The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities
Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA–DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computationa...
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| Veröffentlicht in: | Nano letters 2016-03, Vol.16 (3), p.1746-1753 |
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| container_title | Nano letters |
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| creator | Afonin, Kirill A Viard, Mathias Tedbury, Philip Bindewald, Eckart Parlea, Lorena Howington, Marshall Valdman, Melissa Johns-Boehme, Alizah Brainerd, Cara Freed, Eric O Shapiro, Bruce A |
| description | Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA–DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds. |
| doi_str_mv | 10.1021/acs.nanolett.5b04676 |
| format | Article |
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The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. 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The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.</description><subject>Activation</subject><subject>Cell Line, Tumor</subject><subject>Deoxyribonucleic acid</subject><subject>Design analysis</subject><subject>DNA, Single-Stranded - chemistry</subject><subject>DNA, Single-Stranded - genetics</subject><subject>HeLa Cells</subject><subject>Human</subject><subject>Humans</subject><subject>Models, Molecular</subject><subject>Nanoparticles</subject><subject>Nanoparticles - chemistry</subject><subject>Nanotechnology</subject><subject>Nucleic Acid Hybridization</subject><subject>Nucleotides</subject><subject>Ribonucleic acids</subject><subject>RNA Interference</subject><subject>RNA, Small Interfering - chemistry</subject><subject>RNA, Small Interfering - genetics</subject><subject>Transfection</subject><issn>1530-6984</issn><issn>1530-6992</issn><issn>1530-6992</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkUFrHCEYhqUkNGnaf1CKx1x2q46OM5fAEpI2kKZQds_iOJ-7BnfcqBPov6_T3Szppe1J-XzeFz8ehD5SMqeE0c_apPmgh-Ah57noCK9l_QadU1GRWd227OR4b_gZepfSIyGkrQR5i85Y3bK6atg5Wi03gFcJcLD4mxvcVnv842GBlwE2wfcJ54CX0a3XEHEu6MJk96yzC8PvxOiz23nAt-NgpqH2LjtI79Gp1T7Bh8N5gVa3N8vrr7P771_urhf3My2oyDNdV2B6YqyErmettEb2QnBry9QSoXkZd53ubWuANqZjlFLOakZKXEIvqwt0te_djd0WegNDjtqrXSx7xJ8qaKf-fBncRq3Ds6orLgSbCi4PBTE8jZCy2rpkwHs9QBiTog1pKGOS03-jsuWCCFq1_4FKRjnnZEL5HjUxpBTBHj9PiZo8q-JZvXhWB88l9un14sfQi9gCkD0wxR_DGIua9PfOX4mUudA</recordid><startdate>20160309</startdate><enddate>20160309</enddate><creator>Afonin, Kirill A</creator><creator>Viard, Mathias</creator><creator>Tedbury, Philip</creator><creator>Bindewald, Eckart</creator><creator>Parlea, Lorena</creator><creator>Howington, Marshall</creator><creator>Valdman, Melissa</creator><creator>Johns-Boehme, Alizah</creator><creator>Brainerd, Cara</creator><creator>Freed, Eric O</creator><creator>Shapiro, Bruce A</creator><general>American Chemical Society</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>7X8</scope><scope>7TM</scope><scope>7SR</scope><scope>7U5</scope><scope>8BQ</scope><scope>8FD</scope><scope>JG9</scope><scope>L7M</scope><scope>5PM</scope></search><sort><creationdate>20160309</creationdate><title>The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities</title><author>Afonin, Kirill A ; Viard, Mathias ; Tedbury, Philip ; Bindewald, Eckart ; Parlea, Lorena ; Howington, Marshall ; Valdman, Melissa ; Johns-Boehme, Alizah ; Brainerd, Cara ; Freed, Eric O ; Shapiro, Bruce A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a515t-a63ecd0cf7ebd297fc7d554ffecdf05a4ebdbbadf9ce18cb211142620a517ed73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Activation</topic><topic>Cell Line, Tumor</topic><topic>Deoxyribonucleic acid</topic><topic>Design analysis</topic><topic>DNA, Single-Stranded - chemistry</topic><topic>DNA, Single-Stranded - genetics</topic><topic>HeLa Cells</topic><topic>Human</topic><topic>Humans</topic><topic>Models, Molecular</topic><topic>Nanoparticles</topic><topic>Nanoparticles - chemistry</topic><topic>Nanotechnology</topic><topic>Nucleic Acid Hybridization</topic><topic>Nucleotides</topic><topic>Ribonucleic acids</topic><topic>RNA Interference</topic><topic>RNA, Small Interfering - chemistry</topic><topic>RNA, Small Interfering - genetics</topic><topic>Transfection</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Afonin, Kirill A</creatorcontrib><creatorcontrib>Viard, Mathias</creatorcontrib><creatorcontrib>Tedbury, Philip</creatorcontrib><creatorcontrib>Bindewald, Eckart</creatorcontrib><creatorcontrib>Parlea, Lorena</creatorcontrib><creatorcontrib>Howington, Marshall</creatorcontrib><creatorcontrib>Valdman, Melissa</creatorcontrib><creatorcontrib>Johns-Boehme, Alizah</creatorcontrib><creatorcontrib>Brainerd, Cara</creatorcontrib><creatorcontrib>Freed, Eric O</creatorcontrib><creatorcontrib>Shapiro, Bruce A</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Materials Research Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nano letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Afonin, Kirill A</au><au>Viard, Mathias</au><au>Tedbury, Philip</au><au>Bindewald, Eckart</au><au>Parlea, Lorena</au><au>Howington, Marshall</au><au>Valdman, Melissa</au><au>Johns-Boehme, Alizah</au><au>Brainerd, Cara</au><au>Freed, Eric O</au><au>Shapiro, Bruce A</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities</atitle><jtitle>Nano letters</jtitle><addtitle>Nano Lett</addtitle><date>2016-03-09</date><risdate>2016</risdate><volume>16</volume><issue>3</issue><spage>1746</spage><epage>1753</epage><pages>1746-1753</pages><issn>1530-6984</issn><issn>1530-6992</issn><eissn>1530-6992</eissn><abstract>Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA–DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.</abstract><cop>United States</cop><pub>American Chemical Society</pub><pmid>26926382</pmid><doi>10.1021/acs.nanolett.5b04676</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; ACS Publications |
| subjects | Activation Cell Line, Tumor Deoxyribonucleic acid Design analysis DNA, Single-Stranded - chemistry DNA, Single-Stranded - genetics HeLa Cells Human Humans Models, Molecular Nanoparticles Nanoparticles - chemistry Nanotechnology Nucleic Acid Hybridization Nucleotides Ribonucleic acids RNA Interference RNA, Small Interfering - chemistry RNA, Small Interfering - genetics Transfection |
| title | The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities |
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