ArticleRNA (New York, N.Y.)2001
Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.
Article in RNA (New York, N.Y.), 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 43 citations in OpenAlex.
- Targeting Highly Structured RNA by Cooperative Action of siRNAs and Helper Antisense Oligomers in Living Cells.PloS one · 2015Article
- Labeling native bacterial RNA in live cells.Cell research · 2014Article
- Relieving bottlenecks in RNA drug discovery for retinal diseases.Advances in experimental medicine and biology · 2012Review
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Native mRNA antisense-accessible sites library for the selection of antisense oligonucleotides, PNAs, and siRNAs.RNA (New York, N.Y.) · 2010Article
- Rapid determination of RNA accessible sites by surface plasmon resonance detection of hybridization to DNA arrays.Analytical chemistry · 2009Article
- Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Bottlenecks in development of retinal therapeutic post-transcriptional gene silencing agents.Vision research · 2008Review
- Assays for determining poly(A) tail length and the polarity of mRNA decay in mammalian cells.Methods in enzymology · 2008Article
- Application of the Invader RNA assay to the polarity of vertebrate mRNA decay.Methods in molecular biology (Clifton, N.J.) · 2008Article
- Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.BMC bioinformatics · 2006Article
- Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation.Nucleic acids research · 2006Article
- AOBase: a database for antisense oligonucleotides selection and design.Nucleic acids research · 2006Article
- Secondary structure in the target as a confounding factor in synthetic oligomer microarray design.BMC genomics · 2005Article
- Identification and characterization of high affinity antisense PNAs for the human unr (upstream of N-ras) mRNA which is uniquely overexpressed in MCF-7 breast cancer cells.Nucleic acids research · 2005Article
- A genomic selection strategy to identify accessible and dimerization blocking targets in the 5'-UTR of HIV-1 RNA.Nucleic acids research · 2004Article
- mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides.Nucleic acids research · 2003Article
- Elucidation and characterization of oligonucleotide-accessible sites on HIV-2 leader region RNA.Antisense & nucleic acid drug development · 2003Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A rapid and simple method for determining accessible sites in RNA that is independent of the length of target RNA and does not require RNA labeling is described. In this method, target RNA is allowed to hybridize with sequence-randomized libraries of DNA oligonucleotides linked to a common tag sequence at their 5'-end. Annealed oligonucleotides are extended with reverse transcriptase and the extended products are then amplified by using PCR with a primer corresponding to the tag sequence and a second primer specific to the target RNA sequence. We used the combination of both the lengths of the RT-PCR products and the location of the binding site of the RNA-specific primer to determine which regions of the RNA molecules were RNA extendible sites, that is, sites available for oligonucleotide binding and extension. We then employed this reverse transcription with the random oligonucleotide libraries (RT-ROL) method to determine the accessible sites on four mRNA targets, human activated ras (ha-ras), human intercellular adhesion molecule-1 (ICAM-1), rabbit beta-globin, and human interferon-gamma (IFN-gamma). Our results were concordant with those of other researchers who had used RNase H cleavage or hybridization with arrays of oligonucleotides to identify accessible sites on some of these targets. Further, we found good correlation between sites when we compared the location of extendible sites identified by RT-ROL with hybridization sites of effective antisense oligonucleotides on ICAM-1 mRNA in antisense inhibition studies. Finally, we discuss the relationship between RNA extendible sites and RNA accessibility.
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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.