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Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device

Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed b...

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Autores principales: Shi, Lili, Peng, Pai, Du, Yi, Li, Tao
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416763/
https://www.ncbi.nlm.nih.gov/pubmed/28369541
http://dx.doi.org/10.1093/nar/gkx202
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author Shi, Lili
Peng, Pai
Du, Yi
Li, Tao
author_facet Shi, Lili
Peng, Pai
Du, Yi
Li, Tao
author_sort Shi, Lili
collection PubMed
description Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (C(n-1)T(m)C(n) and C(n)T(m)C(n-1); n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by C(n)T(m)C(n). It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra.
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spelling pubmed-54167632017-05-05 Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device Shi, Lili Peng, Pai Du, Yi Li, Tao Nucleic Acids Res Chemical Biology and Nucleic Acid Chemistry Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (C(n-1)T(m)C(n) and C(n)T(m)C(n-1); n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by C(n)T(m)C(n). It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra. Oxford University Press 2017-05-05 2017-03-23 /pmc/articles/PMC5416763/ /pubmed/28369541 http://dx.doi.org/10.1093/nar/gkx202 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Chemical Biology and Nucleic Acid Chemistry
Shi, Lili
Peng, Pai
Du, Yi
Li, Tao
Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title_full Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title_fullStr Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title_full_unstemmed Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title_short Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device
title_sort programmable i-motif dna folding topology for a ph-switched reversible molecular sensing device
topic Chemical Biology and Nucleic Acid Chemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5416763/
https://www.ncbi.nlm.nih.gov/pubmed/28369541
http://dx.doi.org/10.1093/nar/gkx202
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