Facilitating RNA structure prediction with microarrays.

Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner; Irina E Catrina

doi:10.1021/bi051409+

Home/Archive/PubMed

PubMed · 16401087

Facilitating RNA structure prediction with microarrays.

Elzbieta Kierzek·Ryszard Kierzek·Douglas H Turner·Irina E Catrina

View original source ↗Export metadata ↓

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.

Explore related subjects

Base Pairing Base Sequence Binding Sites Computational Biology Escherichia coli Methylation Molecular Sequence Data Nucleic Acid Conformation Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis RNA Probes RNA, Ribosomal, 5S Ribonuclease H Thermodynamics Thiouridine Comparative Study Journal Article Research Support, N.I.H., Extramural

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Elzbieta Kierzek, Ryszard Kierzek, Douglas H Turner, Irina E Catrina. 2006-01-17. Facilitating RNA structure prediction with microarrays.. https://doi.org/10.1021/bi051409%2B

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2013

Application of mutated miR-206 target sites enables skeletal muscle-specific silencing of transgene expression of cardiotropic AAV9 vectors.

Insertion of completely complementary microRNA (miR) target sites (miRTS) into a transgene has been shown to be a valuable approach to specifically repress transgene expression in non-targeted tissues. miR-122TS have been successfully used to silence transgene expression in the liver following systemic application of cardiotropic adeno-associated virus (AAV) 9 vectors. For miR-206-mediated skeletal muscle-specific silencing of miR-206TS-bearing AAV9 vectors, however, we found this approach failed due to the expression of another member (miR-1) of the same miR family in heart tissue, the intended target. We introduced single-nucleotide substitutions into the miR-206TS and searched for those which prevented miR-1-mediated cardiac repression. Several mutated miR-206TS (m206TS), in particular m206TS-3G, were resistant to miR-1, but remained fully sensitive to miR-206. All these variants had mismatches in the seed region of the miR/m206TS duplex in common. Furthermore, we found that some m206TS, containing mismatches within the seed region or within the 3' portion of the miR-206, even enhanced the miR-206- mediated transgene repression. In vivo expression of m206TS-3G- and miR-122TS-containing transgene of systemically applied AAV9 vectors was strongly repressed in both skeletal muscle and the liver but remained high in the heart. Thus, site-directed mutagenesis of miRTS provides a new strategy to differentiate transgene de-targeting of related miRs.

Base Pairing↗

PubMed2007

15N-15N J-coupling across Hg(II): direct observation of Hg(II)-mediated T-T base pairs in a DNA duplex.

Explore the source record for details and available documents.

Base Pairing↗

PubMed2007

Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory.

The incomplete cancellation of the electron self-interaction can be a serious shortcoming of density-functional theory especially when treating odd-electron systems. In this work, several popular and potentially viable correction schemes are applied in order to characterize the electronic structure of stacked molecular pairs, consisting of a neutral molecule and adjacent radical cation, as a function of separation distance. The unphysical sharing of the positive charge between adjacent molecules separated by 6-7 A is corrected for by applying a new empirical scheme proposed by VandeVondele and Sprik [Phys. Chem. Chem. Phys. 2005, 7, 1363] with a unique choice of parameters. This method is subsequently applied to characterize the electronic structure of two neighboring guanines excised from a canonical Arnott B-DNA structure and will be used in future investigations of certain model DNA fibers.

Base Pairing↗