Disciplines that are now using nucleic acid measurement technologies range from basic biology to medicine to environmental science to biotechnology. Each of these will use the basic data to answer different questions. Below are some of the fundamental questions.
Questions about DNA:
Some very popular analyses include looking at genetic markers, which are readily detected genomic variants. These include single nucleotide polymorphisms (SNPs) and microsatellites. A SNP is a change in a single base in the sequence. A microsatellite is sometimes called a small repeat - a sequence of two or three or four nucleotides which repeat several times in adjacent locations. SNPs are very easy to measure and vary over time scales of thousands of years. Microsatellites are very popular for marking disease associations because they are easy to measure and the number of repeats can vary quite a bit over populations in short time periods compared to other kinds of mutations.
Genome Wide Association Studies (GWAS) involve associating these markers on a genome-wide (or at least single chromosome) scale with phenotypes or traits of interest such as disease stage, tendency to become overweight, having resistance to a pathogen, and so on.
In looking at how organisms of the same species differ, and also organisms the same evolutionary branch differ biologists may also look at genomic duplications and rearrangements. Copy number variation occurs when duplicate copies of the gene (or segment of DNA) gets added to the chromosome. Alternatively, a copy gets deleted and then the individual won't have that gene or express that protein. Studies of copy number variation are quite common when looking at cancer, which often seems to involve large numbers of chromosome defects. Duplications of genes, segments of DNA or even the entire genome are thought to be involved in evolutionary processes.
gene duplication or deletion
Another type of genomic rearrangement is an inversion. The chromosome is cut and segment of DNA is inserted backwards.
A number of molecules bind to the DNA and regulate transcription in various ways. Transcription factors are proteins that bind to promoter regions and regulate gene expression. Small RNAs may also bind to regions of the chromosome and have a role in gene regulation. Methylation involves changes in the DNA molecule but can be measured in a very similar way. Molecular markers are used to bind to the molecules of interest or the methylated sites. The DNA is fragmented. The fragments bound to the markers are retrieved and the other fragments are washed away, enriching the sample of nucleotides for the bound fragments. The binding is reversed and the markers are washed away. What remains are fragments of DNA which can be measured using microarrays or sequencing tools.
Questions about RNA:
Typically questions about RNA involve quantification, as well as identification. We discuss this more in the next section on gene expression.