A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)

Mirco Castoldi; Sabine Schmidt; Vladimir Benes; Mikkel Noerholm; Andreas E. Kulozik; Matthias W. Hentze; Martina U. Muckenthaler

doi:10.1261/rna.2332406

A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA)

¹Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Germany
²Genomics Core Facility
³Gene Expression Unit
⁴Molecular Medicine Partnership Unit, EMBL, Heidelberg, Germany
⁵Research and Development, Exiqon, Vedbaek, Denmark

Abstract

MicroRNAs represent a class of short (∼22 nt), noncoding regulatory RNAs involved in development, differentiation, and metabolism. We describe a novel microarray platform for genome-wide profiling of mature miRNAs (miChip) using locked nucleic acid (LNA)-modified capture probes. The biophysical properties of LNA were exploited to design probe sets for uniform, high-affinity hybridizations yielding highly accurate signals able to discriminate between single nucleotide differences and, hence, between closely related miRNA family members. The superior detection sensitivity eliminates the need for RNA size selection and/or amplification. MiChip will greatly simplify miRNA expression profiling of biological and clinical samples.

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Footnotes

Reprint requests to: Martina U. Muckenthaler, Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Im Neuenheimer Feld 156, D-69120 Heidelberg, Germany; e-mail: martina.muckenthaler{at}med.uni-heidelberg.de; or Matthias W. Hentze, Gene Expression Unit, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany, e-mail: hentze{at}embl.de.
Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2332406.
- Received December 16, 2005.
- Accepted January 19, 2006.