title: Study of pH-induced folding and unfolding kinetics of the DNA i-motif by stopped-flow circular dichroism.
abstract: Using the stopped-flow circular dichroism (SFCD) technique, we investigate the kinetics of the pH-induced folding and unfolding process of the DNA i-motif. The results show that the molecule can fold or unfold on a time scale of 100 ms when the solution pH is changed. It is also found that the folding and unfolding rates strongly depend on the solution pH. On the basis of quantitative data, we propose theoretical models to decipher the folding and unfolding kinetics. Our models suggest that the cooperativity of protons is crucial for both the folding and unfolding process. In the unfolding process, the cooperative neutralization of two protons (out of the total six protons in the i-motif molecule) is the only rate-limiting step. In the folding process, there exists a critical step in which three protons bind cooperatively to the DNA strand. These results offer an in-depth understanding of the folding and unfolding kinetics of the DNA i-motif and may give precise guidance for constructing novel nanodevices based on the DNA i-motif.
authors.affiliation: Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, China.
authors.forename: Chun
authors.initials: C
authors.lastname: Chen
authors.forename: Ming
authors.initials: M
authors.lastname: Li
authors.forename: Yongzheng
authors.initials: Y
authors.lastname: Xing
authors.forename: Yingmei
authors.initials: Y
authors.lastname: Li
authors.forename: Carl-Christian
authors.initials: CC
authors.lastname: Joedecke
authors.forename: Juan
authors.initials: J
authors.lastname: Jin
authors.forename: Zhongqiang
authors.initials: Z
authors.lastname: Yang
authors.forename: Dongsheng
authors.initials: D
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D059372:Nucleotide Motifs
chemical_list: D004247:DNA