scholarly journals l-DNA-Based Catalytic Hairpin Assembly Circuit

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 947 ◽  
Author(s):  
Adam M. Kabza ◽  
Jonathan T. Sczepanski
Keyword(s):  
Nucleic Acid ◽  
Dna Nanotechnology ◽  
Great Promise ◽  
Disease Diagnostics ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Catalytic Hairpin Assembly ◽  
Fetal Bovine ◽  
Dna Strand ◽  
Nuclease Degradation

Isothermal, enzyme-free amplification methods based on DNA strand-displacement reactions show great promise for applications in biosensing and disease diagnostics but operating such systems within biological environments remains extremely challenging due to the susceptibility of DNA to nuclease degradation. Here, we report a catalytic hairpin assembly (CHA) circuit constructed from nuclease-resistant l-DNA that is capable of unimpeded signal amplification in the presence of 10% fetal bovine serum (FBS). The superior biostability of the l-DNA CHA circuit relative to its native d-DNA counterpart was clearly demonstrated through a direct comparison of the two systems (d versus l) under various conditions. Importantly, we show that the l-CHA circuit can be sequence-specifically interfaced with an endogenous d-nucleic acid biomarker via an achiral peptide nucleic acid (PNA) intermediary, enabling catalytic detection of the target in FBS. Overall, this work establishes a blueprint for the detection of low-abundance nucleic acids in harsh biological environments and provides further impetus for the construction of DNA nanotechnology using l-oligonucleotides.

Biocomputing based on DNA strand displacement reactions

ChemPhysChem ◽  
2021 ◽  
Author(s):  
Hui Lv ◽  
Qian Li ◽  
Jiye Shi ◽  
Fei Wang ◽  
Chunhai Fan
Keyword(s):  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

scholarly journals A nucleic acid strand displacement system for the multiplexed detection of tuberculosis-specific mRNA using quantum dots

Nanoscale ◽  
2016 ◽  
Vol 8 (19) ◽  
pp. 10087-10095 ◽  
Author(s):  
H. D. Gliddon ◽  
P. D. Howes ◽  
M. Kaforou ◽  
M. Levin ◽  
M. M. Stevens
Keyword(s):  
Quantum Dots ◽  
Nucleic Acid ◽  
Strand Displacement ◽  
Multiplexed Detection ◽  
Mrna Detection ◽  
Dna Strand Displacement ◽  
Displacement System ◽  
Dna Strand ◽  
Specific Mrna

On the development of a novel multiplexed assay for Tuberculosis-specific mRNA detection using DNA strand displacement and quantum dots.

Connecting localized DNA strand displacement reactions

Nanoscale ◽  
2015 ◽  
Vol 7 (30) ◽  
pp. 12970-12978 ◽  
Author(s):  
Ismael Mullor Ruiz ◽  
Jean-Michel Arbona ◽  
Amitkumar Lad ◽  
Oscar Mendoza ◽  
Jean-Pierre Aimé ◽  
...  
Keyword(s):  
Dna Origami ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand

Design and characterization of a DNA-based localized amplification circuit which, upon tethering on a DNA origami platform, greatly accelerates the catalytic response.

scholarly journals Programming colloidal bonding using DNA strand-displacement circuitry

2020 ◽  
Vol 117 (11) ◽  
pp. 5617-5623 ◽  
Author(s):  
Xiang Zhou ◽  
Dongbao Yao ◽  
Wenqiang Hua ◽  
Ningdong Huang ◽  
Xiaowei Chen ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Thermal Annealing ◽  
Constant Temperature ◽  
Room Temperature ◽  
Dna Nanotechnology ◽  
Structural Transformations ◽  
Temperature Sensitive ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Dna Strand

As a strategy for regulating entropy, thermal annealing is a commonly adopted approach for controlling dynamic pathways in colloid assembly. By coupling DNA strand-displacement circuits with DNA-functionalized colloid assembly, we developed an enthalpy-mediated strategy for achieving the same goal while working at a constant temperature. Using this tractable approach allows colloidal bonding to be programmed for synchronization with colloid assembly, thereby realizing the optimal programmability of DNA-functionalized colloids. We applied this strategy to conditionally activate colloid assembly and dynamically switch colloid identities by reconfiguring DNA molecular architectures, thereby achieving orderly structural transformations; leveraging the advantage of room-temperature assembly, we used this method to prepare a lattice of temperature-sensitive proteins and gold nanoparticles. This approach bridges two subfields: dynamic DNA nanotechnology and DNA-functionalized colloid programming.

scholarly journals A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

2020 ◽  
Vol 17 (167) ◽  
pp. 20190866 ◽  
Author(s):  
Stefan Badelt ◽  
Casey Grun ◽  
Karthik V. Sarma ◽  
Brian Wolfe ◽  
Seung Woo Shin ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Biophysical Model ◽  
Kinetic Properties ◽  
Strand Displacement ◽  
Natural Connection ◽  
Dna Strand Displacement ◽  
Wide Range ◽  
Dna Strand ◽  
High Level ◽  
Domain Level

Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.

scholarly journals DNA nanotechnology approaches for microRNA detection and diagnosis

2019 ◽  
Vol 47 (20) ◽  
pp. 10489-10505 ◽  
Author(s):  
Arun Richard Chandrasekaran ◽  
Jibin Abraham Punnoose ◽  
Lifeng Zhou ◽  
Paromita Dey ◽  
Bijan K Dey ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Dna Origami ◽  
Great Promise ◽  
Dna Nanostructures ◽  
New Class ◽  
Advantages And Disadvantages ◽  
Critical Comparison ◽  
Microrna Detection ◽  
Disease Diagnostics ◽  
Detection And Diagnosis

Abstract MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

The fast detection of streptavidin based on the initial reaction rate of the binding-induced DNA strand-displacement reaction

2016 ◽  
Vol 8 (37) ◽  
pp. 6701-6704 ◽  
Author(s):  
Chenxi Li ◽  
Ruoyun Lin ◽  
Tian Li ◽  
Feng Liu ◽  
Na Li
Keyword(s):  
Small Molecules ◽  
Reaction Rate ◽  
Initial Reaction Rate ◽  
Initial Reaction ◽  
Strand Displacement ◽  
Fast Detection ◽  
Dna Strand Displacement ◽  
Displacement Reactions ◽  
Dna Strand ◽  
Strand Displacement Reaction

Binding-induced DNA strand-displacement reactions diversify the applications beyond nucleic acids and small molecules.

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