Sensing of SNP in HIV-1 Genome Using Fluorescent Oligonucleotide Probes

Single nucleotide polymorphisms (SNPs) are gaining increasing attention in modern diagnostics and research, serving as markers on genetic predispositions, clinically evident disorders and diverse drug responses. Genome of human immunodeficiency virus (HIV-1) contains multiple SNPs due to mistakes of reverse transcriptase converting RNA genome of HIV-1 into cDNA. Some of these SNPs cause resistance to drugs applied for the treatment of HIV/AIDS. Generally, current assays for SNP diagnostics, including HIV-1, can be divided into two broad categories: 1) sophisticated, high-throughput laboratory machines, and 2) easy-to-use, portable devices. Present sophisticated SNP diagnostics of HIV-1 primarily use enzymatic reactions in different formats including sequencing, polymerase-chain reaction (PCR) and microarrays. In doing this, the enzymes help to address the required sensitivity and specificity of the detection. On the other hand, an ideal portable method for the detection of SNP would work by allowing a simple mixing of a cDNA or RNA target with a probe and obtaining a single right away without applying an enzyme or state-ofthe- art equipment. Remarkable progress has been achieved in recent years within both categories of methods. To date, most enzymatic and enzyme-free diagnostic strategies apply fluorescently labeled oligonucleotides - rationally designed probes or primers containing a dye(s) of choice in the desired position(s) of a nucleotide chain. In this chapter, current SNP sensing approaches in HIV-1 cDNA and RNA are described with a main focus on recently developed fluorescent oligonucleotide probes. The chapter includes up-to-date review of sophisticated and portable biosensors for HIV diagnostics, and several exciting emerging technologies are highlighted.

Keywords: Diagnostics, enzyme-free assays, fluorescence, genotyping, HIV-1, imaging, nanoparticles, oligonucleotide probe, PCR, SNP.