Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd
Single-strand conformation polymorphism (SSCP) was used to characterize viroids. Eight cDNA clones, which showed identical profiles in preliminary existing SSCP analysis but had different sequences, were chosen to develop a sensitive SSCP technique for identifying the variability of Peach latent mos...
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| Veröffentlicht in: | Journal of virological methods 2006-08, Vol.135 (2), p.276-280 |
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| container_title | Journal of virological methods |
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| creator | Xu, Wen Xing Hong, Ni Zhang, Jian Kun Wang, Guo Ping |
| description | Single-strand conformation polymorphism (SSCP) was used to characterize viroids. Eight cDNA clones, which showed identical profiles in preliminary existing SSCP analysis but had different sequences, were chosen to develop a sensitive SSCP technique for identifying the variability of
Peach latent mosaic viroid (PLMVd). Polyacrylamide Gel Electrophoresis (PAGE) conditions were optimized to improve the sensitivity of the existing SSCP, and a modified SSCP protocol was developed. The results indicated that the modified SSCP protocol provided an overall sensitivity in identifying the variability of these clones, and showed higher resolution than the existing one and its improved versions. As shown by sequence analyses of cDNA clones of PLMVd and the modified SSCP profiles, there is no close correlation between the number of base changes and variation of the modified SSCP band patterns. The potential use of the modified SSCP analysis is discussed as a tool for viroids characterization. |
| doi_str_mv | 10.1016/j.jviromet.2006.03.004 |
| format | Article |
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Peach latent mosaic viroid (PLMVd). Polyacrylamide Gel Electrophoresis (PAGE) conditions were optimized to improve the sensitivity of the existing SSCP, and a modified SSCP protocol was developed. The results indicated that the modified SSCP protocol provided an overall sensitivity in identifying the variability of these clones, and showed higher resolution than the existing one and its improved versions. As shown by sequence analyses of cDNA clones of PLMVd and the modified SSCP profiles, there is no close correlation between the number of base changes and variation of the modified SSCP band patterns. The potential use of the modified SSCP analysis is discussed as a tool for viroids characterization.</description><identifier>ISSN: 0166-0934</identifier><identifier>EISSN: 1879-0984</identifier><identifier>DOI: 10.1016/j.jviromet.2006.03.004</identifier><identifier>PMID: 16644025</identifier><identifier>CODEN: JVMEDH</identifier><language>eng</language><publisher>London: Elsevier B.V</publisher><subject>Base Sequence ; Biological and medical sciences ; Fundamental and applied biological sciences. Psychology ; Microbiology ; Molecular Sequence Data ; Mosaic Viruses - genetics ; Peach latent mosaic viroid ; Polymorphism, Single-Stranded Conformational ; Prunus - virology ; Sensitivity and Specificity ; SSCP ; Techniques used in virology ; Viroids - genetics ; Virology</subject><ispartof>Journal of virological methods, 2006-08, Vol.135 (2), p.276-280</ispartof><rights>2006 Elsevier B.V.</rights><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c427t-5c7a62aca470163c322c3cf03640400171cf229af77fc84ac1a58189c176dbf73</citedby><cites>FETCH-LOGICAL-c427t-5c7a62aca470163c322c3cf03640400171cf229af77fc84ac1a58189c176dbf73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S016609340600098X$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65534</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17905423$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16644025$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Xu, Wen Xing</creatorcontrib><creatorcontrib>Hong, Ni</creatorcontrib><creatorcontrib>Zhang, Jian Kun</creatorcontrib><creatorcontrib>Wang, Guo Ping</creatorcontrib><title>Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd</title><title>Journal of virological methods</title><addtitle>J Virol Methods</addtitle><description>Single-strand conformation polymorphism (SSCP) was used to characterize viroids. Eight cDNA clones, which showed identical profiles in preliminary existing SSCP analysis but had different sequences, were chosen to develop a sensitive SSCP technique for identifying the variability of
