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Optical mapping of DNA: Single-molecule-based methods for mapping genomes.
Biopolymers. 2011 Jan 4;
Authors: Neely RK, Deen J, Hofkens J
The technologies associated with DNA sequencing are rapidly evolving. Indeed, single-molecule DNA sequencing strategies are cheaper and faster than ever before. Despite this progress, every sequencing platform to date relies on reading the genome in small, abstract fragments, typically of less than a thousand bases in length. The overarching aim of the optical map is to complement the information derived from DNA sequencing by providing long-range context upon which these short sequence reads can be built. This is typically done using an enzyme to target and modify at short DNA sequences of, say, 6-bases in length throughout the genome. By accurately placing these short pieces of sequence on long genomic DNA fragments, up to several millions of bases in length, a scaffold for sequence assembly can be obtained. This review focuses on three enzymatic approaches to optical mapping. Optical mapping was first developed using restriction enzymes to sequence-specifically cleave DNA that is immobilized on a surface. More recently, nicking enzymes have found application in the sequence-specific fluorescent labeling of DNA for optical mapping. Such covalent modification allows the DNA to be imaged in solution and this in combination with developing nanofluidic technologies is enabling new high-throughput approaches to mapping. And finally, this review will discuss the recent development of mapping with sub-diffraction limit precision using methyltransferase enzymes to label the DNA with an ultra-high density. © 2010 Wiley Periodicals, Inc. Biopolymers, 2010.
PMID: 21207457 [PubMed - as supplied by publisher]
More...
Optical mapping of DNA: Single-molecule-based methods for mapping genomes.
Biopolymers. 2011 Jan 4;
Authors: Neely RK, Deen J, Hofkens J
The technologies associated with DNA sequencing are rapidly evolving. Indeed, single-molecule DNA sequencing strategies are cheaper and faster than ever before. Despite this progress, every sequencing platform to date relies on reading the genome in small, abstract fragments, typically of less than a thousand bases in length. The overarching aim of the optical map is to complement the information derived from DNA sequencing by providing long-range context upon which these short sequence reads can be built. This is typically done using an enzyme to target and modify at short DNA sequences of, say, 6-bases in length throughout the genome. By accurately placing these short pieces of sequence on long genomic DNA fragments, up to several millions of bases in length, a scaffold for sequence assembly can be obtained. This review focuses on three enzymatic approaches to optical mapping. Optical mapping was first developed using restriction enzymes to sequence-specifically cleave DNA that is immobilized on a surface. More recently, nicking enzymes have found application in the sequence-specific fluorescent labeling of DNA for optical mapping. Such covalent modification allows the DNA to be imaged in solution and this in combination with developing nanofluidic technologies is enabling new high-throughput approaches to mapping. And finally, this review will discuss the recent development of mapping with sub-diffraction limit precision using methyltransferase enzymes to label the DNA with an ultra-high density. © 2010 Wiley Periodicals, Inc. Biopolymers, 2010.
PMID: 21207457 [PubMed - as supplied by publisher]
More...