scholarly journals DNA nanotechnology assisted nanopore-based analysis

2020 ◽  
Vol 48 (6) ◽  
pp. 2791-2806 ◽  
Author(s):  
Taoli Ding ◽  
Jing Yang ◽  
Victor Pan ◽  
Nan Zhao ◽  
Zuhong Lu ◽  
...  
Keyword(s):  
Single Molecule ◽  
Dna Nanotechnology ◽  
Clinical Diagnostics ◽  
Dna Assembly ◽  
Label Free ◽  
One Pot ◽  
Dna Strand Displacement ◽  
Label Free Detection ◽  
Target Molecules ◽  
Dna Strand

Abstract Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

scholarly journals DNA breathing initiated strand displacement circuits for mimicking ant foraging with nanopore readout

2021 ◽  
Author(s):  
Jinbo Zhu ◽  
Jinglin Kong ◽  
Ulrich Keyser ◽  
Erkang Wang
Keyword(s):  
Single Molecule ◽  
Dna Nanotechnology ◽  
Path Selection ◽  
Strand Displacement ◽  
Initiation Mechanism ◽  
Single Molecule Level ◽  
Sensing Platform ◽  
Dna Strand Displacement ◽  
Dna Strand Exchange ◽  
Dna Strand

Abstract DNA strand displacement reaction is essential for the development of molecular computing based on DNA nanotechnology. Additional DNA strand exchange strategies with high selectivity for input will enable novel complex systems including biosensing applications. Most approaches use bulk readout methods based on fluorescent probes that complicate the monitoring of parallel computations. Herein we propose an autocatalytic strand displacement (ACSD) circuit, which is initiated by DNA breathing and accelerated by seesaw catalytic reaction. The special initiation mechanism of the ACSD circuit enables detection of single base mutations at multiple sites in the input strand with much higher sensitivity than classic toehold-mediated strand displacement. A swarm intelligence model is constructed using the ACSD circuit to mimic foraging behaviour of ants. We introduce a multiplexed nanopore sensing platform to report the output results of a parallel path selection system on the single-molecule level. The ACSD strategy and nanopore multiplexed readout method enhance the toolbox for the future development of DNA computing.

scholarly journals Biological Nanopores: Engineering on Demand

Life ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 27
Author(s):  
Ana Crnković ◽  
Marija Srnko ◽  
Gregor Anderluh
Keyword(s):  
Molecular Biology ◽  
Single Molecule ◽  
Enzymatic Reactions ◽  
Label Free ◽  
Natural Sources ◽  
On Demand ◽  
Label Free Detection ◽  
Long Read ◽  
Inorganic Molecules ◽  
Standard Molecular Biology

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.

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 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.

scholarly journals Single-Molecule Detection of DNA in a Nanochannel by High-Field Strength-Assisted Electrical Impedance Spectroscopy

Micromachines ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 189 ◽  
Author(s):  
Porpin Pungetmongkol ◽  
Takatoki Yamamoto
Keyword(s):  
Single Molecule ◽  
High Intensity ◽  
High Sensitivity ◽  
Electrical Impedance Spectroscopy ◽  
Random Coil ◽  
Label Free ◽  
Electrode Gap ◽  
Label Free Detection ◽  
Intensity Field ◽  
Nanogap Electrodes

Many researchers have fabricated micro and nanofluidic devices incorporating optical, chemical, and electrical detection systems with the aim of achieving on-chip analysis of macromolecules. The present study demonstrates a label-free detection of DNA using a nanofluidic device based on impedance measurements that is both sensitive and simple to operate. Using this device, the electrophoresis and dielectrophoresis effect on DNA conformation and the length dependence were examined. A low alternating voltage was applied to the nanogap electrodes to generate a high intensity field (>0.5 MV/m) under non-faradaic conditions. In addition, a 100 nm thick gold electrode was completely embedded in the substrate to allow direct measurements of a solution containing the sample passing through the gap, without any surface modification required. The high intensity field in this device produced a dielectrophoretic force that stretched the DNA molecule across the electrode gap at a specific frequency, based on back and forth movements between the electrodes with the DNA in a random coil conformation. The characteristics of 100 bp, 500 bp, 1 kbp, 5 kbp, 10 kbp, and 48 kbp λ DNA associated with various conformations were quantitatively analyzed with high resolution (on the femtomolar level). The sensitivity of this system was found to be more than about 10 orders of magnitude higher than that obtained from conventional linear alternating current (AC) impedance for the analysis of bio-polymers. This new high-sensitivity process is expected to be advantageous with regard to the study of complex macromolecules and nanoparticles.

