Formation of a DNA Mini-Dumbbell with a Quasi-Type II Loop
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AbstractQuasi-loops, wherein the backbone has a discontinuous site in the loop, have been found to provide structural flexibility in the formation of DNA three-way junctions. Recently, a highly compact mini-dumbbell (MDB) structure composed of two adjacent CCTG or TTTA type II loops has been reported. Yet, it remains elusive if the presence of a quasi-loop will also facilitate the formation of an MDB. In this study, the possibility of whether an MDB can be formed containing a quasi-type II loop has been investigated. We first demonstrate that two adjacent CTTG type II loops can also form an MDB, which is thermodynamically more stable than those formed by CCTG and TTTA loops. Then, we systematically introduce quasi-type II loops with their discontinuous sites at different backbone positions in the CTTG MDB. Our results show that an MDB can be formed with a quasi-type II loop, in which there is a discontinuous site between the third thymine and the fourth guanine loop residues. The possible inclusion of a quasi-loop in MDBs expands the sequence criteria for the formation of MDBs by natural DNA sequences.
All Author(s) ListYuan Liu, Pei Guo, Sik Lok Lam*
Journal nameThe journal of physical chemistry. B
Year2017
Volume Number121
Issue Number12
Pages2554 - 2560
ISSN1520-6106
LanguagesEnglish-United Kingdom
KeywordsUNPAIRED THYMIDINE BASES, GENETIC INSTABILITY, 3-WAY JUNCTION, NUCLEIC-ACIDS, CCTG REPEATS, NEUTRAL-PH, NMR, SEQUENCE, NANOTECHNOLOGY, CONFORMATION

Last updated on 2021-13-09 at 00:48