Direct detection of unamplified genomic DNA based on photo-induced silver ion reduction by DNA molecules

2013 ◽  
Vol 49 (23) ◽  
pp. 2350 ◽  
Author(s):  
Ye Lim Jung ◽  
Cheulhee Jung ◽  
Jung Hun Park ◽  
Moon Il Kim ◽  
Hyun Gyu Park
Keyword(s):  
Genomic Dna ◽  
Direct Detection ◽  
Silver Ion ◽  
Dna Molecules

Direct detection of genomic DNA with fluidic force discrimination assays

2009 ◽  
Vol 392 (2) ◽  
pp. 139-144 ◽  
Author(s):  
S.P. Mulvaney ◽  
C.N. Ibe ◽  
C.R. Tamanaha ◽  
L.J. Whitman
Keyword(s):  
Genomic Dna ◽  
Direct Detection

scholarly journals Monotonous behavior with 2-propanol converts into reentrant transition with 1-propanol: Higher-order structure of DNA

2019 ◽  
Author(s):  
Y. Ma ◽  
Y. Yoshikawa ◽  
K. Yoshikawa
Keyword(s):  
Secondary Structure ◽  
Genomic Dna ◽  
Conformational Transitions ◽  
Higher Order ◽  
Point Of View ◽  
Order Structure ◽  
Chemical Physics ◽  
Dna Molecules ◽  
Unfolded State ◽  
Compact State

ABSTRACTIn the present study, we measured the changes in the higher-order structure of genomic DNA molecules in the presence of alcohols through single-DNA observation by use of fluorescence microscopy, with particular focus on the different effects of 1-propanol and 2-propanol. The results showed that, with an increasing concentration of 1-propanol, DNA exhibits reentrant conformational transitions from an elongated coil to a folded globule, and then to an unfolded state. On the other hand, with 2-propanol, DNA exhibits monotonous shrinkage into a compact state. Thus, DNA molecules are more effectively condensed/precipitated with 2-propanol than with 1-propanol. The propanol isomers also had different effects on the changes in the secondary structure of DNA, as revealed by circular dichroism (CD) measurements. With 1-propanol, DNA maintains a B-form secondary structure. An A-like conformation appears with the addition of 2-propanol.STATEMENT OF SIGNIFICANCECurrently, 2-propanol has most often been used as the solvent to extract and purify genomic DNA molecules from living cells, according the protocols in molecular biology and biochemistry. Unfortunately, the reason why usage of 2-propanol is recommended instead of ethanol and 1-propanol has never been explained in a clear manner. We believe that the new insight based on chemical physics point of view would play an important role for the development of current chemical procedures/treatments adapted on an empirical basis.

scholarly journals Conversion of Genomic DNA to Proxy Constructs Suitable for Accurate Nanopore Sequencing

2015 ◽  
Author(s):  
Dimitra Tsavachidou
Keyword(s):  
Dna Sequence ◽  
Genomic Dna ◽  
Average Length ◽  
Consensus Sequence ◽  
Whole Genome ◽  
Nanopore Sequencing ◽  
Ion Torrent ◽  
Dna Molecules ◽  
Dna Fragment ◽  
Genome Level

AbstractNanopore sequencing at single-base resolution is challenging. There are developing technologies to convert DNA molecules to expanded constructs. Such constructs can be sequenced by nanopores in place of the original DNA molecules. We present a novel method for converting genomic DNA to expanded constructs (“proxies”) with 99.67% accuracy. Our method “reads” each base in each DNA fragment and appends an oligonucleotide to the DNA fragment after each base “reading”. Each appended oligonucleotide represents a specific base type, so that the proxy construct consisting of all the appended oligonucleotides faithfully represents the original DNA sequence. We generated proxies for genomic DNA and confirmed the identities of both the proxies and their corresponding original DNA sequences by performing sequencing using Ion Torrent sequencer.Conversion to proxies had only 0.33% raw error rate. Errors were: 93.96% deletions, 5.29% insertions, and 0.74% substitutions. The longest sequenced proxy was 170 bases, corresponding to a 17-base original DNA sequence. The short length of the detected proxies reflected restrictions imposed by Ion Torrent’s short reads and was not caused by limitations of our method. The consensus sequence built by using proxies alone (average length: 120 bases; corresponding to original sequences with average length 12 bases) covered 55% of the reference genome with 100% accuracy, and outperformed the Ion Torrent sequencing of the corresponding original DNA fragments in terms of accuracy, coverage and number of aligned sequences. Data and other materials can be found at http://www.vastogen.com/data.html. This proof-of-concept experiment demonstrates highly accurate proxy construction at the whole genome level. To our knowledge, this is the first demonstrated construction of expanded versions of DNA at the whole genome level.

scholarly journals Enhanced nanochannel translocation and localization of genomic DNA molecules using three-dimensional nanofunnels

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Jinsheng Zhou ◽  
Yanqian Wang ◽  
Laurent D. Menard ◽  
Sergey Panyukov ◽  
Michael Rubinstein ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Three Dimensional ◽  
Dna Molecules

scholarly journals A direct detection of Escherichia coli genomic DNA using gold nanoprobes

2012 ◽  
Vol 10 (1) ◽  
pp. 8 ◽  
Author(s):  
Bakthavathsalam Padmavathy ◽  
Rajendran Vinoth Kumar ◽  
Baquir Mohammed Jaffar Ali
Keyword(s):  
Escherichia Coli ◽  
Genomic Dna ◽  
Direct Detection

Methylation-dependent fragment separation: Direct detection of DNA methylation by capillary electrophoresis of PCR products from bisulfite-converted genomic DNA

2006 ◽  
Vol 354 (2) ◽  
pp. 266-273 ◽  
Author(s):  
Victoria L. Boyd ◽  
Kristina I. Moody ◽  
Achim E. Karger ◽  
Kenneth J. Livak ◽  
Gerald Zon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Capillary Electrophoresis ◽  
Genomic Dna ◽  
Direct Detection ◽  
Pcr Products

scholarly journals Direct detection of methylation in genomic DNA

2005 ◽  
Vol 33 (14) ◽  
pp. e124-e124 ◽  
Author(s):  
A. Bart
Keyword(s):  
Genomic Dna ◽  
Direct Detection
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