Use of sodium trichloroacetate and mung bean nuclease to increase sensitivity and precision during transcript mapping
An improved method for mapping RNA transcript boundaries by the nuclease protection technique is presented. This method exploits the large (>20°C) difference in the thermal stability of RNA:DNA and DNA:DNA duplexes in concentrated chaotropic salt solutions. At 45°C in 3.0 m sodium trichloroacetat...
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| Veröffentlicht in: | Anal. Biochem.; (United States) 1986-10, Vol.158 (1), p.165-170 |
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| creator | Murray, Michael G. |
| description | An improved method for mapping RNA transcript boundaries by the nuclease protection technique is presented. This method exploits the large (>20°C) difference in the thermal stability of RNA:DNA and DNA:DNA duplexes in concentrated chaotropic salt solutions. At 45°C in 3.0
m sodium trichloroacetate RNA:DNA hybridization is very efficient but DNA:DNA duplexes remain completely denatured. For many applications, this solvent system can eliminate the need to prepare probes that are free of competing or irrelevant DNA molecules. Fifty- to 100-fold more RNA:DNA hybridization is observed when reassociation is performed in 3.0
m sodium trichloroacetate than in solutions containing high concentrations of formamide. A comparison of the use of S1 nuclease or mung bean nuclease suggests that mung bean nuclease can produce more precise and less ambiguous nuclease protection patterns. |
| doi_str_mv | 10.1016/0003-2697(86)90605-6 |
| format | Article |
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m sodium trichloroacetate RNA:DNA hybridization is very efficient but DNA:DNA duplexes remain completely denatured. For many applications, this solvent system can eliminate the need to prepare probes that are free of competing or irrelevant DNA molecules. Fifty- to 100-fold more RNA:DNA hybridization is observed when reassociation is performed in 3.0
m sodium trichloroacetate than in solutions containing high concentrations of formamide. A comparison of the use of S1 nuclease or mung bean nuclease suggests that mung bean nuclease can produce more precise and less ambiguous nuclease protection patterns.</description><identifier>ISSN: 0003-2697</identifier><identifier>EISSN: 1096-0309</identifier><identifier>DOI: 10.1016/0003-2697(86)90605-6</identifier><identifier>PMID: 2432801</identifier><identifier>CODEN: ANBCA2</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>550201 - Biochemistry- Tracer Techniques ; 550401 - Genetics- Tracer Techniques ; ACETATES ; Applied sciences ; BASIC BIOLOGICAL SCIENCES ; BETA DECAY RADIOISOTOPES ; BETA-MINUS DECAY RADIOISOTOPES ; BIOCHEMISTRY ; Biological and medical sciences ; CARBON 14 COMPOUNDS ; CARBOXYLIC ACID SALTS ; chaotrope ; CHEMISTRY ; DAYS LIVING RADIOISOTOPES ; DNA ; DNA - isolation & purification ; DNA SEQUENCING ; duplex ; Endonucleases ; ENZYMES ; ESTERASES ; Exact sciences and technology ; formamide ; Fundamental and applied biological sciences. Psychology ; Genes. Genome ; GENETIC MAPPING ; HYBRIDIZATION ; hybridization analysis ; HYDROLASES ; ISOTOPE APPLICATIONS ; ISOTOPES ; LABELLED COMPOUNDS ; LIGHT NUCLEI ; MAPPING ; Molecular and cellular biology ; Molecular genetics ; mung bean nuclease ; nuclease ; NUCLEASES ; NUCLEI ; Nucleic Acid Heteroduplexes - isolation & purification ; Nucleic Acid Hybridization ; NUCLEIC ACIDS ; ODD-ODD NUCLEI ; ORGANIC COMPOUNDS ; Other techniques and industries ; PHOSPHODIESTERASES ; PHOSPHORUS 32 ; PHOSPHORUS ISOTOPES ; RADIOISOTOPES ; RNA ; RNA - isolation & purification ; S1 nuclease ; SENSITIVITY ; Single-Strand Specific DNA and RNA