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Whole-body scanning PCR; a highly sensitive method to study the biodistribution of mRNAs, noncoding RNAs and therapeutic oligonucleotides.

Nucleic acids research (2013-06-15)
Julien A Boos, David W Kirk, Mari-Luz Piccolotto, Werner Zuercher, Sandro Gfeller, Philippe Neuner, Andre Dattler, William L Wishart, Fabian Von Arx, Michael Beverly, Jesper Christensen, Karine Litherland, Esther van de Kerkhof, Pieter J Swart, Thomas Faller, Armin Beyerbach, David Morrissey, Juerg Hunziker, Iwan Beuvink
ABSTRACT

Efficient tissue-specific delivery is a crucial factor in the successful development of therapeutic oligonucleotides. Screening for novel delivery methods with unique tissue-homing properties requires a rapid, sensitive, flexible and unbiased technique able to visualize the in vivo biodistribution of these oligonucleotides. Here, we present whole body scanning PCR, a platform that relies on the local extraction of tissues from a mouse whole body section followed by the conversion of target-specific qPCR signals into an image. This platform was designed to be compatible with a novel RT-qPCR assay for the detection of siRNAs and with an assay suitable for the detection of heavily chemically modified oligonucleotides, which we termed Chemical-Ligation qPCR (CL-qPCR). In addition to this, the platform can also be used to investigate the global expression of endogenous mRNAs and non-coding RNAs. Incorporation of other detection systems, such as aptamers, could even further expand the use of this technology.

MATERIALS
Product Number
Brand
Product Description

Sigma-Aldrich
Iodine, ACS reagent, ≥99.8%, solid
Sigma-Aldrich
Iodine, ReagentPlus®, 99.7% trace metals basis, beads, 1-3 mm
Sigma-Aldrich
Dichloromethane, anhydrous, ≥99.8%, contains 40-150 ppm amylene as stabilizer