Controlling the DNA Hybridization Chain Reaction

Figg, C. Adrian; Winegar, Peter H.; Hayes, Oliver G.; Mirkin, Chad A.

doi:10.1021/jacs.0c02892

Cited by 92 publications

(77 citation statements)

References 44 publications

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“…In addition to fundamental genomic processes, DNA nanotechnology exploits strand displacement to create nanoscale gadgets [12][13][14] and computational circuits [15][16][17][18]. Strand displacement also aids in the development of quantitative assays for detection of nucleic acid [19][20][21] and enzymatic activity [22,23] with improved probe specificity [24][25][26].…”

Section: Introductionmentioning

confidence: 99%

First passage time study of DNA strand displacement

Broadwater

Cook

Kim

2020

Preprint

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6DNA strand displacement, where a single-stranded nucleic acid invades a DNA duplex, is perva-7 sive in genomic processes and DNA engineering applications. The kinetics of strand displacement 8 have been studied in bulk; however, the kinetics of the underlying strand exchange were obfus-9 cated by a slow bimolecular association step. Here, we use a novel single-molecule Fluorescence 10 Resonance Energy Transfer (smFRET) approach termed the "fission" assay to obtain the full dis-11 tribution of first passage times of unimolecular strand displacement. At a frame time of 4.4 ms, 12 the first passage time distribution for a 14-nt displacement domain exhibited a nearly monotonic 13 decay with little delay. Among the eight different sequences we tested, the mean displacement time 14 was on average 35 ms and varied by up to a factor of 13. The measured displacement kinetics also 15 varied between complementary invaders and between RNA and DNA invaders of the same base 16 sequence except for T→U substitution. However, displacement times were largely insensitive to 17 the monovalent salt concentration in the range of 0.25 M to 1 M. Using a one-dimensional random 18 walk model, we infer that the single-step displacement time is in the range of ∼30 µs to ∼300 µs 19 depending on the base identity. The framework presented here is broadly applicable to the kinetic 20 analysis of multistep processes investigated at the single-molecule level. 21 * These two authors contributed equally. † harold.kim@physics.gatech.edu 1 Nucleic acids' ability to form hydrogen bonds between complementary Watson-Crick 2 bases allows for a rich set of complicated, multi-step kinetic behaviors such as duplex 3 hybridization[1] and dehybridization[2], Holliday junction structural dynamics[3, 4], and 4 strand invasion[5]. In particular, strand displacement, which is the exchange of bases 5 between two competing nucleic acid strands of identical sequence, occurs in homologous 6 recombination[6, 7], DNA replication[8] and RNA transcription[9], as well as CRISPR/Cas[10] 7 and the related Cascade complex[11]. In addition to fundamental genomic processes, DNA 8 nanotechnology exploits strand displacement to create nanoscale gadgets[12-14] and com-9 putational circuits[15-18]. Strand displacement also aids in the development of quantitative 10 assays for detection of nucleic acid[19-21] and enzymatic activity[22, 23] with improved 11 probe specificity[24-26]. 12For practical applications, strand displacement is implemented with the "invader" 13 strand and a partial duplex composed of the "incumbent" strand and the "substrate" 14 strand[18] (Fig. 1). The partial duplex has two distinct domains: 1) the single-stranded 15 overhang called the toehold which is critical to the speed and efficiency of the reaction[27] 16 and 2) the duplex region called the displacement domain. Toehold-mediated strand dis-17 placement is initiated when the invader strand anneals to the toehold in a bimolecular 18 reaction. Once a stable toehold interaction is formed, the incumben...

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Section: Introductionmentioning

confidence: 99%

First passage time study of DNA strand displacement

Broadwater

Cook

Kim

2020

Preprint

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“…Note that mechano-HCR reflects the traction forces present at earlier time points because of the kinetics of HCR. Assays such as the "exchange-mechano-HCR assay", where the hairpin monomers are barcoded with different dyes and washed into the sample periodically,may offer the ability to time-stamp the mechano-HCR signals.F urthermore, advances in HCR, such as controlled HCR, [22] branched HCR, [37] and FRET HCR, [38] suggest future directions to improve mechano-HCR S/N,c onvenience by reducing wash steps,a nd other advantages in simplifying quantification to address the challenge.F inally,m echano-HCR offers important potential in the adoption for applications such as medium-throughput drug and cell screening in both biological research and clinics.…”

Section: Discussionmentioning

confidence: 99%

Mechanically Triggered Hybridization Chain Reaction

et al. 2021

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Cells transmit piconewton forces to receptors to mediate processes such as migration and immune recognition. Amajor challenge in quantifying such forces is the sparsity of cell mechanical events.A ccordingly,m olecular tension is typically quantified with high resolution fluorescence microscopy, which hinders widespread adoption and application. Here,w er eport am echanically triggered hybridization chain reaction (mechano-HCR) that allows chemicala mplification of mechanical events.The amplification is triggered when acell receptor mechanically denatures ad uplex revealing ac ryptic initiator to activate the HCR reaction in situ. Importantly, mechano-HCR enables direct readout of pN forces using ap late reader.W el everage this capability and measured mechano-IC 50 for aspirin, Y-27632, and eptifibatide.Given that cell mechanical phenotypes are of clinical importance,mechano-HCR may offer ac onvenient route for drug discovery, personalized medicine,and disease diagnosis.

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Section: Design Strategies Of Sdr For Biocomputingmentioning

confidence: 99%

Biocomputing Based on DNA Strand Displacement Reactions

Shi

et al. 2021

ChemPhysChem

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The high sequence specificity and precise base complementary pairing principle of DNA provides a rich orthogonal molecular library for molecular programming, making it one of the most promising materials for developing bio‐compatible intelligence. In recent years, DNA has been extensively studied and applied in the field of biological computing. Among them, the toehold‐mediated strand displacement reaction (SDR) with properties including enzyme free, flexible design and precise control, have been extensively used to construct biological computing circuits. This review provides a systemic overview of SDR design principles and the applications. Strategies for designing DNA‐only, enzymes‐assisted, other molecules‐involved and external stimuli‐controlled SDRs are described. The recently realized computing functions and the application of DNA computing in other fields are introduced. Finally, the advantages and challenges of SDR‐based computing are discussed.

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Controlling the DNA Hybridization Chain Reaction

Cited by 92 publications

References 44 publications

First passage time study of DNA strand displacement

First passage time study of DNA strand displacement

Mechanically Triggered Hybridization Chain Reaction

Biocomputing Based on DNA Strand Displacement Reactions

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