Single base pair changes in the DNA may or may not be responsible for a disease. Not all mutations are harmful. It is true since some changes in the DNA also prove beneficial. Adaptation, evolution, variation, and many other phenomena occur due to single base pair changes in the DNA. Hence, it is important to study both harmful and harmless mutations. A better way to describe single base pair changes involves the following way. The single base pair positions in the DNA are also known as snips or the single nucleotide polymorphisms or SNPs. The single nucleotide polymorphisms involve those types of single base pair changes which show different sequence alternatives. The least frequent allele in a normal individual shows an abundance of 1% or greater. SNPs also encompass low penetrance, quantitative trait loci, and the alleles associated with the risk. These properties also occur in a normal individual to some extent.
Sometimes, the presence of an SNP in a gene disrupts a gene function. Hence, SNPs lead to one base pair change in the DNA. The SNPs effectively serve as markers. Some references point out the comparison of the SNPs with the point mutations. They arise due to the alteration in the sequence of the DNA. It involves a single nucleotide base change, insertion or a deletion. However, the SNPs and point mutations differ only in their frequencies. Point mutations arise as a result of the occurrence of 1% or less than 1% of the variation in a population. Hence, the low-frequency mutations do not serve as good markers. The SNPs occur in the various regions in a genome. Different SNPs exist in the coding as well as the non-coding regions in a genome. The coding regions, also known as exons, code for the specific amino acids. The non-coding regions, known as the introns, do not get involved in coding and hence get spliced out before the translation occurs.
The concept of haplotyping involves grouping the subjects by haplotypes or particular patterns of the sequential SNPs found on a single chromosome. The classification of a single-base position involves three main types. If a chromosome consists of a normal allele, the given single-base position is homozygous for a wild-type base. If there is an altered allele in each chromosome under review, the given single-base position is homozygous for the SNP-base. If one chromosome has a normal allele and the other has an abnormal allele, the condition exhibits heterozygosity. Hence, SNPs serve as the disease gene markers. Every gene may alternatively show the presence of the multiple SNPs. If a coding region involves a smaller percentage of the SNPs, less sequence variation prevails there. The coding sequence codes for an amino acid conferring to a protein structure or a function. The SNPs within this region may alter the protein function, its structure or both. SNP analysis is highly advantageous. SNPs serve as efficient markers for gene mapping. They allow a systematic identification of alleles in normal and diseased individuals.
Image: SNP analysis
Detection of SNPs:
SNPs constitute the most common types of DNA polymorphisms. Most of the SNPs occur in the non-coding regions. Hence, they are known as non-coding SNPs. The coding regions also have SNPs and are also known as cSNPs or coding SNPs. SNPs occurring in the regulatory sequences are known as rSNPs. They also refer to anonymous SNPs occurring in the junk DNA. Most of the cSNPs cause missense mutations. The SNPs also affect the restriction sites. The Southern blotting or PCR techniques help in detecting the SNPs at the restriction sites. The DNA sample first gets a treatment with the restriction enzyme. The resultant fragments get separated using gel electrophoresis. After obtaining the bands of different sizes on the gel, the DNA present on the gel gets transferred to the membrane filter using a Southern blot apparatus. After hybridization with a probe, the bands get visualized using autoradiography technique. Hence, homozygotes and heterozygotes for SNP alleles get detected.
Another way to detect SNPs involves PCR amplification. The PCR technique or Polymerase Chain Reaction technique involves isolation of DNA, amplification, digestion with the restriction enzymes, and gel electrophoresis. Another technique involves allele-specific oligonucleotide hybridization (ASO). Small oligonucleotides help in detecting the single nucleotide polymorphisms. Other techniques for typing thousands of SNPs include DNA microarrays or DNA chips or Gene Chips.
DNA Microarray:
It is an ordered grid of DNA molecules with known sequences. They get fixed at a particular position on a silicon chip or a glass or membrane filter. The automated machines help in depositing the microspots in a known location. The oligonucleotide arrays have a small size similar to a postage stamp. The examples of DNA microarray include GeneChips®. There is no labeling to the DNA molecules fixed on the slide or a glass or a silicon chip. However, the target DNA involves labeling. The target DNA labeling uses fluorescent tags such as a Cy3 dye. After hybridization, laser scanning helps to detect fluorescent molecules and study the pattern across the array. Cancer genomics experiments frequently use DNA microarrays for detecting mutations. Hence, the DNA microarray helps in detecting SNP alleles in an individual. There are two types of spots observed across the array. A green spot indicates a green-labeled target DNA hybridization. A red spot indicates a red-labeled DNA hybridization. The shades of yellow spots indicate hybridization depends on the spot color.
GeneChip technology helps in assessing a large number of SNP alleles. It is easy to map the genes associated with the complex traits using DNA microarray. References:
[1]Forensic DNA Typing: Biology, Technology, and Genetics of STR Markers, John M. Butler
[2] Human Genetics and Genomics, Includes Wiley E-Text, Bruce R. Korf, Mira B. Irons
[3] SNPs, Genetics Home Reference
[4] DNA Microarray, Wikipedia
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