ArticleNucleic acids research2008
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides.Scientific reports · 2019Article
- Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies.Scientific reports · 2017Article
- Incorporating a guanidine-modified cytosine base into triplex-forming PNAs for the recognition of a C-G pyrimidine-purine inversion site of an RNA duplex.Nucleic acids research · 2016Article
- Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease.Nucleic acids research · 2016Article
- Article
- Integration, Regulation, and Long-Term Stability of R2 Retrotransposons.Microbiology spectrum · 2015Review
- Article
- Microarrays for identifying binding sites and probing structure of RNAs.Nucleic acids research · 2015Review
- Article
- Article
- Incorporation of thio-pseudoisocytosine into triplex-forming peptide nucleic acids for enhanced recognition of RNA duplexes.Nucleic acids research · 2014Article
- Article
- Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays.The Journal of biological chemistry · 2012Article
- The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin.PloS one · 2012Article
- Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes.Biochemistry · 2011Article
- NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.RNA (New York, N.Y.) · 2011Article
- Folding and finding RNA secondary structure.Cold Spring Harbor perspectives in biology · 2010Review
- Article
- Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.Biochemistry · 2009Article
- Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.Journal of molecular biology · 2009Article
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Authors and funding
6 authors.
Funding
Abstract
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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