DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants

Tang, Weiyang; Zhong, Weiying; Tan, Yun; Wang, Guan A; Feng, Liang; Liu, Yizhen

doi:10.1007/s41061-019-0274-z

Cited by 48 publications

(35 citation statements)

References 83 publications

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“…With the addition of the corresponding trigger solution, a rapid increase in fluorescence was observed, and no increase in fluorescence for the non-complementary triggers were observed ( Figure S6 ). This corresponds to other studies that showed the highly specific nature of DNA strand displacement and met our design specifications [ 41 , 43 , 53 ]. Additionally, the release curve was fitted with a one phase association model to better model the release behavior.…”

Section: Resultssupporting

confidence: 87%

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Controlled Release in Hydrogels Using DNA Nanotechnology

Veneziano

2022

Biomedicines

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Gelatin is a biopolymer widely used to synthesize hydrogels for biomedical applications, such as tissue engineering and bioinks for 3D bioprinting. However, as with other biopolymer-based hydrogels, gelatin-hydrogels do not allow precise temporal control of the biomolecule distribution to mimic biological signals involved in biological mechanisms. Leveraging DNA nanotechnology tools to develop a responsive controlled release system via strand displacement has demonstrated the ability to encode logic process, which would enable a more sophisticated design for controlled release. However, this unique and dynamic system has not yet been incorporated within any hydrogels to create a complete release circuit mechanism that closely resembles the sequential distribution of biomolecules observed in the native environment. Here, we designed and synthesized versatile multi-arm DNA motifs that can be easily conjugated within a gelatin hydrogel via click chemistry to incorporate a strand displacement circuit. After validating the incorporation and showing the increased stability of DNA motifs against degradation once embedded in the hydrogel, we demonstrated the ability of our system to release multiple model cargos with temporal specificity by the addition of the trigger strands specific to each cargo. Additionally, we were able to modulate the rate and quantity of cargo release by tuning the sequence of the trigger strands.

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Section: Resultssupporting

confidence: 87%

“…The displacement reaction occurs because the trigger strand has a longer hybridization region, known as the toehold region, compared to the initial strand. The displacement kinetics can be tuned by changing the length of the toehold region, thus, making the displacement reaction faster or slower [ 40 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

Controlled Release in Hydrogels Using DNA Nanotechnology

Veneziano

2022

Biomedicines

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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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“…This reaction between two DNA structures initiates at the single-stranded (sticky) end, called a toehold, where the shorter strand in the duplex exchanges with a longer complementary invader strand, requiring no enzymatic mediation . After having been introduced by Yurke et al in 2000, SDR has been used to transfer information in DNA computing, − to amplify signals in catalytic biosensors, − to power the movement of DNA motors and robots, − construct reprogrammable DNA nanostructures, devices, soft materials, and systems, − and even applied in living cells . The reaction rates of SDR increase exponentially with toehold length, making it an easy way to tune kinetics .…”

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confidence: 99%

Kinetics of Toehold-Mediated DNA Strand Displacement Depend on Fe^II₄L₄ Tetrahedron Concentration

et al. 2021

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The toehold-mediated strand displacement reaction (SDR) is a powerful enzyme-free tool for molecular manipulation, DNA computing, signal amplification, etc. However, precise modulation of SDR kinetics without changing the original design remains a significant challenge. We introduce a new means of modulating SDR kinetics using an external stimulus: a water-soluble Fe II 4 L 4 tetrahedral cage. Our results show that the presence of a flexible phosphate group and a minimum toehold segment length are essential for Fe II 4 L 4 binding to DNA. SDRs mediated by toehold ends in different lengths (3–5) were investigated as a function of cage concentration. Their reaction rates all first increased and then decreased as cage concentration increased. We infer that cage binding on the toehold end slows SDR, whereas the stabilization of intermediates that contain two overhangs accelerates SDR. The tetrahedral cage thus serves as a versatile tool for modulation of SDR kinetics.

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DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants

Cited by 48 publications

References 83 publications

Controlled Release in Hydrogels Using DNA Nanotechnology

Controlled Release in Hydrogels Using DNA Nanotechnology

First passage time study of DNA strand displacement

Kinetics of Toehold-Mediated DNA Strand Displacement Depend on Fe^II₄L₄ Tetrahedron Concentration

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DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants

Cited by 48 publications

References 83 publications

Controlled Release in Hydrogels Using DNA Nanotechnology

Controlled Release in Hydrogels Using DNA Nanotechnology

First passage time study of DNA strand displacement

Kinetics of Toehold-Mediated DNA Strand Displacement Depend on FeII4L4 Tetrahedron Concentration

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Kinetics of Toehold-Mediated DNA Strand Displacement Depend on Fe^II₄L₄ Tetrahedron Concentration