Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel
To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (...
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| description | To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution. |
| doi_str_mv | 10.1371/journal.pone.0144422 |
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As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0144422</identifier><identifier>PMID: 26650843</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Acrylic Resins - chemistry ; Base Composition ; Deoxyribonucleic acid ; DNA ; DNA - analysis ; DNA - chemistry ; Drosophila melanogaster ; Dyes ; Electrophoresis, Polyacrylamide Gel - methods ; Fluorescent Dyes - chemistry ; Gel electrophoresis ; Gels ; Inhibition ; Insects ; Methods ; Mutation ; Oligonucleotides ; Organic Chemicals - chemistry ; Physiological aspects ; Polyacrylamide ; Properties ; Proteins ; Sensitivity ; Silver ; Silver - chemistry ; Silver Staining - methods ; Staining ; Stains & staining</subject><ispartof>PloS one, 2015-12, Vol.10 (12), p.e0144422-e0144422</ispartof><rights>COPYRIGHT 2015 Public Library of Science</rights><rights>2015 Tang 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>2015 Tang et al 2015 Tang et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c762t-4a16e1fc4174ea13c1c1f6de49c48f3ac29e5f0f0eb0e4d023b71666def5f9263</citedby><cites>FETCH-LOGICAL-c762t-4a16e1fc4174ea13c1c1f6de49c48f3ac29e5f0f0eb0e4d023b71666def5f9263</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/PMC4674134/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4674134/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,2103,2929,23871,27929,27930,53796,53798</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26650843$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Cotterill, Sue</contributor><creatorcontrib>Tang, Weizhong</creatorcontrib><creatorcontrib>Zhou, Huafu</creatorcontrib><creatorcontrib>Li, Wei</creatorcontrib><title>Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.</description><subject>Acrylic Resins - chemistry</subject><subject>Base Composition</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA - analysis</subject><subject>DNA - chemistry</subject><subject>Drosophila melanogaster</subject><subject>Dyes</subject><subject>Electrophoresis, Polyacrylamide Gel - methods</subject><subject>Fluorescent Dyes - chemistry</subject><subject>Gel electrophoresis</subject><subject>Gels</subject><subject>Inhibition</subject><subject>Insects</subject><subject>Methods</subject><subject>Mutation</subject><subject>Oligonucleotides</subject><subject>Organic Chemicals - chemistry</subject><subject>Physiological aspects</subject><subject>Polyacrylamide</subject><subject>Properties</subject><subject>Proteins</subject><subject>Sensitivity</subject><subject>Silver</subject><subject>Silver - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tang, Weizhong</au><au>Zhou, Huafu</au><au>Li, Wei</au><au>Cotterill, Sue</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2015-12-09</date><risdate>2015</risdate><volume>10</volume><issue>12</issue><spage>e0144422</spage><epage>e0144422</epage><pages>e0144422-e0144422</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>To explore why some oligonucleotides in denaturing polyacrylamide gel could not be silver-stained, 134 different oligonucleotides were analyzed using denaturing polyacrylamide gel electrophoresis stained with silver and asymmetric cyanine. As a result, we found that the sensitivity of oligos (dA), (dC), (dG) and (dT) to silver staining could be ranged as (dA) > (dG) > (dC) > (dT) from high to low. It was unexpected that oligo (dT) was hard to be silver-stained. Moreover, the silver staining of an oligonucleotide containing base T could be partially or completely inhibited by base T. The inhibition of silver staining by base T was a competitive inhibition which could be affected by the amounts of the argyrophil nucleobase and base T, the cis-distance between the argyrophil nucleobase and base T, and the gel concentration. The changes of the intensity of an oligonucleotide band caused by the changes of DNA base composition were diverse and interesting. The intensity of some oligonucleotide bands would significantly change when the changes of DNA base composition accumulated to a certain extent (usually ≥ 4 nt). The sensitivity of cyanine staining of ≤ 11-nt long oligonucleotides could be enhanced about 250-fold by fixing the gels with methanol fixing solution.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>26650843</pmid><doi>10.1371/journal.pone.0144422</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Acrylic Resins - chemistry Base Composition Deoxyribonucleic acid DNA DNA - analysis DNA - chemistry Drosophila melanogaster Dyes Electrophoresis, Polyacrylamide Gel - methods Fluorescent Dyes - chemistry Gel electrophoresis Gels Inhibition Insects Methods Mutation Oligonucleotides Organic Chemicals - chemistry Physiological aspects Polyacrylamide Properties Proteins Sensitivity Silver Silver - chemistry Silver Staining - methods Staining Stains & staining |
| title | Silver and Cyanine Staining of Oligonucleotides in Polyacrylamide Gel |
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