The kinetics of oligonucleotide replacements

Reynaldo, Luis P.; Vologodskii, Alexander; Neri, Bruce; Lyamichev, Victor I.

doi:10.1006/jmbi.2000.3573

Cited by 183 publications

(225 citation statements)

References 27 publications

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“…In the state III, the staple strands of the same sequence compete for the identical binding site in the scaffold DNA, which results in displacing one of the two staple strands. Such DNA displacement process is shown to be highly cooperative 30 , favouring efficient kicking out of one staple by the other rather than stagnant tug-of-war between the staple strands. When all the redundant staple strands are released, folding of the DNA nanostructure is completed (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The second process, hybridization of staple strands with the stretched scaffold DNA is essentially the same as solid-phase oligo hybridization 40 , and should thus be completed within 1 min when each staple strand is present at 200 nM. Time required for the strand displacement reaction depends on the number of strands to be displaced and the length of binding sites 30 . We presume that the ten helices in our honeycomb lattice Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Ten displacement reactions with an average binding site of 8 bp are required to fold one helix in our DNA origami design, which takes about 5 min at room temperature 30 . For more accurate estimation, staple strand exchange should also be considered, because the existence of some staple strand exchange was observed (Supplementary Fig.…”

Section: Discussionmentioning

confidence: 99%

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Programmed folding of DNA origami structures through single-molecule force control

et al. 2014

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Despite the recent development in the design of DNA origami, its folding yet relies on thermal or chemical annealing methods. We here demonstrate mechanical folding of the DNA origami structure via a pathway that has not been accessible to thermal annealing. Using magnetic tweezers, we stretch a single scaffold DNA with mechanical tension to remove its secondary structures, followed by base pairing of the stretched DNA with staple strands. When the force is subsequently quenched, folding of the DNA nanostructure is completed through displacement between the bound staple strands. Each process in the mechanical folding is well defined and free from kinetic traps, enabling us to complete folding within 10 min. We also demonstrate parallel folding of DNA nanostructures through multiplexed manipulation of the scaffold DNAs. Our results suggest a path towards programmability of the folding pathway of DNA nanostructures.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Programmed folding of DNA origami structures through single-molecule force control

et al. 2014

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“…Note that while we have found numerically conditions in which a WTA effect occurs in DNA-only circuits, it is not guaranteed that a unique winner will exist whenever competition for fuel occurs. Strand displacement is prone to leak, which is thought to arise mainly from blunt-end displacement (displacement of a strand from a duplex without the assistance of a toehold) [32,65,66]. Leak is especially problematic for first-order rsif.royalsocietypublishing.org J R Soc Interface 10: 20130212 autocatalytic circuits because they amplify exponentially even a miniscule leak (contrary to second-order amplification which occurs only above a threshold, in the presence of first-order degradation) [31].…”

Section: ð1:8þmentioning

confidence: 99%

Scaling down DNA circuits with competitive neural networks

Genot

Fujii

Rondelez

2013

J. R. Soc. Interface.

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DNA has proved to be an exquisite substrate to compute at the molecular scale. However, nonlinear computations (such as amplification, comparison or restoration of signals) remain costly in term of strands and are prone to leak. Kim et al. showed how competition for an enzymatic resource could be exploited in hybrid DNA/enzyme circuits to compute a powerful nonlinear primitive: the winner-take-all (WTA) effect. Here, we first show theoretically how the nonlinearity of the WTA effect allows the robust and compact classification of four patterns with only 16 strands and three enzymes. We then generalize this WTA effect to DNA-only circuits and demonstrate similar classification capabilities with only 23 strands.

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“…Typically, the hybridization reaction occurs between two complementary DNA strands, and is affected by temperature and strand length. The process has a low rate constant several orders of magnitude less than the hybridization reaction (Reynaldo et al 2000), and by designing a toehold, the process can increase dramatically (Yurke & Mills 2003). Yurke and Mills have determined that for a toehold length of eight bases, the exchange rate increases by six orders of magnitude (Yurke & Mills 2003).…”

Section: Reversibilitymentioning

confidence: 99%