Nucleic acid strand displacement – from DNA nanotechnology to translational regulation

References

• Simmel FC, Yurke B, Singh HR. Principles and applications of nucleic acid strand displacement reactions. Chem Rev 2019 May 22;119(10):6326–6369.
   PubMed Web of Science ®Google Scholar
• Lee CS, Davis RW, Davidson N. A physical study by electron microscopy of the terminally repetitious, circularly permuted DNA from the coliphage particles of Escherichia coli 15. J Mol Biol. 1970;48(1):1–22.
   PubMed Web of Science ®Google Scholar
• Broker TR, Lehman IR. Branched Dna molecules - intermediates in T4 recombination. J Mol Biol. 1971;60(1):131- &.
   PubMed Web of Science ®Google Scholar
• Klein M, Eslami-Mossallam B, Arroyo DG, et al. Hybridization kinetics explains CRISPR-Cas off-targeting rules. Cell Rep. 2018;22(6):1413–1423. DOI:10.1016/j.celrep.2018.01.045
   PubMed Web of Science ®Google Scholar
• Rutkauskas M, Songailiene I, Irmisch P, et al. A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex. Nat Commun. 2022 Dec 3;13(1):7460.
   PubMed Web of Science ®Google Scholar
• Green C, Tibbetts C. Reassociation rate limited displacement of DNA-Strands by branch migration. Nucleic Acids Res. 1981;9(8):1905–1918.
   PubMed Web of Science ®Google Scholar
• Panyutin I, Hsieh P. The kinetics of spontaneous DNA branch migration. Proc Natl Acad Sci USA. 1994;91(6):2021–2025.
   PubMed Web of Science ®Google Scholar
• Cox MM. Motoring along with the bacterial RecA protein. Nat Rev Mol Cell Bio. 2007;8(2):127–138.
   PubMed Web of Science ®Google Scholar
• Murayama Y, Kurokawa Y, Mayanagi K, et al. Formation and branch migration Of holliday junctions mediated by eukaryotic recombinases. Nature. 2008;451(7181):1018–1021. DOI:10.1038/nature06609
   PubMed Web of Science ®Google Scholar
• Neale MJ, Keeney S. Clarifying the mechanics of DNA strand exchange in meiotic recombination. Nature. 2006;442(7099):153–158.
   PubMed Web of Science ®Google Scholar
• Szczelkun MD, Tikhomirova MS, Sinkunas T, et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc Natl Acad Sci USA. 2014;111(27):9798–9803. DOI:10.1073/pnas.1402597111
   PubMed Web of Science ®Google Scholar
• Jones DL, Leroy P, Unoson C, et al. Kinetics of dCas9 target search in Escherichia coli. Science. 2017;357(6358):1420–1424. DOI:10.1126/science.aah7084
   PubMed Web of Science ®Google Scholar
• Radding CM, Beattie KL, Holloman WK, et al. Uptake of homologous single-stranded fragments by superhelical DNA. IV. branch migration. J Mol Biol. 1977;116(4):825–839. DOI:10.1016/0022-2836(77)90273-X
   PubMed Web of Science ®Google Scholar
• Feller. An introduction to probability theory and itsApplications. Vol. 1. New York: Wiley and Sons; 1968.
   Google Scholar
• Reynaldo LP, Vologodskii AV, Neri BP, et al. The kinetics of oligonucleotide replacements11Edited by I. tinoco. J Mol Biol. 2000;297(2):511–520. DOI:10.1006/jmbi.2000.3573
   PubMed Web of Science ®Google Scholar
• Yurke B, Turberfield AJ, Mills AP, et al. A DNA-fuelled molecular machine made of DNA. Nature. 2000;406(6796):605–608. DOI:10.1038/35020524
   PubMed Web of Science ®Google Scholar
• Yurke B, Mills AP. Using DNA to power nanostructures. Genet Program Evolvable Mach. 2003;4(2):111–122.
   Google Scholar
• Zhang DY, Winfree E. Control of DNA strand displacement kinetics using toehold exchange. J Am Chem Soc. 2009;131(47):17303–17314.