Endonucleases ; sodium trichloroacetate ; STRUCTURAL CHEMICAL ANALYSIS ; TRACER TECHNIQUES ; TRANSCRIPTION ; Trichloroacetic Acid</subject><ispartof>Anal. Biochem.; (United States), 1986-10, Vol.158 (1), p.165-170</ispartof><rights>1986</rights><rights>1987 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c473t-5181c2c6e681ed134bda6533de26563ad4399302caa987371fe63f6a1d6ac8553</citedby><cites>FETCH-LOGICAL-c473t-5181c2c6e681ed134bda6533de26563ad4399302caa987371fe63f6a1d6ac8553</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/0003-2697(86)90605-6$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,885,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=8340816$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=8355108$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/2432801$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/6942529$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Murray, Michael G.</creatorcontrib><creatorcontrib>Agrigenetics Advanced Science Co., Madison, WI</creatorcontrib><title>Use of sodium trichloroacetate and mung bean nuclease to increase sensitivity and precision during transcript mapping</title><title>Anal. Biochem.; (United States)</title><addtitle>Anal Biochem</addtitle><description>An improved method for mapping RNA transcript boundaries by the nuclease protection technique is presented. This method exploits the large (>20°C) difference in the thermal stability of RNA:DNA and DNA:DNA duplexes in concentrated chaotropic salt solutions. At 45°C in 3.0
m sodium trichloroacetate RNA:DNA hybridization is very efficient but DNA:DNA duplexes remain completely denatured. For many applications, this solvent system can eliminate the need to prepare probes that are free of competing or irrelevant DNA molecules. Fifty- to 100-fold more RNA:DNA hybridization is observed when reassociation is performed in 3.0
m sodium trichloroacetate than in solutions containing high concentrations of formamide. A comparison of the use of S1 nuclease or mung bean nuclease suggests that mung bean nuclease can produce more precise and less ambiguous nuclease protection patterns.</description><subject>550201 - Biochemistry- Tracer Techniques</subject><subject>550401 - Genetics- Tracer Techniques</subject><subject>ACETATES</subject><subject>Applied sciences</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>BETA DECAY RADIOISOTOPES</subject><subject>BETA-MINUS DECAY RADIOISOTOPES</subject><subject>BIOCHEMISTRY</subject><subject>Biological and medical sciences</subject><subject>CARBON 14 COMPOUNDS</subject><subject>CARBOXYLIC ACID SALTS</subject><subject>chaotrope</subject><subject>CHEMISTRY</subject><subject>DAYS LIVING RADIOISOTOPES</subject><subject>DNA</subject><subject>DNA - isolation & purification</subject><subject>DNA SEQUENCING</subject><subject>duplex</subject><subject>Endonucleases</subject><subject>ENZYMES</subject><subject>ESTERASES</subject><subject>Exact sciences and technology</subject><subject>formamide</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Genes. Genome</subject><subject>GENETIC MAPPING</subject><subject>HYBRIDIZATION</subject><subject>hybridization analysis</subject><subject>HYDROLASES</subject><subject>ISOTOPE APPLICATIONS</subject><subject>ISOTOPES</subject><subject>LABELLED COMPOUNDS</subject><subject>LIGHT NUCLEI</subject><subject>MAPPING</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>mung bean nuclease</subject><subject>nuclease</subject><subject>NUCLEASES</subject><subject>NUCLEI</subject><subject>Nucleic Acid Heteroduplexes - isolation & purification</subject><subject>Nucleic Acid Hybridization</subject><subject>NUCLEIC ACIDS</subject><subject>ODD-ODD NUCLEI</subject><subject>ORGANIC