DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes
Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactio...
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| Veröffentlicht in: | PloS one 2016-07, Vol.11 (7), p.e0160229-e0160229 |
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| creator | Beierlein, Frank R Paradas Palomo, Miguel Sharapa, Dmitry I Zozulia, Oleksii Mokhir, Andriy Clark, Timothy |
| description | Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries. |
| doi_str_mv | 10.1371/journal.pone.0160229 |
| format | Article |
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Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0160229</identifier><identifier>PMID: 27467071</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Biology and Life Sciences ; Cancer ; Chromophores ; Conjugates ; Cytometry ; Deoxyribonucleic acid ; DNA ; DNA - chemistry ; DNA probes ; DNA structure ; Dyes ; Emission spectra ; Energy transfer ; Flow cytometry ; Fluorescence ; Fluorescence microscopy ; Fluorescence Resonance Energy Transfer ; Fluorescent Dyes - chemistry ; Fluorescent indicators ; Influence ; Interdisciplinary aspects ; Localization ; Mathematical analysis ; Microscopy ; Microscopy, Fluorescence ; Molecular dynamics ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Nucleic acids ; Oligonucleotides ; Organic chemistry ; Pharmacy ; Physical Sciences ; Quantum Theory ; Quenching ; Research and Analysis Methods ; Simulation ; Spectrophotometry, Ultraviolet ; Target detection ; Target recognition ; Ultraviolet absorption</subject><ispartof>PloS one, 2016-07, Vol.11 (7), p.e0160229-e0160229</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Beierlein et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Beierlein et al 2016 Beierlein et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c795t-4bc892d1c3e2c52ed66affd6359924decfb114c717c1cdcb43a0d461aae9cd843</citedby><cites>FETCH-LOGICAL-c795t-4bc892d1c3e2c52ed66affd6359924decfb114c717c1cdcb43a0d461aae9cd843</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965132/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965132/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27467071$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Antopolsky, Maxim</contributor><creatorcontrib>Beierlein, Frank R</creatorcontrib><creatorcontrib>Paradas Palomo, Miguel</creatorcontrib><creatorcontrib>Sharapa, Dmitry I</creatorcontrib><creatorcontrib>Zozulia, Oleksii</creatorcontrib><creatorcontrib>Mokhir, Andriy</creatorcontrib><creatorcontrib>Clark, Timothy</creatorcontrib><title>DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. 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| subjects | Analysis Biology and Life Sciences Cancer Chromophores Conjugates Cytometry Deoxyribonucleic acid DNA DNA - chemistry DNA probes DNA structure Dyes Emission spectra Energy transfer Flow cytometry Fluorescence Fluorescence microscopy Fluorescence Resonance Energy Transfer Fluorescent Dyes - chemistry Fluorescent indicators Influence Interdisciplinary aspects Localization Mathematical analysis Microscopy Microscopy, Fluorescence Molecular dynamics Molecular Dynamics Simulation Nucleic Acid Conformation Nucleic acids Oligonucleotides Organic chemistry Pharmacy Physical Sciences Quantum Theory Quenching Research and Analysis Methods Simulation Spectrophotometry, Ultraviolet Target detection Target recognition Ultraviolet absorption |
| title | DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes |
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