Toehold mediated strand displacement

Toehold mediated strand displacement (TMSD) is an enzyme-free molecular tool to exchange one strand of DNA or RNA (output) with another strand (input). It is based on the hybridization of two complementary strands of DNA or RNA via Watson-Crick base pairing (A-T/U and C-G) and makes use of a process called branch migration.[1] Although branch migration has been known to the scientific community since the 1970s, TMSD has not been introduced to the field of DNA nanotechnology until 2000 when Yurke et al. was the first who took advantage of TMSD.[1][2] He used the technique to open and close a set of DNA tweezers made of two DNA helices using an auxiliary strand of DNA as fuel.[1][3] Since its first use, the technique has been modified for the construction of autonomous molecular motors, catalytic amplifiers, reprogrammable DNA nanostructures and molecular logic gates.[3][4] It has also been used in conjunction with RNA for the production of kinetically-controlled ribosensors.[5] TMSD starts with a double-stranded DNA complex composed of the original strand and the protector strand.[2] The original strand has an overhanging region the so-called “toehold” which is complementary to a third strand of DNA referred to as the “invading strand”. The invading strand is a sequence of single-stranded DNA (ssDNA) which is complementary to the original strand.[3][2] The toehold regions initiate the process of TMSD by allowing the complementary invading strand to hybridize with the original strand, creating a DNA complex composed of three strands of DNA.[3][6] This initial endothermic step is rate limiting[1] and can be tuned by varying the strength (length and sequence composition e.g. G-C or A-T rich strands) of the toehold region.[3] The ability to tune the rate of strand displacement over a range of 6 orders of magnitude generates the backbone of this technique and allows the kinetic control of DNA or RNA devices.[4] After the binding of the invading strand and the original strand occurred, branch migration of the invading domain then allows the displacement of the initial hybridized strand (protector strand).[1] The protector strand can possess its own unique toehold and can, therefore, turn into an invading strand itself, starting a strand-displacement cascade.[2][4][7] The whole process is energetically favored and although a reverse reaction can occur its rate is up to 6 orders of magnitude slower.[4] Additional control over the system of toehold mediated strand displacement can be introduced by toehold sequestering.[4][8][9]

A slightly different variant of strand displacement has also been introduced using a strand displacing polymerase enzyme.[10][11] Unlike TMSD, it used the polymerase enzyme as a source of energy and it referred to as polymerase-based strand displacement.[11]

Toehold mediated strand displacement

Toehold sequestering

Toehold sequestering is a technique to “mask” the toehold region, rendering its accessibility.[4][3] There are several ways to do so but the most common approaches are hybridizing the toehold with a complementary strand[7] or by designing the toehold region to form a hairpin loop.[12] Masking and unmasking of the toehold domains together with the ability to precisely control the kinetics of the reaction makes toehold mediated strand displacement a valuable tool in the field of DNA nanotechnology[4] Moreover, biosensors based on toehold mediated strand displacement reaction are useful in single molecule detection of DNA targets and SNP discrimination.[13]

References
  1. Yurke, Bernard (2000). "A DNA-fuelled molecular machine made of DNA". Nature. 406 (6796): 605–8. doi:10.1038/35020524. PMID 10949296.
  2. Guo, Yijun; Wei, Bing; Xiao, Shiyan; Yao, Dongbao; Li, Hui; Xu, Huaguo; Song, Tingjie; Li, Xiang; Liang, Haojun (2017). "Recent advances in molecular machines based on toehold-mediated strand displacement reaction". Quantitative Biology. 5 (1): 25–41. doi:10.1007/s40484-017-0097-2.
  3. Zhang, David Yu; Seelig, Georg (2011). "Dynamic DNA nanotechnology using strand-displacement reactions". Nature Chemistry. 3 (2): 103–13. doi:10.1038/nchem.957. PMID 21258382.
  4. Zhang, David Yu; Winfree, Erik (2009). "Control of DNA strand displacement kinetics using toehold exchange" (PDF). Journal of the American Chemical Society. 131 (47): 17303–17314. doi:10.1021/ja906987s. PMID 19894722.
  5. Burke, Cassandra R; Sparkman- Yager, David; Carothers, James M. "Multi-state design of kinetically-controlled RNA aptamer ribosensors" (PDF). bioRxiv. bioRxiv. Retrieved 30 October 2018.
  6. Yurke, Bernard; Millis, Allen P (2003). "Using DNA to power nanostructures". Genetic Programming and Evolvable Machines. 4 (2): 111–122. doi:10.1023/A:1023928811651.
  7. Zhang, David Yu (2007). "Engineering entropy-driven reactions and networks catalyzed by DNA" (PDF). Science. 318 (5853): 1121–1125. doi:10.1126/science.1148532. PMID 18006742.
  8. Eshra, A.; Shah, S.; Song, T.; Reif, J. (2019). "Renewable DNA hairpin-based logic circuits". IEEE Transactions on Nanotechnology. 18: 252–259. arXiv:1704.06371. doi:10.1109/TNANO.2019.2896189. ISSN 1536-125X.
  9. Garg, Sudhanshu; Shah, Shalin; Bui, Hieu; Song, Tianqi; Mokhtar, Reem; Reif, John (2018). "Renewable Time-Responsive DNA Circuits". Small. 14 (33): 1801470. doi:10.1002/smll.201801470. ISSN 1613-6829. PMID 30022600.
  10. Shah, Shalin; Wee, Jasmine; Song, Tianqi; Ceze, Luis; Strauss, Karin; Chen, Yuan-Jyue; Reif, John (2020-05-27). "Using Strand Displacing Polymerase To Program Chemical Reaction Networks". Journal of the American Chemical Society. 142 (21): 9587–9593. doi:10.1021/jacs.0c02240. ISSN 0002-7863.
  11. Shah, Shalin; Song, Tianqi; Song, Xin; Yang, Ming; Reif, John (2019). Thachuk, Chris; Liu, Yan (eds.). "Implementing Arbitrary CRNs Using Strand Displacing Polymerase". DNA Computing and Molecular Programming. Lecture Notes in Computer Science. Cham: Springer International Publishing: 21–36. doi:10.1007/978-3-030-26807-7_2. ISBN 978-3-030-26807-7.
  12. Green, Simon J; Lubrich, Daniel; Turberfield, Andrew J (2006). "DNA hairpins: fuel for autonomous DNA devices". Biophysical Journal. 91 (8): 2966–2975. CiteSeerX 10.1.1.601.6261. doi:10.1529/biophysj.106.084681. PMC 1578469. PMID 16861269.
  13. Sapkota, K.; et al. (2019). "Single-Step FRET-Based Detection of Femtomoles DNA". Sensors. 19 (16): 3495. doi:10.3390/s19163495.
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