scholarly journals Functionalized carbon nanotube electrodes for controlled DNA sequencing

2020 ◽  
Vol 2 (9) ◽  
pp. 4041-4050 ◽  
Author(s):  
Rameshwar L. Kumawat ◽  
Biswarup Pathak
Keyword(s):  
Carbon Nanotube ◽  
Solid State ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Single Molecule Level ◽  
Sequencing Technique ◽  
Dna Strands ◽  
Functionalized Carbon Nanotube

The TOC features a scheme of the solid-state nanogap-based DNA sequencing technique. DNA strands can be analyzed at the single-molecule level by translocation through the guanine probe-functionalized closed-end cap armchair CNT (6,6) nanogap setup.

scholarly journals Extended topological line defects in graphene for individual identification of DNA nucleobases

2020 ◽  
Vol 1 (8) ◽  
pp. 2908-2916 ◽  
Author(s):  
Rameshwar L. Kumawat ◽  
Biswarup Pathak
Keyword(s):  
Solid State ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Individual Identification ◽  
Single Molecule Level ◽  
Line Defects ◽  
Dna Nucleobases

The TOC features a scheme of solid-state nanochannel-based DNA sequencing techniques. DNA nucleobases can be analyzed at the single-molecule level by adsorption on topologically extended line defects in the graphene-based electrode setup.

scholarly journals Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets

2019 ◽  
Vol 47 (17) ◽  
pp. e101-e101 ◽  
Author(s):  
Boris Breiner ◽  
Kerr Johnson ◽  
Magdalena Stolarek ◽  
Ana-Luisa Silva ◽  
Aurel Negrea ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Dna Polymerases ◽  
Single Molecule Detection ◽  
Synthesis Methods ◽  
Single Nucleotide ◽  
New Approach ◽  
Fluorescent Signal ◽  
Single Molecule Level ◽  
Current Sequence

AbstractA new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.

DNA-Sequencing at the single molecule level

2001 ◽  
Vol 86 (3) ◽  
pp. 161 ◽  
Author(s):  
Rudolf Rigler ◽  
Frank Seela
Keyword(s):  
Dna Sequencing ◽  
Single Molecule ◽  
Single Molecule Level

scholarly journals Nanopore microscope identifies RNA isoforms with structural colors

2021 ◽  
Author(s):  
Filip N Boskovic ◽  
Ulrich Felix Keyser
Keyword(s):  
Single Molecule ◽  
Three Dimensional ◽  
Rna Structures ◽  
Transcript Isoforms ◽  
Single Molecule Level ◽  
Structural Colors ◽  
Rna Targets ◽  
Dna Strands ◽  
One Step ◽  
Simultaneous Identification

Identifying RNA transcript isoforms requires intricate protocols that suffer from various enzymatic biases. Here we design three-dimensional molecular constructs that enable identification of transcript isoforms at the single-molecule level using solid-state nanopore microscopy. We refold target RNA into RNA identifiers (IDs) with designed sets of complementary DNA strands. Each reshaped molecule carries a unique sequence of structural (pseudo)colors. Structural colors consist of DNA structures, protein labels, native RNA structures, or a combination of all three. The sequence of structural colors of RNA IDs enables simultaneous identification and relative quantification of multiple RNA targets without prior amplification. Our Amplification-free RNA TargEt Multiplex Isoform Sensing (ARTEMIS) reveals structural arrangements in native transcripts in agreement with published variants. ARTEMIS discriminates circular and linear transcript isoforms in a one step, enzyme-free reaction in a complex human transcriptome using single-molecule readout.

scholarly journals Application of Solid-State Nanopore in Protein Detection

2020 ◽  
Vol 21 (8) ◽  
pp. 2808 ◽  
Author(s):  
Yuhan Luo ◽  
Linlin Wu ◽  
Jing Tu ◽  
Zuhong Lu
Keyword(s):  
Solid State ◽  
Chemical Modification ◽  
Single Molecule ◽  
Protein Detection ◽  
High Sensitivity ◽  
Protein Sequencing ◽  
Its Sequence ◽  
Sequence Structure ◽  
Single Molecule Level ◽  
Protein Molecules

