Date of Award

Spring 5-10-2013

Degree Type


Degree Name

Doctor of Philosophy (PhD)



First Advisor

Zhen Huang

Second Advisor

Markus Germann

Third Advisor

Gangli Wang

Fourth Advisor

Gabor Patonay


Development of a simple, specific, sensitive and rapid RNA microchip for detection of Head and Neck Cancer (HNC) mRNA, pathogenic bacteria and dengue virus (DENV) RNA is reported. By use of nucleases and polymerases specific RNAs are selectively labeled and detected without separation, reverse transcription and or polymerase chain reaction. This is accomplished by designing specific Hybrid probes consisting of DNA-2’-O-Me-RNA-DNA regions to target the RNA of interest. Upon hybridization with the target RNA, RNase H digestion is used to remove the 3’- RNA sequences which exposes the template for Klenow extension with reporter molecules such as hapten or fluorophore labels. This novel RNA microchip is fast (ca. 1 h detection time), selective as individual RNAs are detected in a synthetic mixture and total RNA mixtures, specific for single nucleotide polymorphisms (SNPs) discrimination and sensitive up to attomole level for chemiluminescence detection and lower femtomole for gold nanoparticles (AuNPs) and silver staining method. Using chemiluminescence, HNC biomarkers, VCAM1 and IL8 are specifically labeled and detected in the presence of thousands of other mRNAs in cancer cell lines and human colon cancer total RNA without interference. Furthermore, the method is highly specific as shown with DENV SNPs discrimination.

Moreover, we report rapid (ca 1hour), selective, specific multi-marker detection of pathogenic mRNAs and HNC mRNAs using AuNPs-silver staining on the RNA microchip. Streptavidin gold nanoparticles technology has a potential in the analysis of specific mRNAs in a wide array of field including infectious diseases diagnosis, viral infections, food safety, gene expression profiling and cancer detection. A simple and rapid NaOH RNA extraction procedure was developed for E. coli total RNA extraction with specific results on the RNA microchip using both chemiluminescence and AuNPs silver staining. This extraction avoids the use of commercial RNA purification kits thus reducing the cost. Furthermore, visual detection on the RNA microchip is simple, does not require electricity or special equipment, and therefore is a good candidate for field diagnostics with minimum resources.