ArticleNucleic acids research1997
A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structures.
Article in Nucleic acids research, 1997. 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, 82 citations in OpenAlex.
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- "Bind, cleave and leave": multiple turnover catalysis of RNA cleavage by bulge-loop inducing supramolecular conjugates.Nucleic acids research · 2022Article
- siRNAs target sites selection of ezrin and the influence of RNA interference on ezrin expression and biological characters of osteosarcoma cells.Molecular and cellular biochemistry · 2012Article
- Ezrin mRNA target site selection for DNAzymes using secondary structure and hybridization thermodynamics.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2011Article
- Variables and strategies in development of therapeutic post-transcriptional gene silencing agents.Journal of ophthalmology · 2011Article
- Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides.Nucleic acids research · 2009Article
- Selection of antisense oligonucleotides based on multiple predicted target mRNA structures.BMC bioinformatics · 2006Article
- Complete, gene-specific siRNA libraries: production and expression in mammalian cells.RNA (New York, N.Y.) · 2005Article
- Probing alternative foldings of the HIV-1 leader RNA by antisense oligonucleotide scanning arrays.Nucleic acids research · 2004Article
- Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry.Nucleic acids research · 2003Article
- mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotides.Nucleic acids research · 2003Article
- Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNA.Biophysical journal · 2002Article
- Utilization of tmRNA sequences for bacterial identification.BMC microbiology · 2001Article
- Determination of optimal sites of antisense oligonucleotide cleavage within TNFalpha mRNA.Nucleic acids research · 2001Article
- 5'-bis-pyrenylated oligonucleotides displaying excimer fluorescence provide sensitive probes of RNA sequence and structure.Nucleic acids research · 2001Article
- Transfer RNA(Ala) recognizes transfer-messenger RNA with specificity; a functional complex prior to entering the ribosome?The EMBO journal · 2001Article
- Identifying ribozyme-accessible sites using NUH triplet-targeting gapmers.Nucleic acids research · 2001Article
- Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond.Nucleic acids research · 2001Article
- Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.RNA (New York, N.Y.) · 2001Article
- Secondary structure prediction and in vitro accessibility of mRNA as tools in the selection of target sites for ribozymes.Nucleic acids research · 2000Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
A technique is described to identify the rare sequences within an RNA molecule that are available for efficient interaction with complementary DNA probes: the target RNA is digested by RNase H in the presence of a random pool of complementary DNA fragments generated from the same DNA preparation that was used for target RNA synthesis. The DNA region was amplified by PCR, partially digested with DNase and denatured prior to RNA binding. In the presence of single-stranded DNA fragments the RNA was digested with RNase H such that, on average, each molecule was cut once. Cleavage sites were detected by gel electrophoresis either directly with end-labeled RNA or by primer extension. The pattern of accessible sites on c- raf mRNA was determined and compared with the known profile of activity of oligonucleotides found in cells, showing the merit of the method for predicting oligonucleotides which are efficient for in vivo antisense targeting. New susceptible sites in the 3'-untranslated region of c- raf mRNA were identified. Also, four RNAs were probed to ascertain to what extent structure predicts accessibility: the P4-P6 domain of the Tetrahymena group I intron, yeast tRNAAsp, Escherichia coli tmRNA and a part of rat 18S rRNA.
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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.