiscip. Rev. Comput. Mol. Sci. 4, 225–248 (2014).
Google Scholar
Hinckley, D. M., Freeman, G. S., Whitmer, J. K. & de Pablo, J. J. An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization. J. Chem. Phys. 139, 10B604_601 (2013).
Google Scholar
Ouldridge, T. E., Louis, A. A. & Doye, J. P. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model. J. Chem. Phys. 134, 02B627 (2011).
Google Scholar
Snodin, B. E. et al. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J. Chem. Phys. 142, 234901 (2015).
Google Scholar
Chakraborty, D., Hori, N. & Thirumalai, D. Sequence-dependent three interaction site model for single-and double-stranded DNA. J. Chem. Theory Comput. 14, 3763–3779 (2018).
Google Scholar
Bernetti, M. & Bussi, G. Integrating experimental data with molecular simulations to investigate RNA structural dynamics. Curr. Opin. Struct. Biol. 78, 102503 (2023).
Google Scholar
Chodera, J. D. & Noé, F. Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol. 25, 135–144 (2014).
Google Scholar
Husic, B. E. & Pande, V. S. Markov state models: from an art to a science. J. Am. Chem. Soc. 140, 2386–2396 (2018).
Google Scholar
Noé, F. et al. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc. Natl Acad. Sci. USA 108, 4822–4827 (2011).
Google Scholar
Remington, J. M., McCullagh, M. & Kohler, B. Molecular dynamics simulations of 2-aminopurine-labeled dinucleoside monophosphates reveal multiscale stacking kinetics. J. Phys. Chem. B 123, 2291–2304 (2019).
Google Scholar
Pinamonti, G. et al. Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput. 13, 926–934 (2017).
Google Scholar
Bozovic, O. et al. Real-time observation of ligand-induced allosteric transitions in a PDZ domain. Proc. Natl Acad. Sci. USA 117, 26031–26039 (2020).
Google Scholar
Wang, H., Xu, Z., Mao, S. & Granick, S. Experimental guidelines to image transient single-molecule events using graphene liquid cell electron microscopy. ACS Nano 16, 18526–18537 (2022).
Google Scholar
Varghese, N. et al. Binding of DNA nucleobases and nucleosides with graphene. ChemPhysChem 10, 206–210 (2009).
Google Scholar
Husale, B. S. et al. ssDNA binding reveals the atomic structure of graphene. Langmuir 26, 18078–18082 (2010).
Google Scholar
Truex, K., Chung, H. S., Louis, J. M. & Eaton, W. A. Testing landscape theory for biomolecular processes with single molecule fluorescence spectroscopy. Phys. Rev. Lett. 115, 018101 (2015).
Google Scholar
Gladrow, J., Ribezzi-Crivellari, M., Ritort, F. & Keyser, U. F. Experimental evidence of symmetry breaking of transition-path times. Nat. Commun. 10, 55 (2019).
Google Scholar
Neupane, K., Hoffer, N. Q. & Woodside, M. Measuring the local velocity along transition paths during the folding of single biological molecules. Phys. Rev. Lett. 121, 018102 (2018).
Google Scholar
Hoffer, N. Q., Neupane, K. & Woodside, M. T. Measuring the average shape of transition paths during the folding of a single biological molecule. Proc. Natl Acad. Sci. USA 116, 8125–8130 (2019).
Google Scholar
Hoffer, N. Q., Neupane, K. & Woodside, M. T. Observing the base-by-base search for native structure along transition paths during the folding of single nucleic acid hairpins. Proc. Natl Acad. Sci. USA 118, e2101006118 (2021).
Google Scholar
Lyons, A., Devi, A., Hoffer, N. Q. & Woodside, M. T. Quantifying the properties of nonproductive attempts at thermally activated energy-barrier crossing through direct observation. Phys. Rev. X 14, 011017 (2024).
Google Scholar
Neupane, K. et al. Transition path times for nucleic acid folding determined from energy-landscape analysis of single-molecule trajectories. Phys. Rev. Lett. 109, 068102 (2012).
Google Scholar
Pyo, A. G., Hoffer, N. Q., Neupane, K. & Woodside, M. T. Transition-path properties for folding reactions in the limit of small barriers. J. Chem. Phys. 149, 115101 (2018).
