Restriction Enzymes in Optical Mapping

Optical mapping is a method that allows production of restriction maps of whole chromosomes or genomes. Learn more about optical mapping. 


What is optical mapping?

Optical mapping is a method that allows production of high resolution restriction maps of whole chromosomes or entire genomes. The method begins with preparation of high molecular weight genomic DNA followed by immobilization of large, individual DNA molecules in a linear configuration, either on a solid support or in microfluidic channels.

How can you use restriction enzymes in optical mapping?

Immobilized DNA is digested with a restriction enzyme, the fragments are stained, and then finally visualized under a microscope. Identification of overlaps between the restriction patterns of different individual DNA molecules leads to the assembly of an optical map that eventually will span an entire chromosome. With around 300 restriction enzymes to choose from, it's relatively easy to select a specificity that gives the optimal cut-site frequency for the genome under investigation.

What is an alternative use of restriction enzymes in optical mapping?

An alternative version of optical mapping uses nicking endonucleases. In this instance, the DNA is treated with a nicking enzyme to nick just on strand of the DNA, and the nick site is then filled in with a fluorescent nucleotide.

What is the future of restriction enzymes in optical mapping?

With the advent of long read sequencing technology, there's been a shift in recent years towards truly finished genome sequences, and optical mapping is often a valuable part of this process because DNA sequence contigs from genome assemblies can be overlaid onto the optical map. This allows the assembly of complex genomes, even in the absence of any reference genome sequence. Since restriction enzymes are so fundamental to this type of optical mapping, they will remain a critical component of the technology.

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