ArticleBiochemistry2006
Facilitating RNA structure prediction with microarrays.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Measuring intramolecular connectivity in long RNA molecules using two-dimensional DNA patch-probe arrays.Nucleic acids research · 2025Article
- Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides.Scientific reports · 2019Article
- Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers.Journal of computational biology : a journal of computational molecular cell biology · 2016Article
- Article
- 2-Thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in RNA and DNA duplexes.Nucleic acids research · 2015Article
- Microarrays for identifying binding sites and probing structure of RNAs.Nucleic acids research · 2015Review
- Article
- Article
- Identifying and characterizing Hfq-RNA interactions.Methods (San Diego, Calif.) · 2013Review
- Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays.The Journal of biological chemistry · 2012Article
- Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes.Biochemistry · 2011Article
- Article
- MicroRNAs align with accessible sites in target mRNAs.Journal of cellular biochemistry · 2010Article
- Chemical synthesis of LNA-2-thiouridine and its influence on stability and selectivity of oligonucleotide binding to RNA.Biochemistry · 2009Article
- Rapid determination of RNA accessible sites by surface plasmon resonance detection of hybridization to DNA arrays.Analytical chemistry · 2009Article
- Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.Nucleic acids research · 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
- Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with locked nucleic acids.Biochemistry · 2009Article
- Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine.Nucleic acids research · 2008Article
- NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon.Journal of the American Chemical Society · 2008Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Determining RNA secondary structure is important for understanding structure-function relationships and identifying potential drug targets. This paper reports the use of microarrays with heptamer 2'-O-methyl oligoribonucleotides to probe the secondary structure of an RNA and thereby improve the prediction of that secondary structure. When experimental constraints from hybridization results are added to a free-energy minimization algorithm, the prediction of the secondary structure of Escherichia coli 5S rRNA improves from 27 to 92% of the known canonical base pairs. Optimization of buffer conditions for hybridization and application of 2'-O-methyl-2-thiouridine to enhance binding and improve discrimination between AU and GU pairs are also described. The results suggest that probing RNA with oligonucleotide microarrays can facilitate determination of secondary structure.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.