Controlling metabolic flux by toehold-mediated strand displacement

Chen, Rebecca P.; Hunt, Victoria M; Mitkas, Alexander A; Siu, Ka-Hei; Chen, Wilfred

doi:10.1016/j.copbio.2020.07.002

Cited by 16 publications

(6 citation statements)

References 37 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The forward reaction TMSD has emerged as the core reaction in dynamic DNA nanotechnology and has been fully developed for constructing biosensors 20 and gene regulators. 21 In TMSD, the target strand binds to the toehold region and initiates branch migration, resulting in reporter strand release. If the fluorophore and quencher are labeled at appropriate positions of the probe, target recognition can be viewed by fluorescence dequenching.…”

Section: Dna Probe Design Guided By Oxdna Simulationmentioning

confidence: 99%

Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems

Liu

Yin

et al. 2021

Preprint

View full text Add to dashboard Cite

Amid of COVID-19 pandemic devastating the public health around the world, it become urgent to maintain a sufficiently large supply of nucleic acid tests to screen suspected cases timely. Reusable molecular probes in current testing method could potentially lead to enormous amount of screening capacity, critical for the disease control. Herein, we for the first time report a kind of self-resetting molecular probes for repeatedly detecting SARS-CoV-2 RNA, enabled by orchestrating a biomimetic fuel dissipative system via dynamic DNA nanotechnology. A set of simulation toolkits was utilized for the design and optimization of the self-resetting probe, allowing for highly consistent signal amplitudes across cyclic detections of SARS-CoV-2 RNA. Idiosyncratically, FWHM regulated by dissipative kinetics exhibits a fingerprint signal for high confidential identification of single-nucleotide mutation in the virus sequence. We further exploited our self-resetting probes to examine multiple human-infectious RNA virus including SARS-CoV-2, ZIKV, MERS-CoV, and SARS-CoV to demonstrate its generic nucleic acid detection capability and superior orthogonality. Self-resetting probes were also deployed for detection of 110 clinical nasopharyngeal swabs and correctly classify all the clinical samples from 55 COVID-19 patients and 55 controls. We anticipate that the DNA nanotechnology-enabled self-resetting probe could circumvent the lack of sustainability in the diagnostics of COVID-19 and other infectious diseases, thus helping disease control and building a broader global public health agenda.

show abstract

Section: Dna Probe Design Guided By Oxdna Simulationmentioning

confidence: 99%

Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems

Liu

Yin

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Nucleic acid-based circuits, i.e. , networks of interacting nucleic acids programmed to process chemical information, are an increasingly useful tool for molecular computation with applications spanning in vitro diagnostics − and biosensing, , synthetic cells, , and cellular computation, − sensing, , and control. − Nucleic acids are an ideal substrate for building molecular circuits because predictable base pairing rules facilitate the rational design of programmable interactions. Compared to transcription factor-based cascades, nucleic acid circuits can operate with faster response times and lower energetic costs. , Many nucleic acid circuits operate via toehold-mediated strand displacement (TMSD), in which a single-stranded toehold domain of a nucleic acid duplex or hairpin recruits a sequence complementary input strand to initiate strand displacement and expose a new domain that enacts a downstream response. , As a testament to the programmability, modularity, and scalability of TMSD reactions, the field of DNA computing has demonstrated in vitro TMSD circuits composed of tens to hundreds of components programmed to execute information processing tasks, such as digital calculations, pattern recognition, , and temporal signaling. − …”

Section: Introductionmentioning

confidence: 99%

“…21,22 Many nucleic acid circuits operate via toehold-mediated strand displacement (TMSD), in which a single-stranded toehold domain of a nucleic acid duplex or hairpin recruits a sequence complementary input strand to initiate strand displacement and expose a new domain that enacts a downstream response. 18,23 As a testament to the programmability, modularity, and scalability of TMSD reactions, the field of DNA computing has demonstrated in vitro TMSD circuits composed of tens to hundreds of components programmed to execute information processing tasks, such as digital calculations, 24 pattern recognition, 25,26 and temporal signaling. 27−30 There is a growing interest in achieving the capabilities of DNA-based TMSD circuits using RNA, 31−34 in part because RNA circuits can be genetically encoded for continuous production in living cells, cell lysates, or samples with nucleases, environments where TMSD components added at fixed concentrations would eventually be degraded.…”

Section: ■ Introductionmentioning

confidence: 99%

Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits

et al. 2023

View full text Add to dashboard Cite

Cotranscriptionally encoded RNA strand displacement (ctRSD) circuits are an emerging tool for programmable molecular computation, with potential applications spanning in vitro diagnostics to continuous computation inside living cells. In ctRSD circuits, RNA strand displacement components are continuously produced together via transcription. These RNA components can be rationally programmed through base pairing interactions to execute logic and signaling cascades. However, the small number of ctRSD components characterized to date limits circuit size and capabilities. Here, we characterize over 200 ctRSD gate sequences, exploring different input, output, and toehold sequences and changes to other design parameters, including domain lengths, ribozyme sequences, and the order in which gate strands are transcribed. This characterization provides a library of sequence domains for engineering ctRSD components, i.e., a toolkit, enabling circuits with up to 4-fold more inputs than previously possible. We also identify specific failure modes and systematically develop design approaches that reduce the likelihood of failure across different gate sequences. Lastly, we show the ctRSD gate design is robust to changes in transcriptional encoding, opening a broad design space for applications in more complex environments. Together, these results deliver an expanded toolkit and design approaches for building ctRSD circuits that will dramatically extend capabilities and potential applications.

show abstract

“…TSDR was first proposed by Yurke et al 18 . It involves three main processes as follows: toehold binding, branching chain migration, and chain dissociation 19 . Specifically, TSDRS is driven by Gibbs free energy.…”

Section: Introductionmentioning

confidence: 99%

Rapid microRNA detection method based on DNA strand displacement for ovarian cancer cells

Sun¹,

Li²,

Hong³

et al. 2023

J. Cancer

View full text Add to dashboard Cite

The current cancer detection methods are heavily dependent on the component analysis of corresponding cancer antigens. There is a lack of effective and simple clinical methods of ovarian cancer screening, which hinders the early identification for ovarian cancer and its treatment. To develop a simple and rapid method for quantitative analysis of ovarian cancer, we developed a DNA strand displacement-based method and finished the rapid detection of miR-21 in ovarian cancer cells within 5 min by a one-step isothermal reaction. The fluorescence intensity trajectory had a good linear relationship with miR-21 concentrations in the range of 100 fM-100 nM, with a lower limit of 6.05 pM. This detection method is simple, faster, and accurate. Besides, it can be applied to detect the miRNA biomarkers of other cancers by changing the preset sequences of toehold.

show abstract

Controlling metabolic flux by toehold-mediated strand displacement

Cited by 16 publications

References 37 publications

Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems

Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems

Design Approaches to Expand the Toolkit for Building Cotranscriptionally Encoded RNA Strand Displacement Circuits

Rapid microRNA detection method based on DNA strand displacement for ovarian cancer cells

Contact Info

Product

Resources

About