COMPOUNDS</subject><subject>Other techniques and industries</subject><subject>PHOSPHODIESTERASES</subject><subject>PHOSPHORUS 32</subject><subject>PHOSPHORUS ISOTOPES</subject><subject>RADIOISOTOPES</subject><subject>RNA</subject><subject>RNA - isolation & purification</subject><subject>S1 nuclease</subject><subject>SENSITIVITY</subject><subject>Single-Strand Specific DNA and RNA Endonucleases</subject><subject>sodium trichloroacetate</subject><subject>STRUCTURAL CHEMICAL ANALYSIS</subject><subject>TRACER TECHNIQUES</subject><subject>TRANSCRIPTION</subject><subject>Trichloroacetic Acid</subject><issn>0003-2697</issn><issn>1096-0309</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1986</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU2L1TAUhoMo43X0HygEEdFFNR_NaboRZPALBtw465CbnDqRNqlJOjD_3vbey106q4Sc503C-xDykrMPnHH4yBiTjYC-e6fhfc-AqQYekR1nPTRMsv4x2Z2Rp-RZKX8Y47xVcEEuRCuFZnxHlpuCNA20JB-WidYc3O2YcrIOq61IbfR0WuJvukcbaVzciHZN1ERDdPmwLxhLqOEu1PsDPmd0oYQUqV9yWKM121hcDnOlk53n9eg5eTLYseCL03pJbr5--XX1vbn--e3H1efrxrWdrI3imjvhAEFz9Fy2e29BSelRgAJpfSv7XjLhrO11Jzs-IMgBLPdgnVZKXpLXx3tTqcEUFyq6W5diRFcN9K1Qol-ht0dozunvgqWaKRSH42gjpqWYrhNSaWgfBHkLigm-ge0RdDmVknEwcw6TzfeGM7O5M5sYs4kxGszBnYE19up0_7Kf0J9DJ1nr_M1pbouz47DWuhZ9xrRUijP9MNYyzbfXPh0xXAXcBcxbPxgd-pC3enwK___uPwU9wnY</recordid><startdate>19861001</startdate><enddate>19861001</enddate><creator>Murray, Michael G.</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QO</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>7X8</scope><scope>OTOTI</scope></search><sort><creationdate>19861001</creationdate><title>Use of sodium trichloroacetate and mung bean nuclease to increase sensitivity and precision during transcript mapping</title><author>Murray, Michael G.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c473t-5181c2c6e681ed134bda6533de26563ad4399302caa987371fe63f6a1d6ac8553</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1986</creationdate><topic>550201 - Biochemistry- Tracer Techniques</topic><topic>550401 - Genetics- Tracer Techniques</topic><topic>ACETATES</topic><topic>Applied sciences</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>BETA DECAY RADIOISOTOPES</topic><topic>BETA-MINUS DECAY RADIOISOTOPES</topic><topic>BIOCHEMISTRY</topic><topic>Biological and medical sciences</topic><topic>CARBON 14 COMPOUNDS</topic><topic>CARBOXYLIC ACID SALTS</topic><topic>chaotrope</topic><topic>CHEMISTRY</topic><topic>DAYS LIVING RADIOISOTOPES</topic><topic>DNA</topic><topic>DNA - isolation & purification</topic><topic>DNA SEQUENCING</topic><topic>duplex</topic><topic>Endonucleases</topic><topic>ENZYMES</topic><topic>ESTERASES</topic><topic>Exact sciences and technology</topic><topic>formamide</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Genes. Genome</topic><topic>GENETIC MAPPING</topic><topic>HYBRIDIZATION</topic><topic>hybridization analysis</topic><topic>HYDROLASES</topic><topic>ISOTOPE APPLICATIONS</topic><topic>ISOTOPES</topic><topic>LABELLED COMPOUNDS</topic><topic>LIGHT NUCLEI</topic><topic>MAPPING</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>mung bean nuclease</topic><topic>nuclease</topic><topic>NUCLEASES</topic><topic>NUCLEI</topic><topic>Nucleic Acid Heteroduplexes - isolation & purification</topic><topic>Nucleic Acid Hybridization</topic><topic>NUCLEIC ACIDS</topic><topic>ODD-ODD NUCLEI</topic><topic>ORGANIC COMPOUNDS</topic><topic>Other techniques and industries</topic><topic>PHOSPHODIESTERASES</topic><topic>PHOSPHORUS 32</topic><topic>PHOSPHORUS ISOTOPES</topic><topic>RADIOISOTOPES</topic><topic>RNA</topic><topic>RNA - isolation & purification</topic><topic>S1 nuclease</topic><topic>SENSITIVITY</topic><topic>Single-Strand Specific DNA and RNA Endonucleases</topic><topic>sodium trichloroacetate</topic><topic>STRUCTURAL CHEMICAL ANALYSIS</topic><topic>TRACER TECHNIQUES</topic><topic>TRANSCRIPTION</topic><topic>Trichloroacetic Acid</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Murray, Michael G.