   PubMed Web of Science ®Google Scholar
• Srinivas N, Ouldridge TE, Sulc P, et al. On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Res. 2013 Dec;41(22):10641–10658.
   PubMed Web of Science ®Google Scholar
• Choi HM, Beck VA, Pierce NA. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. ACS Nano 2014 May 27;8(5):4284–4294.
   PubMed Web of Science ®Google Scholar
• Green AA, Silver PA, Collins JJ, et al. Toehold switches: de-novo-designed regulators of gene expression. Cell. 2014 Nov 6;159(4):925–939.
   PubMed Web of Science ®Google Scholar
• Gillespie DT. EXACT STOCHASTIC SIMULATION of COUPLED CHEMICAL-REACTIONS. J Phys Chem. 1977;81(25):2340–2361.
   Web of Science ®Google Scholar
• Schaeffer JM, Thachuk C, Winfree E, et al. Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. In: Phillips A, and Yin P editor. DNA Computing and Molecular Programming. DNA 2015. Lecture Notes in Computer Science. Vol. 9211. Cham: Springer; 2015.
   Google Scholar
• Doye JPK, Ouldridge TE, Louis AA, et al. Coarse-graining DNA for simulations of DNA nanotechnology. Phys Chem Chem Phys. 2013;15(47):20395–20414. DOI:10.1039/c3cp53545b
   PubMed Web of Science ®Google Scholar
• Machinek RR, Ouldridge TE, Haley NE, et al. Programmable energy landscapes for kinetic control of DNA strand displacement. Nat Commun. 2014 Nov 10;5(1):5324.
   PubMedGoogle Scholar
• Irmisch P, Ouldridge TE, Seidel R. Modeling DNA-Strand displacement reactions in the presence of base-pair mismatches. J Am Chem Soc. 2020;142(26):11451–11463.
   PubMed Web of Science ®Google Scholar
• Sulc P, Ouldridge TE, Romano F, et al. Modelling toehold-mediated RNA strand displacement. Biophys J. 2015;108(5):1238–1247. DOI:10.1016/j.bpj.2015.01.023
   PubMed Web of Science ®Google Scholar
• Genot AJ, Zhang DY, Bath J, et al. Remote toehold: a mechanism for flexible control of DNA hybridization kinetics. 2011;133(7):2177–2182. DOI:10.1021/ja1073239
   Google Scholar
• Dey S, Fan C, Gothelf KV, et al. DNA origami. Nat Rev Methods Primers. 2021;1(1):13. DOI:10.1038/s43586-020-00009-8
   Google Scholar
• Grosso ED, Franco E, Prins LJ, et al. Dissipative DNA nanotechnology. Nat Chem. 2022;14(6):600–613. DOI:10.1038/s41557-022-00957-6
   PubMed Web of Science ®Google Scholar
• Franco E, Friedrichs E, Kim J, et al. Timing molecular motion and production with a synthetic transcriptional clock_SI_appendix. PNAS. 2011;108(40):1–95. DOI:10.1073/pnas.1100060108
   Web of Science ®Google Scholar
• Seelig G, Soloveichik D, Zhang DY, et al. Enzyme-free nucleic acid logic circuits. Science. 2006 Dec 8;314(5805):1585–1588.
   PubMed Web of Science ®Google Scholar
• Yin P, Choi HMT, Calvert CR, et al. Programming biomolecular self-assembly pathways. Nature. 2008;451(7176):318–322. DOI:10.1038/nature06451
   PubMed Web of Science ®Google Scholar
• Green SJ, Lubrich D, Turberfield AJ. DNA hairpins: fuel for autonomous DNA devices. Biophys J. 2006;91(8):2966–2975.
   PubMed Web of Science ®Google Scholar
• Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. Proc Natl Acad Sci 2004 Oct 26;101(43):15275–15278.
   PubMed Web of Science ®Google Scholar
• Li B, Ellington AD, Chen X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res. 2011;39(16):e110.