Google Scholar
Ansari, A. & Kuznetsov, S. V. Is hairpin formation in single-stranded polynucleotide diffusion-controlled? J. Phys. Chem. B 109, 12982–12989 (2005).
Google Scholar
Hori, N., Denesyuk, N. A. & Thirumalai, D. Frictional effects on RNA folding: speed limit and Kramers turnover. J. Phys. Chem. B 122, 11279–11288 (2018).
Google Scholar
Ngo, T. T. et al. Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability. Nat. Commun. 7, 10813 (2016).
Google Scholar
Rossetti, G. et al. The structural impact of DNA mismatches. Nucleic Acids Res. 43, 4309–4321 (2015).
Google Scholar
Sanstead, P. J., Ashwood, B., Dai, Q., He, C. & Tokmakoff, A. Oxidized derivatives of 5-methylcytosine alter the stability and dehybridization dynamics of duplex DNA. J. Phys. Chem. B 124, 1160–1174 (2020).
Google Scholar
Teng, X. & Hwang, W. Effect of methylation on local mechanics and hydration structure of DNA. Biophys. J. 114, 1791–1803 (2018).
Google Scholar
Sabahi, A., Guidry, J., Inamati, G. B., Manoharan, M. & Wittung-Stafshede, P. Hybridization of 2′-ribose modified mixed-sequence oligonucleotides: thermodynamic and kinetic studies. Nucleic Acids Res. 29, 2163–2170 (2001).
Google Scholar
Christensen, U., Jacobsen, N., Rajwanshi, V. K., Wengel, J. & Koch, T. Stopped-flow kinetics of locked nucleic acid (LNA)–oligonucleotide duplex formation: studies of LNA–DNA and DNA–DNA interactions. Biochem. J. 354, 481–484 (2001).
Google Scholar
Rajasekaran, T. et al. Backbone hydrocarbon-constrained nucleic acids modulate hybridization kinetics for RNA. J. Am. Chem. Soc. 144, 1941–1950 (2022).
Google Scholar
Gold, B., Stone, M. P. & Marky, L. A. Looking for Waldo: a potential thermodynamic signature to DNA damage. Acc. Chem. Res. 47, 1446–1454 (2014).
Google Scholar
Gelfand, C. A., Plum, G. E., Grollman, A. P., Johnson, F. & Breslauer, K. J. Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry 37, 7321–7327 (1998).
Google Scholar
Testa, S. M., Disney, M. D., Turner, D. H. & Kierzek, R. Thermodynamics of RNA–RNA duplexes with 2- or 4-thiouridines: implications for antisense design and targeting a group I intron. Biochemistry 38, 16655–16662 (1999).
Google Scholar
Wang, D., Kreutzer, D. A. & Essigmann, J. M. Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions. Mutat. Res. 400, 99–115 (1998).
Google Scholar
Wang, W., Xu, J., Chong, J. & Wang, D. Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair. 71, 43–55 (2018).
Google Scholar
Hardwick, J. S., Lane, A. N. & Brown, T. Epigenetic modifications of cytosine: biophysical properties, regulation, and function in mammalian DNA. BioEssays 40, 1700199 (2018).
Google Scholar
Jones, J. D., Monroe, J. & Koutmou, K. S. A molecular‐level perspective on the frequency, distribution, and consequences of messenger RNA modifications. Wiley Interdiscip. Rev. RNA 11, e1586 (2020).
Google Scholar
Shen, X. & Corey, D. R. Chemistry, mechanism and clinical status of antisense oligonucleotides and duplex RNAs. Nucleic Acids Res. 46, 1584–1600 (2018).
Google Scholar
Bauer, J., Reichl, A. & Tinnefeld, P. Kinetic referencing allows identification of epigenetic cytosine modifications by single-molecule hybridization kinetics and superresolution DNA-PAINT microscopy. ACS Nano 18, 1496–1503 (2023).
Google Scholar
Todisco, M., Ding, D. & Szostak, J. W. Transient states during oligonucleotides hybridization: insights from annealing kinetics of mismatches and bulges. Nucleic Acids Res. 52, 2174–2187 (2023).
