The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide-Nucleic Acid Sequences

Quantum leaps advances in the single-molecule investigative science have been made possible over the past decades through the implication of nanopores, as versatile components on dedicated biosensors. Here, we employed the nanopore-tweezing technique to capture amino acid-functionalized, peptide-nucleic acids (PNA) with -hemolysin-based nanopores, and correlate the ensuing stochastic fluctuations of the ionic current through the nanopore with the composition and order of bases in the PNAs primary structure. We demonstrate that while the system enables detection of distinct bases on homopolymeric PNA or triplet bases on heteropolymeric strands, it also reveals rich insights into the conformational dynamics of the entrapped PNA within the nanopore, relevant for perfecting the recognition capability single-molecule sequencing.

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The Nanopore-Tweezing-Based, Targeted Detection of Nucleobases on Short Functionalized Peptide Nucleic Acid Sequences

Polymers ◽

10.3390/polym13081210 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1210

Author(s):

Isabela S. Dragomir ◽

Alina Asandei ◽

Irina Schiopu ◽

Ioana C. Bucataru ◽

Loredana Mereuta ◽

...

Keyword(s):

Single Molecule ◽

Peptide Nucleic Acid ◽

Conformational Dynamics ◽

Ionic Current ◽

Molecular Medicine ◽

Single Molecule Sequencing ◽

Stochastic Fluctuations ◽

Wide Range ◽

Targeted Detection ◽

Recognition Capability

The implication of nanopores as versatile components in dedicated biosensors, nanoreactors, or miniaturized sequencers has considerably advanced single-molecule investigative science in a wide range of disciplines, ranging from molecular medicine and nanoscale chemistry to biophysics and ecology. Here, we employed the nanopore tweezing technique to capture amino acid-functionalized peptide nucleic acids (PNAs) with α-hemolysin-based nanopores and correlated the ensuing stochastic fluctuations of the ionic current through the nanopore with the composition and order of bases in the PNAs primary structure. We demonstrated that while the system enables the detection of distinct bases on homopolymeric PNA or triplet bases on heteropolymeric strands, it also reveals rich insights into the conformational dynamics of the entrapped PNA within the nanopore, relevant for perfecting the recognition capability of single-molecule sequencing.

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Segmentation of Noisy Signals Generated By a Nanopore

10.1101/014258 ◽

2015 ◽

Author(s):

Jacob Matthew Schreiber ◽

Kevin Karplus

Keyword(s):

Real Time ◽

Single Molecule ◽

Ionic Current ◽

Divide And Conquer ◽

Single Molecule Sequencing ◽

Automated Method ◽

Noisy Signals ◽

Low Pass ◽

Current Steps ◽

Pass Through

Nanopore-based single-molecule sequencing techniques exploit ionic current steps produced as biomolecules pass through a pore to reconstruct properties of the sequence. A key task in analyzing complex nanopore data is discovering the boundaries between these steps, which has traditionally been done in research labs by hand. We present an automated method of analyzing nanopore data, by detecting regions of ionic current corresponding to the translocation of a biomolecule, and then segmenting the region. The segmenter uses a divide-and-conquer method to recursively discover boundary points, with an implementation that works several times faster than real time and that can handle low-pass filtered signals.

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Ionic Current Through a 3 NM in Diameter Nanopore

Volume 12: Micro and Nano Systems, Parts A and B ◽

10.1115/imece2009-11844 ◽

2009 ◽

Author(s):

Yanyan Ge ◽

Yunfei Chen ◽

Dongyan Xu ◽

Juekuan Yang ◽

Deyu Li

Keyword(s):

Single Molecule ◽

Ionic Current ◽

Current Data ◽

Double Layers ◽

The Novel ◽

High Concentration ◽

Electric Double Layers ◽

The Past ◽

Published Research ◽

Significant Attention

Ionic current through highly confined nanochannels receives significant attention over the past decade because of the novel phenomena from the overlapped electric double layers. In addition, nanoscale Coulter-type single molecule sensors detect the modulation of ionic current through individual nanopores to sense the translocation of single molecules or nanoparticles. The baseline ionic current and its noise determine the sensitivity of the Coulter-type single molecule sensors. All published research on ionic current through nanochannels focuses on the effects of overlapped electric double layers without paying much attention to the ionic transport through nanopores for high concentration electrolytes with non-overlapped double layer. Therefore, the ionic current data for high concentration electrolytes through nanochannels are limited and not systematic.

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Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

Physical Chemistry Chemical Physics ◽

10.1039/d0cp05759b ◽

2021 ◽

Vol 23 (1) ◽

pp. 219-228

Author(s):

Nabanita Saikia ◽

Mohamed Taha ◽

Ravindra Pandey

Keyword(s):

Nucleic Acid ◽

Boron Nitride ◽

Nucleic Acids ◽

Dynamic Stability ◽

Peptide Nucleic Acid ◽

Rational Design ◽

Peptide Nucleic Acids ◽

Boron Nitride Nanotubes ◽

Molecular Hybrids ◽

Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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Monitoring the Structural Dynamics of U2 snRNA Via Single-Molecule Förster Resonance Energy Transfer

10.31237/osf.io/9j8gq ◽

2018 ◽

Author(s):

Alexander Carl DeHaven

Keyword(s):

Energy Transfer ◽

Structural Dynamics ◽

Single Molecule ◽

Conformational Dynamics ◽

Resonance Energy Transfer ◽

Resonance Energy ◽

Förster Resonance Energy Transfer ◽

U2 Snrna ◽

Folding Dynamics ◽

The Impact

This thesis contains four topic areas: a review of single-molecule microscropy methods and splicing, conformational dynamics of stem II of the U2 snRNA, the impact of post-transcriptional modifications on U2 snRNA folding dynamics, and preliminary findings on Mango aptamer folding dynamics.

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