Question

1. What is the difference between an STR and a SNP?

2. Describe what an allele is, with respect to STRs.

3.Describe the simplest strategy you could use to clone the insert into the vector if you do not care about which direction it inserts.

4.Describe a second strategy that would ensure that the insert was in the proper direction.

Answer 1

1.Difference between SNP and STR:

SNP: Single nucleotide polymorphism (SNP) is a substitution of single nucleotide that occurs at a specific position in the genome. The frequency with which SNPs occur is very less , about 1% in whole population. Lets look at this with an example. Say there is position in genome where nucleotide C appears in most of the individuals but due to mutations few individuals have A in the same site of the genome.This means there is a SNP in that position with two possible variation A and C which are called alleles for that position.

ATGCCCTAC

ATGCACTAC Point mutation/ SNP at position where C was originally present but A is present in minor people with the mutation

STR: Short tandem repeats in DNA occurs when a pattern of 2 or more nucleotides are repeated and these repeated sequences are present adjacent to each other. These STRs generally occur in non coding regions but when in regulatory or coding region would effect the phenotype of the indivual. They are generally used in DNA profiling, forensic studies and population genetics studies. The polymorphism in STRs is due to presence of different number of repeats of the pattern/DNA sequence.

GATAGATAGATAGATA say the sequence GATA is repeated in the STR. So the number of times the GATA repeat appears may change causing the STR polymorphism.

The mutation rate is different from that of SNP based on the repeats that are present in STR.

2.Alleles w.r.t STR:

Generally alleles in genome are the variations that are present in a location due to mutation or other effects. Though genome is identical across the length for most of the individuals there are locations of variations which can be at any place like in the coding region, regulatory region or non coding regions. Each of them have their effect on the phenotype of the individual based on the region and severity of the variation.

STR contains repeats of DNA sequence units(3-4) and mostly found in the non coding regions. Number of repeats within STR is referred to as allele.

Say a particular STR has repeats from 5-16 then we say there are 12 allele for that particular STR. So different repeat units number refer to different allel in regard to STR.

3. the simplest strategy you could use to clone the insert into the vector if you do not care about which direction the insert is in:

PCR cloning:

Amplification of the site of interest using PCR (Taq DNA polymerase)

Then clone the obtained is inserted into the vector( digestion of vector to form linear and with complementary ends and insertions using ligation).

Here the changes of getting a single direction orientation are 50:50.