A new approach to fragment assembly in DNA sequencing

2001 ◽  
Author(s):  
Pavel A. Pevzner ◽  
Haixu Tang ◽  
Michael S. Waterman
Keyword(s):  
Dna Sequencing ◽  
New Approach ◽  
Fragment Assembly

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.

scholarly journals Botanical Origin of the Brazilian Red Propolis: a New Approach Using DNA analysis

2014 ◽  
Vol 58 (2) ◽  
pp. 79-85 ◽  
Author(s):  
Sona Jain ◽  
Giulia Marchioro ◽  
Lucyana Mendonça ◽  
Marcus Batista ◽  
Edilson Araujo
Keyword(s):  
Dna Sequencing ◽  
Dna Analysis ◽  
Chemical Constituents ◽  
Universal Primers ◽  
Chemical Compositions ◽  
Botanical Origin ◽  
Chemical Marker ◽  
New Approach ◽  
Geographical Regions ◽  
Fast Liquid Chromatography

Abstract Propolis is produced by the honeybees by using resin and other plant secretions. Propolis from different geographical regions have different chemical compositions. This is because the chemical constituents of propolis depend on the vegetation surrounding the apiary. In this report we present a new approach using DNA barcoding for the identification of the botanical origin of propolis. Red propolis samples were collected at different times of the year from the state of Sergipe situated in Northeast Brazil. Extraction of the DNA from propolis was made using a CTA B method. Amplification was done using ITS 2 universal primers, followed by DNA sequencing. Sequence analysis confirmed the presence of Dalbergia ecastaphyllum in the Brazilian red propolis. Formononetin is a chemical marker for the Brazillian red propolis and D. ecastaphyllum. Propolis samples analysed by DNA sequencing, were also checked by Ultra-Fast Liquid Chromatography for the presence of formononetin. Peaks corresponding to formononetin were observed in all the analysed propolis samples. This is the first report of the botanical origin of propolis using DNA technology.

scholarly journals VLSI Structures for DNA Sequencing—A Survey

2020 ◽  
Vol 7 (2) ◽  
pp. 49
Author(s):  
Mohammad A. Islam ◽  
Palash K. Datta ◽  
Harley Myler
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Biomedical Research ◽  
Field Effect ◽  
Field Effect Transistors ◽  
Implementation Strategies ◽  
Metal Oxide Semiconductor ◽  
Oxide Semiconductor ◽  
New Approach ◽  
Technical Advances

DNA sequencing is a critical functionality in biomedical research, and technical advances that improve it have important implications for human health. Novel methods by which sequencing can be accomplished in more accurate, high-throughput, and faster ways are in development. Here, we review VLSI biosensors for nucleotide detection and DNA sequencing. Implementation strategies are discussed and split into function-specific architectures that are presented for reported design examples from the literature. Lastly, we briefly introduce a new approach to sequencing using Gate All-Around (GAA) nanowire Metal Oxide Semiconductor Field Effect Transistors (MOSFETs) that has significant implications for the field.

scholarly journals A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Maitane Ezquerra-Inchausti ◽  
Ander Anasagasti ◽  
Olatz Barandika ◽  
Gonzaga Garay-Aramburu ◽  
Marta Galdós ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Novel Mutations ◽  
New Approach ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Pooled Dna

scholarly journals Microfluidics for rapid detection of isocitrate dehydrogenase 1 mutation for intraoperative application

2016 ◽  
Vol 124 (6) ◽  
pp. 1611-1618 ◽  
Author(s):  
Abudumijiti Aibaidula ◽  
Wang Zhao ◽  
Jin-song Wu ◽  
Hong Chen ◽  
Zhi-feng Shi ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Isocitrate Dehydrogenase ◽  
Soft Lithography ◽  
Idh1 Mutation ◽  
Fluorescence Signal ◽  
Wild Type ◽  
Isocitrate Dehydrogenase 1 ◽  
Tissue Samples ◽  
Mutation Status ◽  
New Approach

OBJECT Conventional methods for isocitrate dehydrogenase 1 (IDH1) detection, such as DNA sequencing and immunohistochemistry, are time- and labor-consuming and cannot be applied for intraoperative analysis. To develop a new approach for rapid analysis of IDH1 mutation from tiny tumor samples, this study used microfluidics as a method for IDH1 mutation detection. METHODS Forty-seven glioma tumor samples were used; IDH1 mutation status was investigated by immunohistochemistry and DNA sequencing. The microfluidic device was fabricated from polydimethylsiloxane following standard soft lithography. The immunoanalysis was conducted in the microfluidic chip. Fluorescence images of the on-chip microcolumn taken by the charge-coupled device camera were collected as the analytical results readout. Fluorescence signals were analyzed by NIS-Elements software to gather detailed information about the IDH1 concentration in the tissue samples. RESULTS DNA sequencing identified IDH1 R132H mutation in 33 of 47 tumor samples. The fluorescence signal for IDH1-mutant samples was 5.49 ± 1.87 compared with 3.90 ± 1.33 for wild type (p = 0.005). Thus, microfluidics was capable of distinguishing IDH1-mutant tumor samples from wild-type samples. When the cutoff value was 4.11, the sensitivity of microfluidics was 87.9% and the specificity was 64.3%. CONCLUSIONS This new approach was capable of analyzing IDH1 mutation status of tiny tissue samples within 30 minutes using intraoperative microsampling. This approach might also be applied for rapid pathological diagnosis of diffuse gliomas, thus guiding personalized resection.

scholarly journals DNA Sequencing with [α-33P]-Labeled ddNTP Terminators: A New Approach to DNA Sequencing with ThermoTM Sequenase DNA Polymerase

BioTechniques ◽  
1996 ◽  
Vol 21 (6) ◽  
pp. 1132-1137 ◽  
Author(s):  
J. Fan ◽  
R.S. Ranu ◽  
C. Smith ◽  
C. Ruan ◽  
C.W. Fuller
Keyword(s):  
Dna Sequencing ◽  
Dna Polymerase ◽  
New Approach

scholarly journals Author Correction: A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Maitane Ezquerra-Inchausti ◽  
Ander Anasagasti ◽  
Olatz Barandika ◽  
Gonzaga Garay-Aramburu ◽  
Marta Galdós ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Novel Mutations ◽  
New Approach ◽  
Inherited Retinal Dystrophies ◽  
Retinal Dystrophies ◽  
Pooled Dna

Targeted DNA sequencing for assessing clonality in multiple lung tumors: A new approach to an old dilemma

Lung Cancer ◽  
2018 ◽  
Vol 122 ◽  
pp. 120-123 ◽  
Author(s):  
I. Eguren-Santamaria ◽  
R. Sanchez-Bayona ◽  
A. Patiño-Garcia ◽  
Ignacio Gil-Bazo ◽  
J.M. Lopez-Picazo
Keyword(s):  
Dna Sequencing ◽  
Lung Tumors ◽  
New Approach
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