   PubMed Web of Science ®Google Scholar
• Tucker BJ, Breaker RR. Riboswitches as versatile gene control elements. Curr Opin Struct Biol. 2005;15(3):342–348.
   PubMed Web of Science ®Google Scholar
• Sherwood AV, Henkin TM. Riboswitch-mediated gene regulation: novel RNA architectures dictate gene expression responses. Annu Rev Microbiol. 2016;70(1):361–374.
   PubMedGoogle Scholar
• Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol. 2004 Jun;5(6):451–463.
   PubMed Web of Science ®Google Scholar
• Isaacs FJ, Dwyer DJ, Ding C, et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol. 2004 Jul;22(7):841–847.
   PubMed Web of Science ®Google Scholar
• Wang T, Simmel FC. Riboswitch-inspired toehold riboregulators for gene regulation in Escherichia coli. Nucleic Acids Res 2022 Apr 21;50(8):4784–4798.
   PubMed Web of Science ®Google Scholar
• Kim J, Zhou Y, Carlson PD, et al. De novo-designed translation-repressing Riboregulators for multi-input cellular logic. Nat Chem Biol. 2019 Dec;15(12):1173–1182.
   PubMed Web of Science ®Google Scholar
• Zhao EM, Mao AS, Puig H, et al. RNA-responsive elements for eukaryotic translational control. Nature Biotechnol. 2022;40(4):539–545. DOI:10.1038/s41587-021-01068-2
   PubMed Web of Science ®Google Scholar
• Kim J, Zhou Y, Carlson P, et al. De-novo-designed translational repressors for multi-input cellular logic. biorxivorg. 2018.
   Google Scholar
• Pardee K, Green AA, Ferrante T, et al. Paper-based synthetic gene networks. Cell. 2014 Nov 6;159(4):940–954.
   PubMed Web of Science ®Google Scholar
• Pardee K, Green AA, Takahashi MK, et al. Rapid, low-cost detection of zika virus using programmable biomolecular components. Cell. 2016;165(5):1255–1266. DOI:10.1016/j.cell.2016.04.059
   PubMed Web of Science ®Google Scholar
• Green AA, Kim J, Ma D, et al. Complex cellular logic computation using ribocomputing devices. Nature. 2017;548(7665):117–121. DOI:10.1038/nature23271
   PubMed Web of Science ®Google Scholar
• Mousavi PS, Smith SJ, Chen JB, et al. A multiplexed, electrochemical interface for gene-circuit-based sensors. Nat Chem. 2019;12(1):48–55. DOI:10.1038/s41557-019-0366-y
   PubMed Web of Science ®Google Scholar
• Carr AR, Dopp JL, Wu K, et al. Toward mail-in-sensors for SARS-CoV‑2 detection: interfacing gel switch resonators with cell-free toehold switches. ACS Sens. 2022;7(3):806–815. DOI:10.1021/acssensors.1c02450
   PubMed Web of Science ®Google Scholar
• Hong F, Ma D, Wu K, et al. Precise and programmable detection of mutations using ultraspecific riboregulators. Cell. 2020;180(5):1018–1032.e16. DOI:10.1016/j.cell.2020.02.011
   PubMed Web of Science ®Google Scholar
• Falgenhauer E, Muckl A, Schwarz-Schilling M, et al. Transcriptional interference in toehold switch-based RNA circuits. ACS Synth Biol. 2022 May 20;11(5):1735–1745.
   PubMed Web of Science ®Google Scholar
• Ma D, Li Y, Wu K, et al. Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics. Nat Biomed Eng. 2022;6(3):298–309. DOI:10.1038/s41551-022-00857-7
   PubMed Web of Science ®Google Scholar
• Chappell J, Takahashi MK, Lucks JB. Creating small transcription activating RNAs. Nat Chem Biol. 2015 Mar;11(3):214–220.
   PubMed Web of Science ®Google Scholar
• Lehr FX, Hanst M, Vogel M, et al. Cell-free prototyping of AND-Logic gates based on heterogeneous RNA activators. ACS Synth Biol. 2019 Sep 20;8(9):2163–2173.
