Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements

Sen, Yi Heng; Jain, Tarun; Aguilar, Carlos A.; Karnik, Rohit

doi:10.1039/c2lc20771k

Cited by 25 publications

(27 citation statements)

References 32 publications

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“…The transient current spike is a serious problem for the nanopore control experiment, since the translocation events during the saturated period will not be detected, and missing a recaptured translocation event will invalidate the ping-pong control process of a single DNA molecule [17][18][19]. To quantitatively analyze the transient spike effects on the nanopore control experiment, we define the saturated period as prohibited time.…”

Section: Methodsmentioning

confidence: 99%

“…It saturates the data acquisition system and prevents the detection of instantly recaptured molecules. As a result, the continuous ping-pong control of a single DNA molecule will fail [19] since the translocation of another molecule will trigger the electronics servo. To diminish membrane capacitance effects, Dimitrov et al [20] designed a complex nanopore structure and modified the electronic system to minimize the transient current spike.…”

Section: Introductionmentioning

confidence: 99%

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Detection and analysis of DNA recapture through a solid-state nanopore

Zhou

Shan

et al. 2014

Chin. Sci. Bull.

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Motion control of a single molecule through a solid-state nanopore offers a new perspective on detecting and analyzing single biomolecules. Repeat recapture of a single DNA molecule reveals the dynamics in DNA translocation through a nanopore and may significantly increase the signal-to-noise ratio for DNA base distinguishing. However, the transient current at the moment of voltage reversal prevents the observation of instantly recaptured molecules and invalidates the continuous DNA ping-pong control. We performed and analyzed the DNA translocation and recapture experiment in a silicon nitride solid-state nanopore. Numerical calculation of molecular motion clearly shows the recapture dynamics with different delay times. The prohibited time when the data acquisition system is saturated by the transient current is derived by equivalent circuit analysis and finite element simulation. The COMSOL simulation reveals that the membrane capacitance plays an important role in determining the electric field distribution during the charging process. As a result of the transient charging process, a non-constant driving force pulls the DNA back to nanopores faster than theoretically predicted. The observed long time constant in the transient current trace is explained by the dielectric absorption of the membrane capacitor.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Detection and analysis of DNA recapture through a solid-state nanopore

Zhou

Shan

et al. 2014

Chin. Sci. Bull.

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“…For example, fragmented genomic DNA can be sized by measuring the translocation time through a nanochannel shorter than the contour length in pulsed electrical fields 50 . A benefit of this method is that molecules can be detected electronically, obviating the need for molecular labeling and expensive optical equipment that limits portability 51 . However, improvements in sizing resolution would be necessary, for example by performing multiple measurements on each molecule for statistical averaging 51 .…”

Section: Assessment Modalitiesmentioning

confidence: 99%

Analysis of single nucleic acid molecules in micro- and nano-fluidics

2016

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Nucleic acid analysis has enhanced our understanding of biological processes and disease progression, elucidated the association of genetic variants and disease, and led to the design and implementation of new treatment strategies. These diverse applications require analysis of a variety of characteristics of nucleic acid molecules: size or length, detection or quantification of specific sequences, mapping of the general sequence structure, full sequence identification, analysis of epigenetic modifications, and observation of interactions between nucleic acids and other biomolecules. Strategies that can detect rare or transient species, characterize population distributions, and analyze small sample volumes enable the collection of richer data from biosamples. Platforms that integrate micro- and nano- fluidic operations with high sensitivity single molecule detection facilitate manipulation and detection of individual nucleic acid molecules. In this review, we will highlight important milestones and recent advances in single molecule nucleic acid analysis in micro- and nano- fluidic platforms. We focus on assessment modalities for single nucleic acid molecules and highlight the role of micro- and nano- structures and fluidic manipulation. We will also briefly discuss future directions and the current limitations and obstacles impeding even faster progress toward these goals.

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“…75 Multiple measurements made on ss-DNA with a PDMS nanopore increases measurement precision. 76 Recapture of ss-DNA is accomplished with a solid state nanopore for dynamic information of strand conformation. 77 Nanoparticle dynamics are measured by multiple passes through a single glass nanopipette 78 and a single track-etched pore in a PET membrane.…”

Section: Multiple Resistive-pulse Measurements On Single Particlesmentioning

confidence: 99%

Conductivity-based detection techniques in nanofluidic devices

Harms

Haywood

Kneller

et al. 2015

Analyst

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This review covers conductivity detection in fabricated nanochannels and nanopores. Improvements in nanoscale sensing are a direct result of advances in fabrication techniques, which produce devices with channels and pores with reproducible dimensions and in a variety of materials. Analytes of interest are detected by measuring changes in conductance as the analyte accumulates in the channel or passes transiently through the pore. These detection methods take advantage of phenomena enhanced at the nanoscale, such as ion current rectification, surface conductance, and dimensions comparable to the analytes of interest. The end result is the development of sensing technologies for a broad range of analytes, e.g., ions, small molecules, proteins, nucleic acids, and particles.

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Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements

Cited by 25 publications

References 32 publications

Detection and analysis of DNA recapture through a solid-state nanopore

Detection and analysis of DNA recapture through a solid-state nanopore

Analysis of single nucleic acid molecules in micro- and nano-fluidics

Conductivity-based detection techniques in nanofluidic devices

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