title: Effects of Structural Flexibility on the Kinetics of DNA Y-Junction Assembly and Gelation.
abstract: The kinetics of DNA assembly is determined not only by temperature but also by the flexibility of the DNA tiles. In this work, the flexibility effect was studied with a model system of Y-junctions, which contain single-stranded thymine (T) loops in the center. It was demonstrated that the incorporation of a loop with only one thymine prominently improved the assembly rate and tuned the final structure of the assembly, whereas the incorporation of a loop of two thymines exhibited the opposite effect. These observations could be explained by the conformation adjustment rate and the intermotif binding strength. Increasing DNA concentration hindered the conformational adjustment rate of DNA strands, leading to the formation of hydrogels in which the network was connected by ribbons. Therefore, the gel can be treated as a metastable state during the phase transition.
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Niu
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
authors.forename: Xuyan
authors.initials: X
authors.lastname: Yang
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Pan
authors.affiliation: Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University , Beijing 100084, China.
authors.forename: Tao
authors.initials: T
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University , Beijing 100084, China.
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Liu
authors.affiliation: Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States.
authors.forename: Chengde
authors.initials: C
authors.lastname: Mao
authors.affiliation: Beijing National Laboratory for Molecular Sciences, Department of Polymer Science and Engineering and the Key Laboratory of Polymer Chemistry and Physics of the Ministry of Education, College of Chemistry and Molecular Engineering, Peking University , Beijing 100871, China.
authors.forename: Dehai
authors.initials: D
authors.lastname: Liang
mesh_terms: D004247:DNA / Q000737:chemistry*; D020100:Hydrogels; D007700:Kinetics; D009690:Nucleic Acid Conformation; D044367:Phase Transition; D013941:Thymine / Q000737:chemistry*
chemical_list: D020100:Hydrogels; D004247:DNA; D013941:Thymine