scholarly journals Photonic Biosensor for Label-Free Detection Based on Photonic Nanostructures on Si-Waveguide Ring Resonator

2021 ◽  
Vol 6 (1) ◽  
pp. 39
Author(s):  
Hoang Anh Truong ◽  
Yugang Shang ◽  
Shunsuke Abe ◽  
Nobuyuki Matsuda ◽  
Hirohito Yamada
Keyword(s):  
Quality Factor ◽  
Ring Resonator ◽  
Clinical Diagnostics ◽  
Label Free ◽  
Electromagnetic Simulations ◽  
Label Free Detection ◽  
Matter Interaction ◽  
Light Matter Interaction ◽  
Conventional Structure ◽  
Waveguide Ring

A new structure of a micro-ring resonator for label-free biosensing is proposed. The structure includes sidewall-grating Si waveguide and periodical side-blocks that can enhance the light–matter interaction. From the electromagnetic simulations, the proposed structure exhibits a four-fold improvement in terms of sensitivity compared with the conventional structure. Moreover, the quality factor of the proposed structure is not degraded from that of the conventional structure. The improved sensitivity is promising for the detection of nanoparticles that can be applied to the environmental field and clinical diagnostics.

scholarly journals Cross-Inhibitor: a time-sensitive molecular circuit based on DNA strand displacement

2020 ◽  
Vol 48 (19) ◽  
pp. 10691-10701
Author(s):  
Chanjuan Liu ◽  
Yuan Liu ◽  
Enqiang Zhu ◽  
Qiang Zhang ◽  
Xiaopeng Wei ◽  
...  
Keyword(s):  
Input Signal ◽  
Dna Nanotechnology ◽  
Strand Displacement ◽  
Important Goal ◽  
Molecular Systems ◽  
Molecular Programming ◽  
Dna Strand Displacement ◽  
Input Signals ◽  
Biochemical Systems ◽  
Dna Strand

Abstract Designing biochemical systems that can be effectively used in diverse fields, including diagnostics, molecular computing and nanomachines, has long been recognized as an important goal of molecular programming and DNA nanotechnology. A key issue in the development of such practical devices on the nanoscale lies in the development of biochemical components with information-processing capacity. In this article, we propose a molecular device that utilizes DNA strand displacement networks and allows interactive inhibition between two input signals; thus, it is termed a cross-inhibitor. More specifically, the device supplies each input signal with a processor such that the processing of one input signal will interdict the signal of the other. Biochemical experiments are conducted to analyze the interdiction performance with regard to effectiveness, stability and controllability. To illustrate its feasibility, a biochemical framework grounded in this mechanism is presented to determine the winner of a tic-tac-toe game. Our results highlight the potential for DNA strand displacement cascades to act as signal controllers and event triggers to endow molecular systems with the capability of controlling and detecting events and signals.

One-pot dual product synthesis of hierarchical Co3O4@N-rGO for supercapacitors, N-GDs for label-free detection of metal ion and bio-imaging applications

2018 ◽  
Vol 44 (3) ◽  
pp. 2869-2883 ◽  
Author(s):  
Raji Atchudan ◽  
Thomas Nesakumar Jebakumar Immanuel Edison ◽  
Dasagrandhi Chakradhar ◽  
Namachivayam Karthik ◽  
Suguna Perumal ◽  
...  
Keyword(s):  
Metal Ion ◽  
Label Free ◽  
One Pot ◽  
Label Free Detection ◽  
Bio Imaging
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