Editing Repeated sequence (DNA) (section)

== Biotechnology ==
Repetitive DNA is hard to [[DNA sequencing|sequence]] using [[next-generation sequencing]] techniques because [[sequence assembly]] from short reads simply cannot determine the length of a repetitive part. This issue is particularly serious for microsatellites, which are made of tiny 1-6bp repeat units.<ref name=":5">{{cite journal | vauthors = De Bustos A, Cuadrado A, Jouve N | title = Sequencing of long stretches of repetitive DNA | journal = Scientific Reports | volume = 6 | issue = 1 | pages = 36665 | date = November 2016 | pmid = 27819354 | pmc = 5098217 | doi = 10.1038/srep36665 | bibcode = 2016NatSR...636665D | doi-access = free }}</ref> Although they are difficult to sequence, these short repeats have great value in DNA fingerprinting and evolutionary studies. Many researchers have historically left out repetitive sequences when analyzing and publishing whole genome data due to technical limitations.<ref>{{cite journal | vauthors = Slotkin RK | title = The case for not masking away repetitive DNA | journal = Mobile DNA | volume = 9 | issue = 1 | pages = 15 | date = 1 May 2018 | pmid = 29743957 | pmc = 5930866 | doi = 10.1186/s13100-018-0120-9 | doi-access = free }}</ref>

Bustos. et al. proposed one method of sequencing long stretches of repetitive DNA.<ref name=":5" /> The method combines the use of a linear vector for stabilization and exonuclease III for deletion of continuing simple sequence repeats (SSRs) rich regions. First, SSR-rich fragments are cloned into a linear vector that can stably incorporate tandem repeats up to 30kb. Expression of repeats is prohibited by the transcriptional terminators in the vector. The second step involves the use of exonuclease III. The enzyme can delete nucleotide at the 3' end which results in the production of a unidirectional deletion of SSR fragments. Finally, this product which has deleted fragments is multiplied and analyzed with colony PCR. The sequence is then built by an ordered sequencing of a set of clones containing different deletions.