Watson, J. D. & Crick, F. H. Molecular construction of nucleic acids; a construction for deoxyribose nucleic acid. Nature 171, 737–738 (1953).
Kool, E. T. Hydrogen bonding, base stacking, and steric results in DNA replication. Annu. Rev. Biophys. Biomol. Struct. 30, 1–22 (2001).
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).
Schulz, E. C. et al. Intermolecular base stacking mediates RNA–RNA interplay in a crystal construction of the RNA chaperone Hfq. Sci. Rep. 7, 9903 (2017).
Kervio, E., Hochgesand, A., Steiner, U. E. & Richert, C. Templating effectivity of bare DNA. Proc. Natl Acad. Sci. USA 107, 12074–12079 (2010).
Gerling, T., Wagenbauer, Okay. F., Neuner, A. M. & Dietz, H. Dynamic DNA units and assemblies shaped by shape-complementary, non-base pairing 3D elements. Science 347, 1446–1452 (2015).
Uehara, S. et al. 3′ Poly (dA)-tailed thrombin DNA aptamer to extend DNase-resistance and clotting inhibitory exercise. Bull. Chem. Soc. Jpn 81, 1485–1491 (2008).
Do, N. Q., Lim, Okay. W., Teo, M. H., Heddi, B. & Phan, A. T. Stacking of G-quadruplexes: NMR construction of a G-rich oligonucleotide with potential anti-HIV and anticancer exercise. Nucleic Acids Res. 39, 9448–9457 (2011).
Modi, S. et al. A DNA nanomachine that maps spatial and temporal pH modifications inside dwelling cells. Nat. Nanotechnol. 4, 325–330 (2009).
Surana, S., Shenoy, A. R. & Krishnan, Y. Designing DNA nanodevices for compatibility with the immune system of upper organisms. Nat. Nanotechnol. 10, 741–747 (2015).
Sigl, C. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021).
Hellmeier, J. et al. DNA origami show the distinctive stimulatory energy of single pMHCs as T cell antigens. Proc. Natl Acad. Sci. USA 118, e2016857118 (2021).
Woo, S. & Rothemund, P. W. Okay. Programmable molecular recognition based mostly on the geometry of DNA nanostructures. Nat. Chem. 3, 620–627 (2011).
Wang, R., Kuzuya, A., Liu, W. & Seeman, N. C. Blunt-ended DNA stacking interactions in a 3-helix motif. Chem. Commun. 46, 4905–4907 (2010).
Pumm, A.-Okay. et al. A DNA origami rotary ratchet motor. Nature 607, 492–498 (2022).
Bommarito, S., Peyret, N. & SantaLucia, J. Jr Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res. 28, 1929–1934 (2000).
Petersheim, M. & Turner, D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry 22, 256–263 (1983).
Gotoh, O. & Tagashira, Y. Stabilities of nearest-neighbor doublets in double-helical DNA decided by becoming calculated melting profiles to noticed profiles. Biopolymers 20, 1033–1042 (1981).
Vologodskii, A. V., Amirikyan, B., Lyubchenko, Y. L. & Frank-Kamenetskii, M. Allowance for heterogeneous stacking within the DNA helix-coil transition idea. J. Biomol. Struct. Dyn. 2, 131–148 (1984).
Breslauer, Okay. J., Frank, R., Blöcker, H. & Marky, L. A. Predicting DNA duplex stability from the bottom sequence. Proc. Natl Acad. Sci. USA 83, 3746–3750 (1986).
Delcourt, S. G. & Blake, R. Stacking energies in DNA. J. Biol. Chem. 266, 15160–15169 (1991).
Doktycz, M. J., Goldstein, R. F., Paner, T. M., Gallo, F. J. & Benight, A. S. Research of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with completely different duplex stem sequences linked by T4 endloops: Analysis of the closest‐neighbor stacking interactions in DNA. Biopolymers 32, 849–864 (1992).
SantaLucia, J., Allawi, H. T. & Seneviratne, P. A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555–3562 (1996).
Sugimoto, N., Nakano, S.-i, Yoneyama, M. & Honda, Okay.-I. Improved thermodynamic parameters and helix initiation issue to foretell stability of DNA duplexes. Nucleic Acids Res. 24, 4501–4505 (1996).
SantaLucia, J. Jr A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460–1465 (1998).
Protozanova, E., Yakovchuk, P. & Frank-Kamenetskii, M. D. Stacked–unstacked equilibrium on the nick web site of DNA. J. Mol. Biol. 342, 775–785 (2004).
Lane, M. J. et al. The thermodynamic benefit of DNA oligonucleotide ‘stacking hybridization’ reactions: energetics of a DNA nick. Nucleic Acids Res. 25, 611–617 (1997).
