Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

Levy‐Sakin, Michal; Ebenstein, Yuval

doi:10.1016/j.copbio.2013.01.009

Cited by 104 publications

(72 citation statements)

References 44 publications

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“…These massive stretches of labeled DNA greatly facilitate the assembly of genomic maps for anchoring sequencing data, 2 and they are especially important for the analysis of structural variations. 3,15 Understanding the probability distribution governing the polymer extension between labeled points along nanochannelconfined DNA is critical to accurately map the physical distance X (in nm) between probes to their genomic distance, L (in base pairs (bp)). However, the theory surrounding DNA confinement for channel sizes D ≈ l p is contentious.…”

Section: Introductionmentioning

confidence: 99%

“…The importance of this problem extends beyond chemical physics, as these channel sizes form the basis for an emerging method of genomic mapping. [1][2][3] Here, the DNA is stretched by confinement in a nanochannel 4,5 and the genomic information is then read by fluorescence microscopy, either using sequencespecific probes, [6][7][8][9][10][11] the absence of fluorescence due to localized melting of AT-rich regions, 12,13 or competitive binding. 14 Genome mapping in nanochannels uses intact genomic DNA molecules that are hundreds of kilobases (and even megabases) in contour length.…”

Section: Introductionmentioning

confidence: 99%

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Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension. C 2015 AIP Publishing LLC. [http://dx

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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“…The characteristics and features of Bionano technology have been reviewed elsewhere (Levy-Sakin and Ebenstein, 2013;Tang et al, 2015;Chaney et al, 2016;Yuan et al, 2017). Briefly, the method involves purifying high molecular weight (HMW) DNA and treating with a nickase, a modified restriction enzyme that creates single stranded nicks.…”

Section: Validation Of Sequence Assemblymentioning

confidence: 99%

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Udall

Dawe

2017

Plant Cell

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ORCID ID: 0000-0003-0978-4764 (J.A.U.)Long-read single-molecule sequencing, Hi-C sequencing, and improved bioinformatic tools are ushering in an era where complete genome assembly will become common for species with few or no classical genetic resources. There are no guidelines for how to proceed in such cases. Ideally, such genomes would be sequenced by two different methods so that one assembly serves as confirmation of the other; however, cost constraints make this approach unlikely. Overreliance on synteny as a means of confirming and ordering contigs will lead to compounded errors. Optical mapping is an accessible and relatively mature technology that can be used for genome assembly validation. We discuss how optical mapping can be used as a validation tool for genome assemblies and how to interpret the results. In addition, we discuss methods for using optical map data to enhance genome assemblies derived from both traditional sequence contigs and Hi-C pseudomolecules.

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“…MTase‐based labeling of methylated DNA could easily be combined with single‐molecule detection in nanochannels 76b. Since MTase‐based labeling can be targeted towards either adenine or cytosine, the method could be combined with optical mapping in order to localize regions of (un)methylation.…”

Section: Current and Future Applicationsmentioning

confidence: 99%

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

et al. 2017

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Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S‐adenosyl‐l‐Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly‐activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet‐dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.

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Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy

Cited by 104 publications

References 44 publications

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Is It Ordered Correctly? Validating Genome Assemblies by Optical Mapping

Methyltransferase‐Directed Labeling of Biomolecules and its Applications

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