Google Scholar
Zhao, X.-C. et al. 5-Methyl-cytosine stabilizes DNA but hinders DNA hybridization revealed by magnetic tweezers and simulations. Nucleic Acids Res. 50, 12344–12354 (2022).
Google Scholar
Liu, B. et al. A quantitative model predicts how m6A reshapes the kinetic landscape of nucleic acid hybridization and conformational transitions. Nat. Commun. 12, 5201 (2021).
Google Scholar
Tawa, K. & Knoll, W. Mismatching base‐pair dependence of the kinetics of DNA–DNA hybridization studied by surface plasmon fluorescence spectroscopy. Nucleic Acids Res. 32, 2372–2377 (2004).
Google Scholar
Rajasekaran, T. et al. Systematic investigation of tether length and phosphorus configuration in backbone constrained macrocyclic nucleic acids to modulate binding kinetics for RNA. J. Org. Chem. 88, 3599–3614 (2023).
Google Scholar
Naiser, T., Kayser, J., Mai, T., Michel, W. & Ott, A. Position dependent mismatch discrimination on DNA microarrays — experiments and model. BMC Bioinformatics 9, 509 (2008).
Google Scholar
Chen, J., Dupradeau, F.-Y., Case, D. A., Turner, C. J. & Stubbe, J. DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res. 36, 253–262 (2008).
Google Scholar
Kierzek, R., Burkard, M. E. & Turner, D. H. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38, 14214–14223 (1999).
Google Scholar
Woodside, M. T. et al. Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid. Science 314, 1001–1004 (2006).
Google Scholar
Manuel, A. P., Lambert, J. & Woodside, M. T. Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories. Proc. Natl Acad. Sci. USA 112, 7183–7188 (2015).
Google Scholar
McCauley, M. J. et al. Quantifying the stability of oxidatively damaged DNA by single-molecule DNA stretching. Nucleic Acids Res. 46, 4033–4043 (2018).
Google Scholar
Nguyen, H. T., Hori, N. & Thirumalai, D. Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics. Nat. Chem. 14, 775–785 (2022).
Google Scholar
Bellini, T. et al. Liquid crystal self-assembly of random-sequence DNA oligomers. Proc. Natl Acad. Sci. USA 109, 1110–1115 (2012).
Google Scholar
Snodin, B. E. et al. Direct simulation of the self-assembly of a small DNA origami. ACS Nano 10, 1724–1737 (2016).
Google Scholar
Ouldridge, T. E. DNA nanotechnology: understanding and optimisation through simulation. Mol. Phys. 113, 1–15 (2015).
Google Scholar
Fonseca, P. et al. Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly. J. Chem. Phys. 148, 134910 (2018).
Google Scholar
Wang, J. et al. Probing heterogeneous folding pathways of DNA origami self-assembly at the molecular level with atomic force microscopy. Nano Lett. 22, 7173–7179 (2022).
Google Scholar
Simmel, F. C., Yurke, B. & Singh, H. R. Principles and applications of nucleic acid strand displacement reactions. Chem. Rev. 119, 6326–6369 (2019).
Google Scholar
Srinivas, N. et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 41, 10641–10658 (2013).
Google Scholar
James, P. L., Brown, T. & Fox, K. R. Thermodynamic and kinetic stability of intermolecular triple helices containing different proportions of C+*GC and T*AT triplets. Nucleic Acids Res. 31, 5598–5606 (2003).
Google Scholar
Hu, Y., Cecconello, A., Idili, A., Ricci, F. & Willner, I. Triplex DNA nanostructures: from basic properties to applications. Angew. Chem. Int. Ed. Engl. 56, 15210–15233 (2017).
Google Scholar
Ouldridge, T. E., Johnston, I. G., Louis, A. A. & Doye, J. P. The self-assembly of DNA holliday junctions studied with a minimal model. J. Chem. Phys. 130, 065101 (2009).
Google Scholar
Wang, W. et al. Holliday junction thermodynamics and structure: coarse-grained simulations and experiments. Sci. Rep. 6, 22863 (2016).
Google Scholar
Zhou, L. et al. Non-enzymatic primer extension with strand displacement. eLife 8, e51888 (2019).
