The Effect of Basepair Mismatch on DNA Strand Displacement

Broadwater, Bo; Kim, Harold D.

doi:10.1016/j.bpj.2016.02.027

“…19 However, the only previous attempt to systematically probe the consequences of mismatch repair did not see any signal of enhanced displacement, due to the use of much longer toeholds. 30 Interestingly, we note that oxDNA predicts reaction acceleration even for longer toeholds if concentrations are high enough to access the first order limit (Supplementary Material S1.2). In this context, mismatch repair might be used to increase the fundamental speed limit of displacement reactions occuring, for example, at high effective concentrations between surface-localized reactants.…”

Section: Discussionmentioning

confidence: 85%

Rational design of hidden thermodynamic driving through DNA mismatch repair

Haley

¹

,

Ouldridge

²

,

Geraldini

³

et al. 2018

Preprint

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Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a new mechanism for enhancing thermodynamic drive of DNA strand displacement reactions whilst barely perturbing forward reaction rates -introducing mismatches in an internal location within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a strand-displacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of nonequilibrium systems that rely on catalytic control and must be robust to leak reactions.One of the signature features of living systems is that they operate continuously, expending free energy, rather than relaxing to equilibrium. Key molecular components are not consumed by these reactions but recovered -they act as catalysts. 1 Examples include metabolic enzymes, signal-processing kinases, molecular motors, polymerases and even nucleic acids undergoing replication, transcription and translation. 2 Designing synthetic analogues of such complex molecular systems is a key goal of nanotechnology. This task is complicated by the requirements that reactions must be thermodynamically favourable to proceed while stable equilibrium states that lock up the key catalytic components, and accidental leak reactions, must be avoided. Overall reaction thermodynamics and kinetics must therefore be carefully tuned.Due to its predictable base-pairing interactions, DNA has proved to be a remarkable material for the construction of static nanoscale structures 3-7 and systems that perform single-shot computations. 8,9 Continuouly operating dynamic systems, including reaction network architectures 9-11 and synthetic molecular machinery, 12-14 have also been developed, but the state of the art is far from the power and flexibility of natural analogs.Toehold-mediated strand displacement (TMSD) 15 and toehold exchange, 16 illustrated in Fig. 1, are the key reactions underlying much of DNA nanotechnology. In these processes, an invading strand replaces another strand in a duplex by competing for base pairs. A

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“…This prediction is consistent with the results of Broadwater et al, who observed no kinetic consequences of mismatch elimination when using toeholds of length 10 (ref. 30 ).…”

Section: Resultsmentioning

confidence: 99%

Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

Haley

¹

,

Ouldridge

²

,

Ruiz

³

et al. 2020

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Recent years have seen great advances in the development of synthetic self-assembling molecular systems. Designing out-of-equilibrium architectures, however, requires a more subtle control over the thermodynamics and kinetics of reactions. We propose a mechanism for enhancing the thermodynamic drive of DNA strand-displacement reactions whilst barely perturbing forward reaction rates: the introduction of mismatches within the initial duplex. Through a combination of experiment and simulation, we demonstrate that displacement rates are strongly sensitive to mismatch location and can be tuned by rational design. By placing mismatches away from duplex ends, the thermodynamic drive for a stranddisplacement reaction can be varied without significantly affecting the forward reaction rate. This hidden thermodynamic driving motif is ideal for the engineering of non-equilibrium systems that rely on catalytic control and must be robust to leak reactions.

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“…9a). A probe containing a hairpin has a higher target specificity than an unmasked probe with the same cognate sequence 1,43,44 ( Supplementary Figs. 15 and 16).…”

Section: Resultsmentioning

confidence: 99%

Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP

Garcia

¹

,

Leach

²

,

Wadsworth

³

et al. 2020

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RNase P and MRP are highly conserved, multi-protein/RNA complexes with essential roles in processing ribosomal and tRNAs. Three proteins found in both complexes, Pop1, Pop6, and Pop7 are also telomerase-associated. Here, we determine how temperature sensitive POP1 and POP6 alleles affect yeast telomerase. At permissive temperatures, mutant Pop1/6 have little or no effect on cell growth, global protein levels, the abundance of Est1 and Est2 (telomerase proteins), and the processing of TLC1 (telomerase RNA). However, in pop mutants, TLC1 is more abundant, telomeres are short, and TLC1 accumulates in the cytoplasm. Although Est1/2 binding to TLC1 occurs at normal levels, Est1 (and hence Est3) binding is highly unstable. We propose that Pop-mediated stabilization of Est1 binding to TLC1 is a prerequisite for formation and nuclear localization of the telomerase holoenzyme. Furthermore, Pop proteins affect TLC1 and the RNA subunits of RNase P/MRP in very different ways.

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The Effect of Basepair Mismatch on DNA Strand Displacement

Cited by 35 publications

References 47 publications

Rational design of hidden thermodynamic driving through DNA mismatch repair

Rational design of hidden thermodynamic driving through DNA mismatch repair

Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP

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