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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. 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. 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. 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. It has also been used in conjunction with RNA for the production of kinetically-controlled ribosensors. TMSD starts with a double-stranded DNA complex composed of the original strand and the protector strand. 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. 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. This initial endothermic step is rate limiting 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. 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. 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). The protector strand can possess its own unique toehold and can, therefore, turn into an invading strand itself, starting a strand-displacement cascade. The whole process is energetically favored and although a reverse reaction can occur its rate is up to 6 orders of magnitude slower. Additional control over the system of toehold mediated strand displacement can be introduced by toehold sequestering.
TectoRNAs are modular RNA units able to self-assemble into larger nanostructures in a programmable fashion. They are generated by rational design through an approach called RNA architectonics, which make use of RNA structural modules identified in natural RNA molecules to form pre-defined 3D structures spontaneously.
References
- ↑ "Lulu Qian | Caltech Directory". directory.caltech.edu. Retrieved 2023-03-05.
- ↑ "Introducing ISNSCE Vice President Lulu Qian". ISNSCE. 2021-12-11. Retrieved 2023-03-05.
- ↑ "Programming DNA for Molecular Robots: An Interview with Lulu Qian – Pasadena Now". www.pasadenanow.com. Retrieved 2023-03-05.
- ↑ Qian, Lulu; Winfree, Erik (2011-06-03). "Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades". Science. 332 (6034): 1196–1201. Bibcode:2011Sci...332.1196Q. doi:10.1126/science.1200520. ISSN 0036-8075. PMID 21636773. S2CID 10053541.
- ↑ "Lulu Qian's CV" (PDF).
- ↑ Major, Mario L. (2017-09-16). "Scientists Build DNA Robots That Could One Day Deliver Medicine Inside Your Body". interestingengineering.com. Retrieved 2023-03-04.
- ↑ "Caltech researchers build largest biochemical circuit out of small synthetic DNA molecules". EurekAlert!. Retrieved 2023-03-04.
- 1 2 Andy Extance2017-12-07T14:30:00+00:00. "DNA origami makes it big". Chemistry World. Retrieved 2023-03-04.
{{cite web}}: CS1 maint: numeric names: authors list (link) - 1 2 Qian, Lulu; Winfree, Erik; Bruck, Jehoshua (July 2011). "Neural network computation with DNA strand displacement cascades". Nature. 475 (7356): 368–372. doi:10.1038/nature10262. ISSN 1476-4687. PMID 21776082. S2CID 1735584.
- ↑ Mehar, Pranjal (2018-07-10). "Scientists created AI from DNA". Tech Explorist. Retrieved 2023-03-04.
- ↑ "Foresight Institute Awards 2019 Feynman Prizes in Nanotechnology to Qian, Galli; awards presented by Nobelist, Sir Fraser Stoddart". PRWeb. Retrieved 2023-03-04.
- ↑ "Two Professors Receive Caltech's Highest Honors for Teaching and Mentorship". California Institute of Technology. 2023-02-21. Retrieved 2023-03-04.
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