Google Scholar
Hong, F. & Šulc, P. An emergent understanding of strand displacement in RNA biology. J. Struct. Biol. 207, 241–249 (2019).
Google Scholar
Machinek, R. R., Ouldridge, T. E., Haley, N. E., Bath, J. & Turberfield, A. J. Programmable energy landscapes for kinetic control of DNA strand displacement. Nat. Commun. 5, 5324 (2014).
Google Scholar
Irmisch, P., Ouldridge, T. E. & Seidel, R. Modeling DNA-strand displacement reactions in the presence of base-pair mismatches. J. Am. Chem. Soc. 142, 11451–11463 (2020).
Google Scholar
Broadwater, D. B., Cook, A. W. & Kim, H. D. First passage time study of DNA strand displacement. Biophys. J. 120, 2400–2412 (2021).
Google Scholar
Broadwater, D. B. & Kim, H. D. The effect of basepair mismatch on DNA strand displacement. Biophys. J. 110, 1476–1484 (2016).
Google Scholar
Šulc, P., Ouldridge, T. E., Romano, F., Doye, J. P. & Louis, A. A. Modelling toehold-mediated RNA strand displacement. Biophys. J. 108, 1238–1247 (2015).
Google Scholar
Smith, F. G., Goertz, J. P., Jurinović, K., Stevens, M. M. & Ouldridge, T. E. Strong sequence–dependence in RNA/DNA hybrid strand displacement kinetics. Nanoscale 16, 17624–17637 (2024).
Google Scholar
Ratajczyk, E. J. et al. Controlling DNA-RNA strand displacement kinetics with base distribution. Preprint at bioRxiv https://doi.org/10.1101/2024.08.06.606789v1 (2024).
Zhang, D. Y. & Winfree, E. Control of DNA strand displacement kinetics using toehold exchange. J. Am. Chem. Soc. 131, 17303–17314 (2009).
Google Scholar
Yurke, B. & Mills, A. P. Using DNA to power nanostructures. Genet. Program. Evol. Mach. 4, 111–122 (2003).
Google Scholar
Reynaldo, L. P., Vologodskii, A. V., Neri, B. P. & Lyamichev, V. I. The kinetics of oligonucleotide replacements. J. Mol. Biol. 297, 511–520 (2000).
Google Scholar
Di Michele, L. et al. Effect of inert tails on the thermodynamics of DNA hybridization. J. Am. Chem. Soc. 136, 6538–6541 (2014).
Google Scholar
Todisco, M., Radakovic, A. & Szostak, J. W. RNA complexes with nicks and gaps: thermodynamic and kinetic effects of coaxial stacking and dangling ends. J. Am. Chem. Soc. 146, 18083–18094 (2024).
Google Scholar
Abraham Punnoose, J. et al. High-throughput single-molecule quantification of individual base stacking energies in nucleic acids. Nat. Commun. 14, 631 (2023).
Google Scholar
Walbrun, A. et al. Single-molecule force spectroscopy of toehold-mediated strand displacement. Nat. Commun. 15, 7564 (2024).
Google Scholar
Ivani, I. et al. Parmbsc1: a refined force field for DNA simulations. Nat. Methods 13, 55–58 (2016).
Google Scholar
Chaudhury, S. & Makarov, D. E. A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements. J. Chem. Phys. 133, 034118 (2010).
Google Scholar
Marky, L. A. & Breslauer, K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26, 1601–1620 (1987).
Google Scholar
Mergny, J.-L. & Lacroix, L. Analysis of thermal melting curves. Oligonucleotides 13, 515–537 (2003).
Google Scholar
Majikes, J. M., Zwolak, M. & Liddle, J. A. Best practice for improved accuracy: a critical reassessment of van’t Hoff analysis of melt curves. Biophys. J. 121, 1986–2001 (2022).
Google Scholar
Bernasconi, C. Relaxation Kinetics (Academic, 1976).
Hopfinger, M. C., Kirkpatrick, C. C. & Znosko, B. M. Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides. Nucleic Acids Res. 48, 8901–8913 (2020).
Google Scholar
Denisov, V. P., Carlström, G., Venu, K. & Halle, B. Kinetics of DNA hydration. J. Mol. Biol. 268, 118–136 (1997).
