Dynamically elongated associative toehold for tuning DNA circuit kinetics and thermodynamics
نویسندگان
چکیده
منابع مشابه
Control of DNA strand displacement kinetics using toehold exchange.
DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchang...
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Hybridization of DNA strands can be used to build molecular devices, and control of the kinetics of DNA hybridization is a crucial element in the design and construction of functional and autonomous devices. Toehold-mediated strand displacement has proved to be a powerful mechanism that allows programmable control of DNA hybridization. So far, attempts to control hybridization kinetics have mai...
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We explore a method of designing algorithms using two types of DNA strands, namely rule strands (rules) and input strands. Rules are fixed in advance, and their task is to bind with the input strands in order to produce an output. We present algorithms for divisibility and primality testing as well as for square root computation. We measure the complexity of our algorithms in terms of the neces...
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The rates of duplex formation for two octamers of DNA (5' d-CACGGCTC/5' d-GAGCCGTG and 5' d-CACAGCAC/5' d-GTGCTGTG), the homologous RNA, and both sets of hybrids in 1 M NaCl buffer have been measured using stopped-flow spectroscopy. In addition, the thermodynamic parameters, ΔH° and ΔS°, have been determined for the same sequences under the same buffer conditions using optical melting technique...
متن کاملOn the biophysics and kinetics of toehold-mediated DNA strand displacement Supplementary Information
Niranjan Srinivas,∗,† Thomas E. Ouldridge,∗,‡ Petr Šulc,‡ Joseph M. Schaeffer,† Bernard Yurke,¶ Ard A. Louis,‡ Jonathan P. K. Doye§ and Erik Winfree† ∗Both these authors contributed equally to this work. Email: [email protected], [email protected] †California Institute of Technology, 1200 E California Blvd., Pasadena, CA 91125 ‡Rudolph Peierls Centre for Theoretical Physics, 1 Ke...
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ژورنال
عنوان ژورنال: Nucleic Acids Research
سال: 2021
ISSN: 0305-1048,1362-4962
DOI: 10.1093/nar/gkab212