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Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function

LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding...

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Detalles Bibliográficos
Autores principales: Kierzek, Elzbieta, Kierzek, Ryszard, Moss, Walter N., Christensen, Shawn M., Eickbush, Thomas H., Turner, Douglas H.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346776/
https://www.ncbi.nlm.nih.gov/pubmed/18252773
http://dx.doi.org/10.1093/nar/gkm1085
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author Kierzek, Elzbieta
Kierzek, Ryszard
Moss, Walter N.
Christensen, Shawn M.
Eickbush, Thomas H.
Turner, Douglas H.
author_facet Kierzek, Elzbieta
Kierzek, Ryszard
Moss, Walter N.
Christensen, Shawn M.
Eickbush, Thomas H.
Turner, Douglas H.
author_sort Kierzek, Elzbieta
collection PubMed
description LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5′ coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5′ RNA). This R2Bm 5′ RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5′ RNA.
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spelling pubmed-23467762008-05-05 Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function Kierzek, Elzbieta Kierzek, Ryszard Moss, Walter N. Christensen, Shawn M. Eickbush, Thomas H. Turner, Douglas H. Nucleic Acids Res RNA LNA (locked nucleic acids, i.e. oligonucleotides with a methyl bridge between the 2′ oxygen and 4′ carbon of ribose) and 2,6-diaminopurine were incorporated into 2′-O-methyl RNA pentamer and hexamer probes to make a microarray that binds unpaired RNA approximately isoenergetically. That is, binding is roughly independent of target sequence if target is unfolded. The isoenergetic binding and short probe length simplify interpretation of binding to a structured RNA to provide insight into target RNA secondary structure. Microarray binding and chemical mapping were used to probe the secondary structure of a 323 nt segment of the 5′ coding region of the R2 retrotransposon from Bombyx mori (R2Bm 5′ RNA). This R2Bm 5′ RNA orchestrates functioning of the R2 protein responsible for cleaving the second strand of DNA during insertion of the R2 sequence into the genome. The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5′ RNA. Oxford University Press 2008-04 2008-02-05 /pmc/articles/PMC2346776/ /pubmed/18252773 http://dx.doi.org/10.1093/nar/gkm1085 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Kierzek, Elzbieta
Kierzek, Ryszard
Moss, Walter N.
Christensen, Shawn M.
Eickbush, Thomas H.
Turner, Douglas H.
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title_full Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title_fullStr Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title_full_unstemmed Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title_short Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
title_sort isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an rna element orchestrating r2 retrotransposon protein function
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2346776/
https://www.ncbi.nlm.nih.gov/pubmed/18252773
http://dx.doi.org/10.1093/nar/gkm1085
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