Steve Turner on "Single Molecule Real Time DNA Sequencing"

SciVee ◽  
2009 ◽  
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule

Long-Read, Single Molecule, Real-Time (SMRT) DNA Sequencing for Metagenomic Applications

2015 ◽  
pp. 25-38 ◽  
Author(s):  
Brett Bowman ◽  
Mincheol Kim ◽  
Yong-Joon Cho ◽  
Jonas Korlach
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Long Read

scholarly journals Five Closed Salmonella enterica Genome Sequences from a 2017–2018 Multistrain, Multistate Kratom Outbreak

2020 ◽  
Vol 9 (3) ◽  
Author(s):  
Hallie E. Rauch ◽  
Julie Haendiges ◽  
Maria Balkey ◽  
Maria Hoffmann
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Salmonella Enterica ◽  
Genome Sequences ◽  
Circular Chromosome ◽  
Content Type ◽  
Single Plasmid

We report here the closed genomes of Salmonella enterica strains from the 2017–2018 multistrain, multistate kratom outbreak using single-molecule real-time DNA sequencing. Four of the genomes consist of one circular chromosome, and the fifth has a circular chromosome and a single plasmid.

scholarly journals Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

2011 ◽  
Vol 40 (4) ◽  
pp. e29-e29 ◽  
Author(s):  
Tyson A. Clark ◽  
Iain A. Murray ◽  
Richard D. Morgan ◽  
Andrey O. Kislyuk ◽  
Kristi E. Spittle ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Dna Methyltransferase

Abstract 1154: Direct detection of DNA methylation and mutagenic damage through single-molecule, real-time (SMRTTM) DNA sequencing

2010 ◽  
Author(s):  
Benjamin Flusberg ◽  
Dale Webster ◽  
Kevin Travers ◽  
Eric Olivares ◽  
Jonas Korlach ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Direct Detection

HLA-DPB1*64:01N and DPB1*701:01 sequence extensions by single molecule real-time DNA sequencing

HLA ◽  
2018 ◽  
Vol 92 (6) ◽  
pp. 426-427 ◽  
Author(s):  
Charlotte A. Cambridge ◽  
Thomas R. Turner ◽  
Jashan P. Abraham ◽  
Steven G. E. Marsh ◽  
Neema P. Mayor
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule

scholarly journals Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array

2016 ◽  
Vol 113 (19) ◽  
pp. 5233-5238 ◽  
Author(s):  
Carl W. Fuller ◽  
Shiv Kumar ◽  
Mintu Porel ◽  
Minchen Chien ◽  
Arek Bibillo ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Lipid Bilayers ◽  
Dna Polymerase ◽  
Single Molecule ◽  
High Throughput Sequencing ◽  
Electrical Current ◽  
Sequencing Data ◽  
Sequencing By Synthesis ◽  
Dna Strand

DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5′-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform. We designed and synthesized several polymer-tagged nucleotides using tags that produce different electrical current blockade levels and verified they are active substrates for DNA polymerase. A highly processive DNA polymerase was conjugated to the nanopore, and the conjugates were complexed with primer/template DNA and inserted into lipid bilayers over individually addressable electrodes of the nanopore chip. When an incoming complementary-tagged nucleotide forms a tight ternary complex with the primer/template and polymerase, the tag enters the pore, and the current blockade level is measured. The levels displayed by the four nucleotides tagged with four different polymers captured in the nanopore in such ternary complexes were clearly distinguishable and sequence-specific, enabling continuous sequence determination during the polymerase reaction. Thus, real-time single-molecule electronic DNA sequencing data with single-base resolution were obtained. The use of these polymer-tagged nucleotides, combined with polymerase tethering to nanopores and multiplexed nanopore sensors, should lead to new high-throughput sequencing methods.

Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines

HLA ◽  
2017 ◽  
Vol 91 (2) ◽  
pp. 88-101 ◽  
Author(s):  
T. R. Turner ◽  
J. D. Hayhurst ◽  
D. R. Hayward ◽  
W. P. Bultitude ◽  
D. J. Barker ◽  
...  
Keyword(s):  
High Resolution ◽  
Dna Sequencing ◽  
Real Time ◽  
Cell Lines ◽  
Single Molecule ◽  
Hla Genes

Single molecule real‐time DNA sequencing of the full HLA‐E gene for 212 reference cell lines

HLA ◽  
2020 ◽  
Vol 95 (6) ◽  
pp. 561-572 ◽  
Author(s):  
Jonathan A. M. Lucas ◽  
James D. Hayhurst ◽  
Thomas R. Turner ◽  
Arthur W. Gymer ◽  
Gayle Leen ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Cell Lines ◽  
Single Molecule ◽  
Reference Cell ◽  
E Gene

A review of DNA sequencing techniques

2002 ◽  
Vol 35 (2) ◽  
pp. 169-200 ◽  
Author(s):  
Lilian T. C. França ◽  
Emanuel Carrilho ◽  
Tarso B. L. Kist
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Fluorescent Dyes ◽  
Read Length ◽  
Chemical Methods ◽  
Single Molecule Sequencing ◽  
Exonuclease Digestion ◽  
Speed Accuracy ◽  
Sanger Method

1. Summary 1692. Introduction 1703. Sanger's method and other enzymic methods 1703.1 Random approach 1713.2 Direct approach 1713.3 Enzyme technology 1753.4 Sample preparation 1753.5 Labels and DNA labelling 1763.5.1 Radioisotopes 1763.5.2 Chemiluminescent detection 1763.5.3 Fluorescent dyes 1773.6 Fragment separation and analysis 1803.6.1 Electrophoresis 1803.6.2 Mass spectrometry – an alternative 1824. Maxam & Gilbert and other chemical methods 1835. Pyrosequencing – DNA sequencing in real time by the detection of released PPi 1876. Single molecule sequencing with exonuclease 1907. Conclusion 1928. Acknowledgements 1929. References 193The four best known DNA sequencing techniques are reviewed. Important practical issues covered are read-length, speed, accuracy, throughput, cost, as well as the automation of sample handling and preparation. The methods reviewed are: (i) the Sanger method and its most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other chemical methods; (iii) the PyrosequencingTM method – DNA sequencing in real time by the detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with exonuclease (exonuclease digestion of a single molecule composed of a single strand of fluorescently labelled deoxynucleotides). Each method is briefly described, the current literature is covered, advantages, disadvantages, and the most suitable applications of each method are discussed.

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