Chromosome Markers in the DNA Tests - Research Paper Example

Forensic DNA testing is currently performed by using the complex STR multiplex systems. This testing allows the testing of several loci in a single – tube PCR system. A highly variable STR is chosen for the analysis such that they should be within the detection range of 90 – 500 base pairs. These STRs should also be present in the other chromosomes too. Highly polymorphic markers and gender identifying markers are widely used in the STR multiplex systems. All these loci are labeled with different fluorescent dyes for the automated Genotyping.

The fluorescent dye is attached to the PCR primers and these dyes get incorporated into the target DNA sequence during the process of amplification.  5-FAM (blue) dye is used for the STR loci D3S1358 and NED (Yellow) dye is used for D19S433 STR loci. By using the two different fluorescent dyes, it was observed that the height and the peaks of the STR loci D3S1358 and D19S433 are similar between them. If we use the same fluorescent dye then it may lead to confusion whether the source of DNA is from a single person or from multiple persons because the peak areas are very important for the determination of the amount of DNA.

If the sample is homozygous and have only one peak with the area equal to the two individual peaks then it will be very difficult to analyze the results. This is very frequent if we use the same fluorescent dye for D3S1358 and D19S433. Since D3S1358 and D19S433 are similar to each other, the use of two different dyes will easily differentiate them. (Thompson 2006). The specific dye is incorporated into the PCR product and the level of emission of light and the intensity of light emission gives the details about the size of the DNA.

The level of emission may vary for the two STR loci but since they are of same size, the emission level will be same and it will be very difficult to identify the two STRs. The factors for choosing the Fluorescent dye are based on the dyes, optical filters, laser and matrix to which it binds. The D3S1358 is 119 bp to 147 bp in size with the average repeats of 15. These loci will accept the blue dye more readily than the yellow dye. Similarly D19S433 is 206 bp with 9 repeats. (Foster and Laurin 2012).

This also will absorb yellow dye more readily than the blue dye. The variation in the base pair is thus an important factor for the choice of fluorescent dyes. The peak heights of the two STR loci D3S1358 and D19S433 vary with the annealing temperatures. Similarly the relative intensity of the loci also varies. (Foster and Laurin 2012). First generation dyes were used for the analysis of the loci initially; later the development of the second generation dyes with more specificity replaced them.

The fluorescent dyes used for the multiplex were amandine dyes that emits the color when bind properly to the DNA fragments. The fluorescent dyes NED and 6 - FAM currently for the identification of the D19S433 and D3S1358 produces standard results for the different populations in many parts of the world. (Li et al. 2013). Thus it is concluded that D3S1358 and D19S433 STR loci cannot have same fluorescent dye because they have the similar base pair length and produce the same peak. (Butler 2005).

If the same dye is used then they will form only one peak but with