Google Scholar
Duboué-Dijon, E., Fogarty, A. C., Hynes, J. T. & Laage, D. Dynamical disorder in the DNA hydration shell. J. Am. Chem. Soc. 138, 7610–7620 (2016).
Google Scholar
Dewey, T. & Turner, D. H. Laser temperature-jump study of stacking in adenylic acid polymers. Biochemistry 18, 5757–5762 (1979).
Google Scholar
Lieblein, A. L., Buck, J., Schlepckow, K., Fürtig, B. & Schwalbe, H. Time‐resolved NMR spectroscopic studies of DNA i‐motif folding reveal kinetic partitioning. Angew. Chem. Int. Ed. Engl. 51, 250–253 (2012).
Google Scholar
Stellwagen, E., Lu, Y. & Stellwagen, N. C. Unified description of electrophoresis and diffusion for DNA and other polyions. Biochemistry 42, 11745–11750 (2003).
Google Scholar
Wirth, A. J., Liu, Y., Prigozhin, M. B., Schulten, K. & Gruebele, M. Comparing fast pressure jump and temperature jump protein folding experiments and simulations. J. Am. Chem. Soc. 137, 7152–7159 (2015).
Google Scholar
Su, H. et al. Massively parallelized molecular force manipulation with on-demand thermal and optical control. J. Am. Chem. Soc. 143, 19466–19473 (2021).
Google Scholar
Yin, Y. et al. Dynamics of spontaneous flipping of a mismatched base in DNA duplex. Proc. Natl Acad. Sci. USA 111, 8043–8048 (2014).
Google Scholar
Applequist, J. & Damle, V. Thermodynamics of the helix-coil equilibrium in oligoadenylic acid from hypochromicity studies. J. Am. Chem. Soc. 87, 1450–1458 (1965).
Google Scholar
Menssen, R. J., Kimmel, G. J. & Tokmakoff, A. Investigation into the mechanism and dynamics of DNA association and dissociation utilizing kinetic Monte Carlo simulations. J. Chem. Phys. 154, 045101 (2021).
Google Scholar
Hudson, G. A., Bloomingdale, R. J. & Znosko, B. M. Thermodynamic contribution and nearest-neighbor parameters of pseudouridine–adenosine base pairs in oligoribonucleotides. RNA 19, 1474–1482 (2013).
Google Scholar
Nardo, L. et al. Effects of non-CpG site methylation on DNA thermal stability: a fluorescence study. Nucleic Acids Res. 43, 10722–10733 (2015).
Google Scholar
Kierzek, E. et al. Secondary structure prediction for RNA sequences including N6-methyladenosine. Nat. Commun. 13, 1271 (2022).
Google Scholar
Zhou, H. et al. m1A and m1G disrupt A-RNA structure through the intrinsic instability of Hoogsteen base pairs. Nat. Struct. Mol. Biol. 23, 803–810 (2016).
Google Scholar
Gruber, D. R. et al. Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation. Nucleic Acids Res. 46, 10827–10839 (2018).
Google Scholar
Ovcherenko, S. S. et al. Dynamics of 8-oxoguanine in DNA: decisive effects of base pairing and nucleotide context. J. Am. Chem. Soc. 145, 5613–5617 (2023).
Google Scholar
Rangadurai, A. et al. Measuring thermodynamic preferences to form non-native conformations in nucleic acids using ultraviolet melting. Proc. Natl Acad. Sci. USA 119, e2112496119 (2022).
Google Scholar
Dai, Q. et al. Weakened N3 hydrogen bonding by 5-formylcytosine and 5-carboxylcytosine reduces their base-pairing stability. ACS Chem. Biol. 11, 470–477 (2016).
Google Scholar
Kou, Y., Koag, M.-C. & Lee, S. N7 methylation alters hydrogen-bonding patterns of guanine in duplex DNA. J. Am. Chem. Soc. 137, 14067–14070 (2015).
Google Scholar
Afek, A. et al. DNA mismatches reveal conformational penalties in protein–DNA recognition. Nature 587, 291–296 (2020).
Google Scholar
Rohs, R. et al. Origins of specificity in protein–DNA recognition. Annu. Rev. Biochem. 79, 233–269 (2010).
Google Scholar