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Nucleic Acids Res. 2013 Sep;41(17):e168. doi: 10.1093/nar/gkt668. Epub 2013 Aug 1.

A multidimensional platform for the purification of non-coding RNA species.

Author information

1
Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670.

Abstract

A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.

PMID:
23907385
PMCID:
PMC3783195
DOI:
10.1093/nar/gkt668
[Indexed for MEDLINE]
Free PMC Article

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