RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour
We have probed the effects of altering buffer conditions on the behaviour of two aptamer RNAs for the bacterio-phage MS2 coat protein using site-specific substitution of 2'-deoxy-2-aminopurine nucleotides at key adenosine positions. These have been compared to the wild-type operator stem-loop o...
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| Veröffentlicht in: | Nucleic acids research 2000-01, Vol.28 (2), p.489-497 |
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| creator | Parrott, A M Lago, H Adams, C J Ashcroft, A E Stonehouse, N J Stockley, P G |
| description | We have probed the effects of altering buffer conditions on the behaviour of two aptamer RNAs for the bacterio-phage MS2 coat protein using site-specific substitution of 2'-deoxy-2-aminopurine nucleotides at key adenosine positions. These have been compared to the wild-type operator stem-loop oligonucleotide, which is the natural target for the coat protein. The fluorescence emission spectra show a position and oligonucleotide sequence dependence which appears to reflect local conformational changes. These are largely similar between the differing oligonucleotides and deviations can be explained by the individual features of each sequence. Recognition by coat protein is enhanced, unaffected or decreased depending on the site of substitution, consistent with the known protein-RNA contacts seen in crystal structures of the complexes. These data suggest that the detailed conformational dynamics of aptamers and wild-type RNA ligands for the same protein target are remarkably similar. |
| doi_str_mv | 10.1093/nar/28.2.489 |
| format | Article |
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These have been compared to the wild-type operator stem-loop oligonucleotide, which is the natural target for the coat protein. The fluorescence emission spectra show a position and oligonucleotide sequence dependence which appears to reflect local conformational changes. These are largely similar between the differing oligonucleotides and deviations can be explained by the individual features of each sequence. Recognition by coat protein is enhanced, unaffected or decreased depending on the site of substitution, consistent with the known protein-RNA contacts seen in crystal structures of the complexes. 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These data suggest that the detailed conformational dynamics of aptamers and wild-type RNA ligands for the same protein target are remarkably similar.</description><subject>2'-deoxy-2-aminopurine nucleotides</subject><subject>Base Sequence</subject><subject>Capsid Proteins - genetics</subject><subject>Levivirus - genetics</subject><subject>oligonucleotides</subject><subject>Phage MS2</subject><subject>RNA, Viral - chemistry</subject><subject>RNA, Viral - genetics</subject><subject>RNA-Binding Proteins - genetics</subject><subject>Solutions</subject><subject>Spectrometry, Fluorescence</subject><issn>1362-4962</issn><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUtv1TAQhSNERUthxxpZLLoit7bj2PGCRVXxkvqQeKytiTPudZXEwXaK-u9xuRW6sGE1o5lvjmbmVNUrRjeM6uZ0hnjKuw3fiE4_qY5YI3kttORP9_LD6nlKt5QywVrxrDpkVFIphTqq4perMwJLhgljIi5EkrdILr9y0oPNGH1YtnCDxAbIZIkho58JzMNv7KcfhzrfL0geVMKCEXJR2MIdkuQnP0IkKYxr9mEmPZa6D2t8UR04GBO-fIzH1fcP77-df6ovrj9-Pj-7qK1oVK4V8q5RtmOuaXvHUNDWskF01jkuqNWMD9BTyZzkrWM90h6UBtRMd0xTIZvj6t1Od1n7CQeLc44wmiX6CeK9CeDN353Zb81NuDOM8paKMn_yOB_DjxVTNpNPFscRZgxrMooqrTpB_wsyVbYpogV88w94W_4xlycYTqlsuNJtgd7uIBtDShHdn40ZNQ-Om-K44Z3hpjhe8Nf7V-7BO4ubX3WJqDc</recordid><startdate>20000115</startdate><enddate>20000115</enddate><creator>Parrott, A M</creator><creator>Lago, H</creator><creator>Adams, C J</creator><creator>Ashcroft, A E</creator><creator>Stonehouse, N J</creator><creator>Stockley, P G</creator><general>Oxford Publishing Limited (England)</general><general>Oxford University Press</general><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>7QL</scope><scope>7QO</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20000115</creationdate><title>RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour</title><author>Parrott, A M ; 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| source | MEDLINE; Oxford Journals Open Access Collection; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | 2'-deoxy-2-aminopurine nucleotides Base Sequence Capsid Proteins - genetics Levivirus - genetics oligonucleotides Phage MS2 RNA, Viral - chemistry RNA, Viral - genetics RNA-Binding Proteins - genetics Solutions Spectrometry, Fluorescence |
| title | RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour |
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