</creatorcontrib><creatorcontrib>Agrigenetics Advanced Science Co., Madison, WI</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><jtitle>Anal. Biochem.; (United States)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Murray, Michael G.</au><aucorp>Agrigenetics Advanced Science Co., Madison, WI</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Use of sodium trichloroacetate and mung bean nuclease to increase sensitivity and precision during transcript mapping</atitle><jtitle>Anal. Biochem.; (United States)</jtitle><addtitle>Anal Biochem</addtitle><date>1986-10-01</date><risdate>1986</risdate><volume>158</volume><issue>1</issue><spage>165</spage><epage>170</epage><pages>165-170</pages><issn>0003-2697</issn><eissn>1096-0309</eissn><coden>ANBCA2</coden><abstract>An improved method for mapping RNA transcript boundaries by the nuclease protection technique is presented. This method exploits the large (>20°C) difference in the thermal stability of RNA:DNA and DNA:DNA duplexes in concentrated chaotropic salt solutions. At 45°C in 3.0
m sodium trichloroacetate RNA:DNA hybridization is very efficient but DNA:DNA duplexes remain completely denatured. For many applications, this solvent system can eliminate the need to prepare probes that are free of competing or irrelevant DNA molecules. Fifty- to 100-fold more RNA:DNA hybridization is observed when reassociation is performed in 3.0
m sodium trichloroacetate than in solutions containing high concentrations of formamide. A comparison of the use of S1 nuclease or mung bean nuclease suggests that mung bean nuclease can produce more precise and less ambiguous nuclease protection patterns.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>2432801</pmid><doi>10.1016/0003-2697(86)90605-6</doi><tpages>6</tpages></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0003-2697 |
| ispartof | Anal. Biochem.; (United States), 1986-10, Vol.158 (1), p.165-170 |
| issn | 0003-2697 1096-0309 |
| language | eng |
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| source | MEDLINE; Access via ScienceDirect (Elsevier) |
| subjects | 550201 - Biochemistry- Tracer Techniques 550401 - Genetics- Tracer Techniques ACETATES Applied sciences BASIC BIOLOGICAL SCIENCES BETA DECAY RADIOISOTOPES BETA-MINUS DECAY RADIOISOTOPES BIOCHEMISTRY Biological and medical sciences CARBON 14 COMPOUNDS CARBOXYLIC ACID SALTS chaotrope CHEMISTRY DAYS LIVING RADIOISOTOPES DNA DNA - isolation & purification DNA SEQUENCING duplex Endonucleases ENZYMES ESTERASES Exact sciences and technology formamide Fundamental and applied biological sciences. Psychology Genes. Genome GENETIC MAPPING HYBRIDIZATION hybridization analysis HYDROLASES ISOTOPE APPLICATIONS ISOTOPES LABELLED COMPOUNDS LIGHT NUCLEI MAPPING Molecular and cellular biology Molecular genetics mung bean nuclease nuclease NUCLEASES NUCLEI Nucleic Acid Heteroduplexes - isolation & purification Nucleic Acid Hybridization NUCLEIC ACIDS ODD-ODD NUCLEI ORGANIC COMPOUNDS Other techniques and industries PHOSPHODIESTERASES PHOSPHORUS 32 PHOSPHORUS ISOTOPES RADIOISOTOPES RNA RNA - isolation & purification S1 nuclease SENSITIVITY Single-Strand Specific DNA and RNA Endonucleases sodium trichloroacetate STRUCTURAL CHEMICAL ANALYSIS TRACER TECHNIQUES TRANSCRIPTION Trichloroacetic Acid |
| title | Use of sodium trichloroacetate and mung bean nuclease to increase sensitivity and precision during transcript mapping |
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