G-Quadruplex conformational change driven by pH variation with potential application as a nanoswitch

Yi Yong Yan, Jia Heng Tan, Yu Jing Lu, Siu Cheong Yan, Kwok Yin Wong, Ding Li, Lian Quan Gu, Zhi Shu Huang

Research output: Journal article publicationJournal articleAcademic researchpeer-review

16 Citations (Scopus)

Abstract

Background G-Quadruplex is a highly polymorphic structure, and its behavior in acidic condition has not been well studied. Methods Circular dichroism (CD) spectra were used to study the conformational change of G-quadruplex. The thermal stabilities of the G-quadruplex were measured with CD melting. Interconversion kinetics profiles were investigated by using CD kinetics. The fluorescence of the inserted 2-Aminopurine (Ap) was monitored during pH change and acrylamide quenching, indicating the status of the loop. Proton NMR was adopted to help illustrate the change of the conformation. Results G-Quadruplex of specific loop was found to be able to transform upon pH variation. The transformation was resulted from the loop rearrangement. After screening of a library of diverse G-quadruplex, a sequence exhibiting the best transformation property was found. A pH-driven nanoswitch with three gears was obtained based on this transition cycle. Conclusions Certain G-quadruplex was found to go through conformational change at low pH. Loop was the decisive factor controlling the interconversion upon pH variation. G-Quadruplex with TT central loop could be converted in a much milder condition than the one with TTA loop. It can be used to design pH-driven nanodevices such as a nanoswitch. General significance These results provide more insights into G-quadruplex polymorphism, and also contribute to the design of DNA-based nanomachines and logic gates.
Original languageEnglish
Pages (from-to)4935-4942
Number of pages8
JournalBiochimica et Biophysica Acta - General Subjects
Volume1830
Issue number10
DOIs
Publication statusPublished - 2 Oct 2013

Keywords

  • Acidic pH
  • Conformational interconversion
  • G-Quadruplex
  • Nanoswitch
  • pH-driven Thiazole orange (TO)

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

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