Structural analysis of hepatitis C RNA genome using DNA microarrays

Nucleic Acids Research
María MartellJordi Gomez

Abstract

Many studies have tried to identify specific nucleotide sequences in the quasispecies of hepatitis C virus (HCV) that determine resistance or sensitivity to interferon (IFN) therapy, unfortunately without conclusive results. Although viral proteins represent the most evident phenotype of the virus, genomic RNA sequences determine secondary and tertiary structures which are also part of the viral phenotype and can be involved in important biological roles. In this work, a method of RNA structure analysis has been developed based on the hybridization of labelled HCV transcripts to microarrays of complementary DNA oligonucleotides. Hybridizations were carried out at non-denaturing conditions, using appropriate temperature and buffer composition to allow binding to the immobilized probes of the RNA transcript without disturbing its secondary/tertiary structural motifs. Oligonucleotides printed onto the microarray covered the entire 5' non-coding region (5'NCR), the first three-quarters of the core region, the E2-NS2 junction and the first 400 nt of the NS3 region. We document the use of this methodology to analyse the structural degree of a large region of HCV genomic RNA in two genotypes associated with different responses to IFN ...Continue Reading

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Citations

Oct 16, 2012·Nucleic Acids Research·Cristina Romero-LópezAlfredo Berzal-Herranz
Sep 21, 2013·Nucleic Acids Research·Cristina Romero-LópezAlfredo Berzal-Herranz
Jul 11, 2007·BMC Evolutionary Biology·Michael StichSusanna C Manrubia
Sep 28, 2010·Journal of Medical Virology·Mónica Viviana Alvarado MoraJoão Renato Rebello Pinho
Nov 9, 2010·Virology·Noemí FernándezEncarnación Martínez-Salas
Aug 30, 2007·Journal of the American Chemical Society·Dorota I RozkiewiczDavid N Reinhoudt

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