Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays: Next Generation Double‐, and Four‐Stranded DNA and RNA Microarrays

Abstract

Many different types of nucleic acids, with unique structures, play important roles in prokaryotic and eukaryotic regulation of an organisms genome, e.g., canonical double‐stranded (ds‐) right‐handed B‐DNA, alternative left‐handed ds‐Z‐DNA, triplex DNA, G4‐quadruplex DNA, i‐motif DNA, slipped‐strand DNA and cruciform DNA. These canonical and exotic (e.g., Z‐DNA, and four‐stranded G4‐quadruplex DNA) nucleic acid structures also regulate many different pathological conditions. The application of exotic nucleic acids, based on its structure, has not been applied to commercial, conventional DNA microarrays. Conventional DNA microarrays are powerful tools that allow for gene expression studies, however, they have severe limitations. The basic principle behind conventional DNA microarrays is that complementary sequences of DNA molecules will bind to each other. Commercial DNA microarrays measure the relative abundance of mRNA sequences isolated from cells by taking advantage of complementary DNA base pairing. Researchers employ DNA microarrays to quantify the different levels of gene expression involving very large numbers of genes simultaneously, or to genotype numerous areas of an organisms genomic makeup. DNA microarrays needs to evolve beyond these limitations. The novel, next generation DNA and RNA microarrays, i.e., Canonical, and Multistranded, Alternative and Transitional Helical (C‐MATH) Nucleic Acid Microarrays, allow for a completely different approach to studying gene expression [e.g., genes (B‐DNA, Z‐DNA) and telomers (G4‐quadruplex DNA)], based on the different structure of ds‐DNA and RNA, and multi‐stranded DNA and RNA molecules. It also allows for the characterization of different drugs and biologics that can directly bind to nucleic acids and inhibit gene expression (or enhance it). C‐MATH DNA microarrays can enhance the “drug discovery” part of “drug discovery and development”, resulting in new drugs, new uses for old drugs and lower coast for drug‐based research. Recent advances in the novel C‐MATH nucleic acid microarrays allow for more precise quantification of multiple fluorescent signals coming from a single immobilized DNA molecule (fluorescently labelled), i.e., B‐DNA, Z‐DNA and G4‐quadruplex DNA. Fluorescent and colorimetric DNA microarrays scanners were employed. The C‐MATH microarrays allow for superior analysis of colocalization, and permits competitive binding assays involving two or more fluorescently labelled drugs or biologicals binding to a gene sequence. Positive and negative controls involve direct binding by DNA‐binding chemicals and anti‐DNA antibodies. Conventional image analysis software was used, along with the development of novel algorithms to differentiate multiple fluorescence signals and intensity. The C‐MATH DNA and RNA microarrays will allow for development of new classes of DNA and RNA structure‐based drugs, and biologics (e.g., antibody, transcription factors), i.e., sequence‐specific and non‐sequence‐specific DNA and RNA binding therapeutics. Additionally, it will also allow for characterization of nucleic acids under different environmental conditions similar to a cell.