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Precision length determination and in silico simulation in PCR of microsatellite repeat sequences
Author(s) -
Shioi Seijiro,
Shimamoto Akiyoshi,
Nakagami Yuki,
Qin Lexin,
Shimokawa Mototsugu,
Oda Shinya
Publication year - 2021
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.202100021
Subject(s) - microsatellite , in silico , polymerase chain reaction , polymerase , computational biology , biology , in silico pcr , primer (cosmetics) , genetics , slippage , dna , chemistry , gene , multiplex polymerase chain reaction , materials science , allele , organic chemistry , composite material
Despite being commonplace, polymerase chain reactions (PCRs) still contain many unknown aspects. One example is microsatellite PCR, which is now widely used for various purposes from ecology to cancer medicine. Since this category of repetitive DNA sequences induces polymerase slippage not only in vivo but also in vitro , microsatellite PCR products comprise a complex combination of DNA fragments with various lengths and have, therefore, been empirically interpreted. The primary obstacle for understanding microsatellite PCR was the intrinsic inaccuracy in sizing of DNA fragments in capillary electrophoresis (CE), which, however, has been overcome by elucidating intrinsic sizing errors in each fragment length range. Secondly, the slippage properties of the thermostable polymerases were first clarified in detail using primer extension assays. Furthermore, using the obtained slippage parameters and our original program, we have first reconstructed microsatellite PCR in silico . The entire processes of complex microsatellite PCR have, thus, been more clearly understood.