A protein is a kind of major biomacromolecule of life. Its sequence, structure, and content in organisms contains quite important information for normal or pathological physiological process. However, research of proteomics is facing certain obstacles. Only a few technologies are available for protein analysis, and their application is limited by chemical modification or the need for a large amount of sample. Solid-state nanopore overcomes some shortcomings of the existing technology, and has the ability to detect proteins at a single-molecule level, with its high sensitivity and robustness of device. Many works on detection of protein molecules and discriminating structure have been carried out in recent years. Single-molecule protein sequencing techniques based on solid-state nanopore are also been proposed and developed. Here, we categorize and describe these efforts and progress, as well as discuss their advantages and drawbacks.

Solid-state nanopores for biosensing with submolecular resolution

2012 ◽  
Vol 40 (4) ◽  
pp. 624-628 ◽  
Author(s):  
Azadeh Bahrami ◽  
Fatma Doğan ◽  
Deanpen Japrung ◽  
Tim Albrecht
Keyword(s):  
Solid State ◽  
Dna Sequencing ◽  
Single Molecule ◽  
Dna Interactions ◽  
Patch Clamp Technique ◽  
New Class ◽  
Protein Dna Interactions ◽  
Transmembrane Pores ◽  
Recent Developments ◽  
Detection Of Biomolecules

Biological cell membranes contain various types of ion channels and transmembrane pores in the 1–100 nm range, which are vital for cellular function. Individual channels can be probed electrically, as demonstrated by Neher and Sakmann in 1976 using the patch-clamp technique [Neher and Sakmann (1976) Nature 260, 799–802]. Since the 1990s, this work has inspired the use of protein or solid-state nanopores as inexpensive and ultrafast sensors for the detection of biomolecules, including DNA, RNA and proteins, but with particular focus on DNA sequencing. Solid-state nanopores in particular have the advantage that the pore size can be tailored to the analyte in question and that they can be modified using semi-conductor processing technology. This establishes solid-state nanopores as a new class of single-molecule biosensor devices, in some cases with submolecular resolution. In the present review, we discuss a few of the most important recent developments in this field and how they might be applied to studying protein–protein and protein–DNA interactions or in the context of ultra-fast DNA sequencing.

scholarly journals Single molecule based SNP detection using designed DNA carriers and solid-state nanopores

2017 ◽  
Vol 53 (2) ◽  
pp. 436-439 ◽  
Author(s):  
Jinglin Kong ◽  
Jinbo Zhu ◽  
Ulrich F. Keyser
Keyword(s):  
Solid State ◽  
Single Molecule ◽  
Strand Displacement ◽  
Snp Detection ◽  
Single Molecule Level ◽  
Dna Strand Displacement ◽  
Dna Strand ◽  
Dna Carriers

A novel nanopore-DNA carrier method is demonstrated for SNP detection and following DNA strand displacement kinetics at the single molecule level.

scholarly journals Impact of Small Molecules on Intermolecular G-Quadruplex Formation

Molecules ◽  
2019 ◽  
Vol 24 (8) ◽  
pp. 1570 ◽  
Author(s):  
Prabesh Gyawali ◽  
Keshav GC ◽  
Yue Ma ◽  
Sanjaya Abeysirigunawardena ◽  
Kazuo Nagasawa ◽  
...  
Keyword(s):  
Small Molecules ◽  
Single Molecule ◽  
The Other ◽  
Single Molecule Level ◽  
G Quadruplex ◽  
Dna Strands ◽  
Order Of Magnitude ◽  
Single Molecule Studies ◽  
Quadruplex Formation ◽  
The Impact

We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC3) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.

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