   PubMed Web of Science ®Google Scholar
• Kozak M. Downstream secondary structure facilitates recognition of initiator codons by eukaryotic ribosomes. Proc Nat Acad Sci. 1990;87(21):8301–8305.
   PubMed Web of Science ®Google Scholar
• Zadeh JN, Steenberg CD, Bois JS, et al. NUPACK: analysis and design of nucleic acid systems. J Comput Chem. 2010;32(1):170–173. DOI:10.1002/jcc.21596
   Web of Science ®Google Scholar
• Fornace NJP, Niles APME, Pierce NA. A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synth Biol. 2020;9(10):1–14.
   PubMed Web of Science ®Google Scholar
• Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 2003 Jul 1;31(13):3406–3415.
   PubMed Web of Science ®Google Scholar
• Lorenz R, Bernhart SH, Honer Z, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011 Nov 24;6(1):26.
   PubMed Web of Science ®Google Scholar
• Boussebayle A, Torka D, Ollivaud S, et al. Next-level riboswitch development—implementation of Capture-SELEX facilitates identification of a new synthetic riboswitch. Nucleic Acids Res. 2019;47(9):4883–4895. DOI:10.1093/nar/gkz216
   PubMed Web of Science ®Google Scholar
• Groher A-C, Jager S, Schneider C, et al. Tuning the performance of synthetic riboswitches using machine learning. ACS Synth Biol. 2019;8(1):34–44. DOI:10.1021/acssynbio.8b00207
   PubMed Web of Science ®Google Scholar
• Angenent-Mari NM, Garruss AS, Soenksen LR, et al. A deep learning approach to programmable RNA switches. Nat Commun. 2020 Oct 7;11(1):5057.
   PubMed Web of Science ®Google Scholar
• Valeri JA, Collins KM, Ramesh P, et al. Sequence-to-function deep learning frameworks for engineered riboregulators. Nat Commun. 2020 Oct 7;11(1):5058.
   PubMed Web of Science ®Google Scholar
• Loughrey D, Watters KE, Settle AH, et al. SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic Acids Res. 2014;42(21):e165. DOI:10.1093/nar/gku909
   PubMed Web of Science ®Google Scholar
• Watters KE, Abbott TR, Lucks JB. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic Acids Res. 2015;44(2):e12.
   PubMed Web of Science ®Google Scholar
• Wilusz JE, JnBaptiste CK, Lu LY, et al. A triple helix stabilizes the 3’ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev. 2012;26(21):2392–2407. DOI:10.1101/gad.204438.112
   PubMed Web of Science ®Google Scholar
• Zhang Q, Ma D, Wu F, et al. Predictable control of RNA lifetime using engineered degradation-tuning RNAs. Nat Chem Biol. 2021;17(7):828–836. DOI:10.1038/s41589-021-00816-4
   PubMed Web of Science ®Google Scholar
• Cetnar DP, Salis HM. Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons. ACS Synth Biol. 2021;10(2):318–332.
   PubMed Web of Science ®Google Scholar
• Vogel J, Luisi BF. Hfq and its constellation of RNA. Nat Rev Microbiol 2011 Aug 15;9(8):578–589.
   PubMed Web of Science ®Google Scholar
• Lee N, Moss Walter N, Yario Therese A, et al. EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA. Cell. 2015;160(4):607–618. DOI:10.1016/j.cell.2015.01.015
   PubMed Web of Science ®Google Scholar
• Statello L, Guo C-J, Chen L-L, et al. Gene regulation by long non-coding RNAs and its biological functions. Nat Rev Mol Cell Bio. 2021;22(2):96–118. DOI:10.1038/s41580-020-00315-9
   PubMed Web of Science ®Google Scholar
• Mayer T, Oesinghaus L, Simmel FC. Toehold-mediated strand displacement in random sequence pools. J. Am. Chem. Soc. 2023;146:634–644 .
   Google Scholar
• Mihailovic MK, Vazquez-Anderson J, Li Y, et al. High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites. Nat Commun. 2018;9(1):4084. DOI:10.1038/s41467-018-06207-z
   PubMedGoogle Scholar