Question: Pcr Primer In Highly Repetitive Region
0
gravatar for PoGibas
7.6 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

Is there any way to design a PCR primer if region of interest is highly repetitive (tens of kilobases only SINE's & LINE's)?

pcr • 3.3k views
ADD COMMENTlink modified 7.6 years ago by deanna.church1.1k • written 7.6 years ago by PoGibas4.8k
2
gravatar for seidel
7.6 years ago by
seidel6.8k
United States
seidel6.8k wrote:

If you can find a unique sequence within the repetitive region, then you should be able to find a primer. It might help to utilize LNA nucleotides (locked nucleic acids). They are nucleotides with higher melting temperatures than regular nucleotides and thus allow one to design shorter oligos for PCR, or to have leeway in your design specs. Perhaps you can utilize ePCR to check your designs.

ADD COMMENTlink written 7.6 years ago by seidel6.8k
1
gravatar for deanna.church
7.6 years ago by
deanna.church1.1k
Bethesda, MD
deanna.church1.1k wrote:

Try using Primer BLAST: http://www.ncbi.nlm.nih.gov/tools/primer-blast/ Make sure you look at all of the options (scroll the page) as there is an option of checking primer specificity in a list of genomes of interest.

ADD COMMENTlink written 7.6 years ago by deanna.church1.1k
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