title: Chitosan: a novel platform in proton-driven DNA strand rearrangement actuation.
abstract: Nanometre-scaled DNA machine based on molecular recognition properties of DNA has now become a powerful tool in nanodevices, miniaturized structure, and nanofabrication. The common principle behind designing a DNA nanomachine is DNA strand exchange or rearrangement, which is solely controlled by the stabilization through associative and dissociative forces arising from base pair interaction of DNA molecules. Thus, highly effective DNA reaction actuator will make DNA nanomachine more flexible, controllable, and powerful device. Here, we report the novel polymer-mediated platform in proton-driven DNA strand rearrangement actuation. This cationic low molecular weight water-soluble chitosan (LMWSC) exhibited pH-dependent complexation with oligodeoxynucleotides (ODN). It formed complex with ODN only at low pH and accelerated the DNA strand exchange (or rearrangement) reaction between dsDNA and its complementary ssDNA at pH 5.0. However, no complexation was observed between LMWSC and ODN at neutral pH. We assume that at physiological pH, LMWSC is not protonated enough for formation of complex with ODN. Therefore, it can not diminish the electrostatic repulsion among the negatively charged DNA strands of the three-stranded intermediate formed during the strand exchange reaction. In contrast, LMWSC becomes positively charged at acidic pH, and it stabilizes the three-stranded intermediate by spreading out the accumulated counter-ions and increasing the entropy of the system. This fascinating observation prompted us to believe that this intelligent proton-driven DNA reaction actuator has a potential for the precise control of DNA nanomachine and would be applied for operating and controlling nanoscaled machine.
authors.affiliation: Department of Chemistry, The Brain Korea 21 Project, Polymer Research Institute, Pohang University of Science and Technology, San 31, Hyoja-dong, Pohang 790-784, Korea.
authors.forename: Dami
authors.initials: D
authors.lastname: Lee
authors.forename: Kaushik
authors.initials: K
authors.lastname: Singha
authors.forename: Mi-Kyeong
authors.initials: MK
authors.lastname: Jang
authors.forename: Jae-Woon
authors.initials: JW
authors.lastname: Nah
authors.forename: In-Kyu
authors.initials: IK
authors.lastname: Park
authors.forename: Won Jong
authors.initials: WJ
authors.lastname: Kim
mesh_terms: D048271:Chitosan / Q000737:chemistry* / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D031541:Fluorescence Resonance Energy Transfer; D015321:Gene Rearrangement; D006863:Hydrogen-Ion Concentration; D008970:Molecular Weight; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011522:Protons; D013050:Spectrometry, Fluorescence
chemical_list: D009838:Oligodeoxyribonucleotides; D011522:Protons; D004247:DNA; D048271:Chitosan