Quantification of plasma HIV RNA using chemically engineered peptide nucleic acids

Chao Zhao, Travis Hoppe, Mohan Kumar Haleyur Giri Setty, Danielle Murray, Tae-Wook Chun, Indira Hewlett and Daniel H. Appella ()
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Chao Zhao: Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Travis Hoppe: Laboratory of Biochemistry and Genetics, NIDDK, NIH, DHHS, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Mohan Kumar Haleyur Giri Setty: Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, FDA, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Danielle Murray: Laboratory of Immunoregulation, NIAID, NIH, DHHS, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Tae-Wook Chun: Laboratory of Immunoregulation, NIAID, NIH, DHHS, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Indira Hewlett: Laboratory of Molecular Virology, Center for Biologics Evaluation and Research, FDA, 9000 Rockville Pike, Bethesda, Maryland 20892, USA
Daniel H. Appella: Laboratory of Bioorganic Chemistry, NIDDK, NIH, DHHS, 9000 Rockville Pike, Bethesda, Maryland 20892, USA

Nature Communications, 2014, vol. 5, issue 1, 1-9

Abstract: Abstract The remarkable stability of peptide nucleic acids (PNAs) towards enzymatic degradation makes this class of molecules ideal to develop as part of a diagnostic device. Here we report the development of chemically engineered PNAs for the quantitative detection of HIV RNA at clinically relevant levels that are competitive with current PCR-based assays. Using a sandwich hybridization approach, chemical groups were systematically introduced into a surface PNA probe and a reporter PNA probe to achieve quantitative detection for HIV RNA as low as 20 copies per millilitre of plasma. For the surface PNA probe, four cyclopentane groups were incorporated to promote stronger binding to the target HIV RNA compared with PNA without the cyclopentanes. For the reporter PNA probe, 25 biotin groups were attached to promote strong signal amplification after binding to the target HIV RNA. These general approaches to engineer PNA probes may be used to detect other RNA target sequences.

Date: 2014
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DOI: 10.1038/ncomms6079

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