scholarly journals Erratum: Corrigendum: Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lena K. Nyberg ◽  
Saair Quaderi ◽  
Gustav Emilsson ◽  
Nahid Karami ◽  
Erik Lagerstedt ◽  
...  
Keyword(s):  
Bacterial Resistance ◽  
Optical Mapping ◽  
Rapid Identification ◽  
Dna Molecules ◽  
Single Dna Molecules ◽  
Resistance Plasmids

scholarly journals Rapid identification of intact bacterial resistance plasmids via optical mapping of single DNA molecules

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Lena K. Nyberg ◽  
Saair Quaderi ◽  
Gustav Emilsson ◽  
Nahid Karami ◽  
Erik Lagerstedt ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Bacterial Resistance ◽  
Clinical Epidemiology ◽  
Rapid Identification ◽  
Sequence Information ◽  
Dna Molecules ◽  
Structural Variations ◽  
Mapping Procedure ◽  
Single Dna Molecules ◽  
Nanofluidic Channels

Abstract The rapid spread of antibiotic resistance – currently one of the greatest threats to human health according to WHO – is to a large extent enabled by plasmid-mediated horizontal transfer of resistance genes. Rapid identification and characterization of plasmids is thus important both for individual clinical outcomes and for epidemiological monitoring of antibiotic resistance. Toward this aim, we have developed an optical DNA mapping procedure where individual intact plasmids are elongated within nanofluidic channels and visualized through fluorescence microscopy, yielding barcodes that reflect the underlying sequence. The assay rapidly identifies plasmids through statistical comparisons with barcodes based on publicly available sequence repositories and also enables detection of structural variations. Since the assay yields holistic sequence information for individual intact plasmids, it is an ideal complement to next generation sequencing efforts which involve reassembly of sequence reads from fragmented DNA molecules. The assay should be applicable in microbiology labs around the world in applications ranging from fundamental plasmid biology to clinical epidemiology and diagnostics.

Molecular microscopy of DNA for genome analysis: optical mapping of restriction digests

1995 ◽  
Vol 53 ◽  
pp. 50-51
Author(s):  
Edward J. Huff ◽  
Weiwen Cai ◽  
Xinghua Hu ◽  
John Huang ◽  
Junping Jing ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Analysis ◽  
Optical Mapping ◽  
Ccd Camera ◽  
Dna Molecules ◽  
Specific Sequence ◽  
Single Dna Molecules ◽  
Single Clone ◽  
Rapid Generation ◽  
Glass Surfaces

Optical microscopy of individual DNA molecules has been an interesting technique for the past 15 years, but until recently has not been useful for genome analysis. We have developed Optical Mapping an emerging single molecule approach for the rapid generation of ordered restriction maps. Many identical individual DNA molecules from a single clone are elongated and fixed onto derivatized glass surfaces, digested with a restriction enzyme which cuts the DNA wherever a specific sequence pattern is found, stained with YOYO, and imaged with a cooled CCD camera attached to an automated epi-fluorescence microscope. Images are automatically processed to correct for non-uniform illumination, remove background, locate the DNA fragments, reject objects which do not look like single DNA molecules, recognize which fragments originate from an original uncut molecule, and calculate the relative sizes of the fragments by apparent length and fluorescence intensity. Results from many molecules are combined by clustering to recognize a consistent cutting pattern. Molecules which match the pattern are averaged to improve the sizing accuracy.

Thermoplastic Nanofluidic Devices for Identifying Abasic Sites in Single DNA Molecules

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Steven A Soper ◽  
Swarnagowri Vaidyanathan ◽  
Franklin Uba ◽  
Bo Hu ◽  
David Kaufman ◽  
...  
Keyword(s):  
Dna Damage ◽  
Therapeutic Efficacy ◽  
Double Strand Breaks ◽  
Dna Molecules ◽  
Strand Breaks ◽  
Single Dna Molecules ◽  
Abasic Sites ◽  
Nanofluidic Devices ◽  
Ap Sites

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy...

scholarly journals Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing

Nano Letters ◽  
2018 ◽  
Vol 18 (12) ◽  
pp. 8003-8010 ◽  
Author(s):  
Xin Shi ◽  
Daniel V. Verschueren ◽  
Cees Dekker
Keyword(s):  
Optical Sensing ◽  
Label Free ◽  
Dna Molecules ◽  
Single Dna Molecules

scholarly journals Molecular conformations of DNA targets captured by model nanoarrays

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13419-13424 ◽  
Author(s):  
X. Hao ◽  
E. A. Josephs ◽  
Q. Gu ◽  
T. Ye
Keyword(s):  
Dna Molecules ◽  
Molecular Conformations ◽  
Single Dna Molecules

We generated nanoarrays with tailored surface functionalities and morphologies to probe how single DNA molecules interact with surface heterogeneities.

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