Peach latent mosaic viroid (PLMVd). Polyacrylamide Gel Electrophoresis (PAGE) conditions were optimized to improve the sensitivity of the existing SSCP, and a modified SSCP protocol was developed. The results indicated that the modified SSCP protocol provided an overall sensitivity in identifying the variability of these clones, and showed higher resolution than the existing one and its improved versions. As shown by sequence analyses of cDNA clones of PLMVd and the modified SSCP profiles, there is no close correlation between the number of base changes and variation of the modified SSCP band patterns. The potential use of the modified SSCP analysis is discussed as a tool for viroids characterization.</description><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Mosaic Viruses - genetics</subject><subject>Peach latent mosaic viroid</subject><subject>Polymorphism, Single-Stranded Conformational</subject><subject>Prunus - virology</subject><subject>Sensitivity and Specificity</subject><subject>SSCP</subject><subject>Techniques used in virology</subject><subject>Viroids - genetics</subject><subject>Virology</subject><issn>0166-0934</issn><issn>1879-0984</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU1v1DAQhi0EokvhL1S-gOCQMP6IndxAqxYqbUWlAlfL69jUqyRebG-k_fd12aAee7I1eua1Zx6ELgjUBIj4vKt3s49htLmmAKIGVgPwF2hFWtlV0LX8JVoVUJQ742foTUo7AGgkY6_RWalzDrRZofF63Mcw--kPzvcWJzsln_3s8xEHh1OpD7ZKOeqpxyZMLsRRZx8mvA_DcQxxf-_TiD_e3a1vP-EccMqH_vgvatbR660flqjbzc3v_i165fSQ7LvlPEe_ri5_rr9Xmx_frtdfN5XhVOaqMVILqo3msozADKPUMOOACQ4cgEhiHKWddlI603JtiG5a0naGSNFvnWTn6MMpt8z292BTVqNPxg6Dnmw4JCVa6ARjzbMgkcC6ltICihNoYkgpWqf20Y86HhUB9WhE7dR_I-rRiAKmipHSeLG8cNiOtn9qWxQU4P0C6GT04MqqjU9PnOyg4ZQV7suJs2Vxs7dRJePtZGzvozVZ9cE_95cH0c2uAw</recordid><startdate>20060801</startdate><enddate>20060801</enddate><creator>Xu, Wen Xing</creator><creator>Hong, Ni</creator><creator>Zhang, Jian Kun</creator><creator>Wang, Guo Ping</creator><general>Elsevier B.V</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>7U9</scope><scope>H94</scope><scope>7X8</scope></search><sort><creationdate>20060801</creationdate><title>Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd</title><author>Xu, Wen Xing ; Hong, Ni ; Zhang, Jian Kun ; Wang, Guo Ping</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c427t-5c7a62aca470163c322c3cf03640400171cf229af77fc84ac1a58189c176dbf73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2006</creationdate><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Mosaic Viruses - genetics</topic><topic>Peach latent mosaic viroid</topic><topic>Polymorphism, Single-Stranded Conformational</topic><topic>Prunus - virology</topic><topic>Sensitivity and Specificity</topic><topic>SSCP</topic><topic>Techniques used in virology</topic><topic>Viroids - genetics</topic><topic>Virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Xu, Wen Xing</creatorcontrib><creatorcontrib>Hong, Ni</creatorcontrib><creatorcontrib>Zhang, Jian Kun</creatorcontrib><creatorcontrib>Wang, Guo Ping</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>Virology and AIDS Abstracts</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of virological methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Xu, Wen Xing</au><au>Hong, Ni</au><au>Zhang, Jian Kun</au><au>Wang, Guo Ping</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd</atitle><jtitle>Journal of virological methods</jtitle><addtitle>J Virol Methods</addtitle><date>2006-08-01</date><risdate>2006</risdate><volume>135</volume><issue>2</issue><spage>276</spage><epage>280</epage><pages>276-280</pages><issn>0166-0934</issn><eissn>1879-0984</eissn><coden>JVMEDH</coden><abstract>Single-strand conformation polymorphism (SSCP) was used to characterize viroids. Eight cDNA clones, which showed identical profiles in preliminary existing SSCP analysis but had different sequences, were chosen to develop a sensitive SSCP technique for identifying the variability of
Peach latent mosaic viroid (PLMVd). Polyacrylamide Gel Electrophoresis (PAGE) conditions were optimized to improve the sensitivity of the existing SSCP, and a modified SSCP protocol was developed. The results indicated that the modified SSCP protocol provided an overall sensitivity in identifying the variability of these clones, and showed higher resolution than the existing one and its improved versions. As shown by sequence analyses of cDNA clones of PLMVd and the modified SSCP profiles, there is no close correlation between the number of base changes and variation of the modified SSCP band patterns. The potential use of the modified SSCP analysis is discussed as a tool for viroids characterization.</abstract><cop>London</cop><cop>Amsterdam</cop><cop>New York, NY</cop><pub>Elsevier B.V</pub><pmid>16644025</pmid><doi>10.1016/j.jviromet.2006.03.004</doi><tpages>5</tpages></addata></record> |
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| ispartof | Journal of virological methods, 2006-08, Vol.135 (2), p.276-280 |
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| subjects | Base Sequence Biological and medical sciences Fundamental and applied biological sciences. Psychology Microbiology Molecular Sequence Data Mosaic Viruses - genetics Peach latent mosaic viroid Polymorphism, Single-Stranded Conformational Prunus - virology Sensitivity and Specificity SSCP Techniques used in virology Viroids - genetics Virology |
| title | Improving the sensitivity of single-strand conformation polymorphism (SSCP) to study the variability of PLMVd |
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