Optical mapping of DNA: Single‐molecule‐based methods for mapping genomes
- 4 January 2011
- journal article
- review article
- Published by Wiley in Peptide Science
- Vol. 95 (5), 298-311
- https://doi.org/10.1002/bip.21579
Abstract
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 1000 bases in length. The overarching aim of the optical map is to complement the information derived from DNA sequencing by providing long‐range context on 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, six 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 subdiffraction‐limit precision using methyltransferase enzymes to label the DNA with an ultrahigh density. © 2011 Wiley Periodicals, Inc. Biopolymers 95: 298–311, 2011.Keywords
This publication has 73 references indexed in Scilit:
- Assembly of large genomes using second-generation sequencingGenome Research, 2010
- The sequence and de novo assembly of the giant panda genomeNature, 2009
- Sequencing technologies — the next generationNature Reviews Genetics, 2009
- Perspectives and Challenges of Emerging Single‐Molecule DNA Sequencing TechnologiesSmall, 2009
- Single-molecule sequencing of an individual human genomeNature Biotechnology, 2009
- Genome assembly reborn: recent computational challengesBriefings in Bioinformatics, 2009
- Sequence assemblyComputational Biology and Chemistry, 2009
- Real-Time DNA Sequencing from Single Polymerase MoleculesScience, 2009
- Single-molecule DNA sequencing technologies for future genomics researchTrends in Biotechnology, 2008
- Single-Molecule DNA Sequencing of a Viral GenomeScience, 2008