STR Sites

STR Sites

FGA:

• This site is a tetranucleotide repeat CTTT

• Lies on chromosome #4 Intron #3

When strand dissociates then there will be no self-annealing.

CTTT sequence does not have complementary nucleotides. Thus, the double-stranded structure will not form. Therefore, it is not a strong STR site as there is not polymorphism.

A good STR site is that which has more polymorphism.

• 3rd intron of human * fibrinogen.

• It is flanked by degenerate primers, primers have to be designed from a distance to flanking regions because they are not stable & primers may not bind i.e no product formation. This also means that it ill has a large product size.

Small product size is required because work has to be done with degraded DNA. There may be such a sample that is very old so fragments will be small so the chance of having full STR will be difficult.

The more the sample is old the more will be the degraded DNA.

• These repeats can be 12.2 and up to 51.2 (micro variants).

• There can be a deletion of 2 nucleotides i.e CT.

If there is some replication slippage with a good copy number then there will be some utility. If there are some repeats present then strand binds.

 CT

 T  T

  T    T

_____C     l_____

There are 80 alleles reported & more polymorphism. It means it has more variety in population because of which it is being used in CODIS.

TH01:

• Tetranucleotide repeats TCAT.

• Lies in intron 1 of the tyrosine hydroxylase gene.

• Value in Caucasians is 9.3

The more the polymorphism in a state the more is its utility. Example:
D18S51 is more polymorphic as compared to TPOX.

It means there is more variation in D18S51 hence it is more useful from a forensic point of view. More polymorphic sites have more chances of occurrence of micro variants. D18S51 has more chances.

• TPOX has less.

In micro variants

Null Allele (Allele Dropout)

Mutations occur within the repeat, flanking region & primer binding site. More important mutations are those occurring in primer binding sites as o primer will bind. If a mutation is at 3’ end then there will be no product formation.

Product formation depends on the annealing of the primer. If decreased then there will be product formation.

The following solutions can be implemented to avoid null alleles.

1. The more the mutations the weak will be the binding so to promote binding annealing temperature can be decreased.

2. By changing/redesigning the primers.

Make primers against those regions which are not changing frequently but it cannot be ensured that change will not come.

3. Drop the site.

4. Add degenerate primes → mix preparation of primers with the difference of 1-2 nucleotides.

Either amount of degenerate primers should be used more as the product will come less in such a case or the second option is to change/drop the STR site.

Editor's Recommendation:

• Analysing Metabolic Pathways
• Protein Threading Sequence
• Ab Initio Protein Structure Prediction
• Homology Modeling
• Hot Start PCR, Multiplex PCR, Avoiding Contamination In PCR, Advantages, and Disadvantages in PCR
• DNA Damage
• Docking | Protein-Protein Docking | Protein-Ligand Docking 
• Functional Regulation | Genetic Aspect | Indirect Aspects 
• Database Development 
• Functional Analysis At Structure Level
• PTMs and Functional Regulations
• Modeling Cellular Processes
• PCR Reagents | Stochastic Effect | STR Classification
• DNA Degradation
• DNA Quantification | Human DNA Quantification Method | Advantages  
• Desirable Characteristics of STR used in Forensic DNA typing
• DNA Ladders
• Metabolic Pathways
• Non-Human DNA
• Mitochondrial DNA 
• Integrated Genomic Circuits 
• Shutter Product Formation 
• Mini STR Sites 
• Real-Time PCR
• Molecular Diagnosis of Genetic Diseases
• Immuno Quantitative Assay