Pyshnyi, D. & Ivanova, E. Thermodynamic parameters of coaxial stacking on stacking hybridization of oligodeoxyribonucleotides. Russ. Chem. Bull. 51, 1145–1155 (2002).
Kilchherr, F. et al. Single-molecule dissection of stacking forces in DNA. Science 353, aaf5508 (2016).
Abraham Punnoose, J. et al. Excessive-throughput single-molecule quantification of particular person base stacking energies in nucleic acids. Nat. Commun. 14, 631 (2023).
Rieu, M. et al. Parallel, linear, and subnanometric 3D monitoring of microparticles with Stereo Darkfield Interferometry. Sci. Adv. 7, eabe3902 (2021).
Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. Tremendous-resolution microscopy with DNA-PAINT. Nat. Protoc. 12, 1198–1228 (2017).
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).
Ganji, M., Schlichthaerle, T., Eklund, A. S., Strauss, S. & Jungmann, R. Quantitative evaluation of labeling probes for super-resolution microscopy utilizing designer DNA nanostructures. ChemPhysChem 22, 911–914 (2021).
Vasiliskov, V. A., Prokopenko, D. V. & Mirzabekov, A. D. Parallel multiplex thermodynamic evaluation of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips. Nucleic Acids Res. 29, 2303–2313 (2001).
Strauss, S. & Jungmann, R. As much as 100-fold speed-up and multiplexing in optimized DNA-PAINT. Nat. Strategies 17, 789–791 (2020).
Schickinger, M., Zacharias, M. & Dietz, H. Tethered multifluorophore movement reveals equilibrium transition kinetics of single DNA double helices. Proc. Natl Acad. Sci. USA 115, E7512–E7521 (2018).
Eklund, A. S., Ganji, M., Gavins, G., Seitz, O. & Jungmann, R. Peptide-PAINT super-resolution imaging utilizing transient coiled coil interactions. Nano Lett. 20, 6732–6737 (2020).
Cisse, I. I., Kim, H. & Ha, T. A rule of seven in Watson–Crick base-pairing of mismatched sequences. Nat. Struct. Mol. Biol. 19, 623–627 (2012).
Wong, Okay.-Y. & Pettitt, B. M. The pathway of oligomeric DNA melting investigated by molecular dynamics simulations. Biophys. J. 95, 5618–5626 (2008).
Andrews, R. et al. Transient DNA binding to gapped DNA substrates hyperlinks DNA sequence to the single-molecule kinetics of protein–DNA interactions. Preprint at bioRxiv https://doi.org/10.1101/2022.02.27.482175 (2022).
Ganji, M., Docter, M., Le Grice, S. F. & Abbondanzieri, E. A. DNA binding proteins discover a number of native configurations throughout docking through speedy rebinding. Nucleic Acids Res. 44, 8376–8384 (2016).
Hertel, S. et al. The soundness and variety of nucleating interactions decide DNA hybridization charges within the absence of secondary construction. Nucleic Acids Res. 50, 7829–7841 (2022).
Zacharias, M. Base-pairing and base-stacking contributions to double-stranded DNA formation. J. Phys. Chem. B 124, 10345–10352 (2020).
Pyshnyi, D. V. et al. Thermodynamic evaluation of stacking hybridization of oligonucleotides with DNA template. J. Biomol. Struct. Dyn. 19, 555–570 (2001).
Krueger, A., Protozanova, E. & Frank-Kamenetskii, M. D. Sequence-dependent basepair opening in DNA double helix. Biophys. J. 90, 3091–3099 (2006).
Ouldridge, T. E., Louis, A. A. & Doye, J. P. Okay. Structural, mechanical, and thermodynamic properties of a coarse-grained DNA mannequin. J. Chem. Phys. 134, 085101 (2011).
Maffeo, C., Luan, B. & Aksimentiev, A. Finish-to-end attraction of duplex DNA. Nucleic Acids Res. 40, 3812–3821 (2012).
Rohloff, J. C. et al. Nucleic acid ligands with protein-like aspect chains: modified aptamers and their use as diagnostic and therapeutic brokers. Mol. Ther. Nucleic Acids 3, e201 (2014).
He, Y. et al. Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra. Nature 452, 198–201 (2008).
Wade, O. Okay. et al. 124-color super-resolution imaging by engineering DNA-PAINT blinking kinetics. Nano Lett. 19, 2641–2646 (2019).
Ho, H. N., Zalami, D., Köhler, J., van Oijen, A. M. & Ghodke, H. Identification of a number of kinetic populations of DNA-binding proteins in dwell cells. Biophys. J. 117, 950–961 (2019).
Jungmann, R. et al. Multiplexed 3D mobile super-resolution imaging with DNA-PAINT and Change-PAINT. Nat. Strategies 11, 313–318 (2014).
