期刊
JOURNAL OF PHYSICAL CHEMISTRY B
卷 -, 期 -, 页码 -出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.2c05611
关键词
-
资金
- National Key Technology R&D Program of China
- National Natural Science Foundation of China
- LiaoNing Revitalization Talents Program
- Innovation and Entrepreneurship Team of Dalian University
- Natural Science Foundation of Liaoning Province
- [2018YFC0910500]
- [62272079]
- [61751203]
- [61972266]
- [61802040]
- [XLYC2008017]
- [XQN202008]
- [2021-MS-344]
- [2021-KF-11-03]
- [2022-KF-12-14]
This study proposes a new DNA triplex design approach (TripDesign) based on interaction forces. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, which can promote the application of DNA triplexes in nanotechnology.
A DNA triplex has the advantages of improved nanostructure stability and pH environment responsiveness compared with single-stranded and double-stranded nucleic acids. However, sequence stability and low design efficiency hinder the application of DNA triplexes. Therefore, a DNA triplex design approach (TripDesign) based on interaction forces is proposed. First, we present the stacking force constraint, torsional stress constraint, and G-quadruplex motif constraint and then use an improved memetic algorithm to design triplex sequences under combinatorial constraints. Finally, to quantify the process of triplex formation, we also explore the minimum length of the triplex-forming oligos (TFOs) required to form the triplex and the factors that produce depletion in cyclic pH-jump experiments. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, and the proposed approach achieves efficient and automatic sequence design. In addition, this study characterizes multiple basic parameters of DNA triplex formation and promotes the wider application of DNA triplexes in nanotechnology.
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