Sequencing by ligation

Sequencing by ligation is a DNA sequencing method that uses the enzyme DNA ligase to identify the nucleotide present at a given position in a DNA sequence. Unlike most currently popular DNA sequencing methods, this method does not use a DNA polymerase to create a second strand. Instead, the mismatch sensitivity of a DNA ligase enzyme is used to determine the underlying sequence of the target DNA molecule.

Process
DNA ligase is an enzyme that binds joins together ends of DNA molecules. Although commonly represented as joining two pairs of ends at once, as in the ligation of restriction enzyme fragments, ligase can also join the ends on only one of the two strands (for example, when the other strand either already continuous or lacks a terminal phosphate necessary for ligation). DNA ligase is sensitive to the structure of DNA and has very low efficiency when there are mismatches between the bases of the two strands.

Sequencing by ligation relies upon the sensitivity of DNA ligase for base-pairing mismatches. The target molecule to be sequenced is a single strand of unknown DNA sequence, flanked on at least one end by a known sequence. A short "anchor" strand is brought in to bind the known sequence.

A mixed pool of oligonucleotides is then brought in (eight or nine bases long), labeled according to the position that will be sequenced. These molecules hybridize to the target DNA sequence, next to the anchor sequence, and DNA ligase preferentially joins the molecule to the anchor when its bases match the unknown DNA sequence. Based on the fluorescence produced by the molecule, one can infer the identity of the nucleotide at this position in the unknown sequence.

To sequence other positions, the anchor and ligated oligonucleotide must be stripped off the target DNA sequence to allow for another round of sequencing by hybridization.