Genomic DNA i-motifs as fast sensors responsive to near-physiological pH microchanges.
作者： Anton V. Turaev , Ekaterina A. Isaakova , Vjacheslav V. Severov , Alexandra N. Bogomazova , Timofei S. Zatsepin
DOI: 10.1016/J.BIOS.2020.112864
关键词: Chemistry 、 DNA 、 genomic DNA 、 Förster resonance energy transfer 、 Kinetics 、 Fluorescence 、 Biophysics 、 Intracellular pH 、 Transcription (biology) 、 Intracellular
摘要: Abstract We report the design of robust sensors for measuring intracellular pH, based on native DNA i-motifs (iMs) found in neurodegeneration- or carcinogenesis-related genes. Those iMs appear to be genomic regulatory elements and might modulate transcription response pH stimuli. Given their intrinsic sensitivity minor changes within physiological range, such noncanonical structures can used as sensor core without additional modules other than fluorescent labels quenchers. focused several that exhibited fast folding/unfolding kinetics. Using stopped-flow techniques FRET-melting/annealing assays, we confirmed rates temperature-driven iM-ssDNA transitions correlate with pH-driven transitions. Thus, propose FRET-based hysteresis analysis an express method selecting desired kinetic characteristics. For leading fast-response sensor, optimized labelling scheme performed calibration. Unlike commonly small-molecule indicators, was transferred efficiently cell nuclei. Considering its favourable characteristics, monitoring proton dynamics nucleus. These results argue ‘genome-inspired’ is a productive approach development biocompatible molecular tools.
sci-hub.st 参考文章(47)
Alzbeta Hulikova, Pawel Swietach, Nuclear proton dynamics and interactions with calcium signaling Journal of Molecular and Cellular Cardiology. ,vol. 96, pp. 26- 37 ,(2016) , 10.1016/J.YJMCC.2015.07.003
Masaki TORIMURA, Shinya KURATA, Kazutaka YAMADA, Toyokazu YOKOMAKU, Yoichi KAMAGATA, Takahiro KANAGAWA, Ryuichiro KURANE, Fluorescence-quenching phenomenon by photoinduced electron transfer between a fluorescent dye and a nucleotide base. Analytical Sciences. ,vol. 17, pp. 155- 160 ,(2001) , 10.2116/ANALSCI.17.155
Chun Chen, Ming Li, Yongzheng Xing, Yingmei Li, Carl-Christian Joedecke, Juan Jin, Zhongqiang Yang, Dongsheng Liu, Study of pH-induced folding and unfolding kinetics of the DNA i-motif by stopped-flow circular dichroism. Langmuir. ,vol. 28, pp. 17743- 17748 ,(2012) , 10.1021/LA303851A
Vernon A. Ruffin, Ahlam I. Salameh, Walter F. Boron, Mark D. Parker, Intracellular pH regulation by acid-base transporters in mammalian neurons Frontiers in Physiology. ,vol. 5, pp. 43- 43 ,(2014) , 10.3389/FPHYS.2014.00043
Robert Sjöback, Jan Nygren, Mikael Kubista, Characterization of fluorescein–oligonucleotide conjugates and measurement of local electrostatic potential Biopolymers. ,vol. 46, pp. 445- 453 ,(1998) , 10.1002/(SICI)1097-0282(199812)46:7<445::AID-BIP2>3.0.CO;2-5
Henry A. Day, Pavlos Pavlou, Zoë A.E. Waller, i-Motif DNA: Structure, stability and targeting with ligands Bioorganic & Medicinal Chemistry. ,vol. 22, pp. 4407- 4418 ,(2014) , 10.1016/J.BMC.2014.05.047
Souvik Modi, Clément Nizak, Sunaina Surana, Saheli Halder, Yamuna Krishnan, Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell Nature Nanotechnology. ,vol. 8, pp. 459- 467 ,(2013) , 10.1038/NNANO.2013.92
Christy Agbavwe, Mark M. Somoza, Sequence-Dependent Fluorescence of Cyanine Dyes on Microarrays PLoS ONE. ,vol. 6, pp. e22177- ,(2011) , 10.1371/JOURNAL.PONE.0022177
Irina V. Nesterova, Evgueni E. Nesterov, Rational Design of Highly Responsive pH Sensors Based on DNA i-Motif Journal of the American Chemical Society. ,vol. 136, pp. 8843- 8846 ,(2014) , 10.1021/JA501859W
Antony K. Chen, Zhiliang Cheng, Mark A. Behlke, Andrew Tsourkas, Assessing the sensitivity of commercially available fluorophores to the intracellular environment. Analytical Chemistry. ,vol. 80, pp. 7437- 7444 ,(2008) , 10.1021/AC8011347