Are there any points to be taken into account for primers used in aptamer designing. Can we use any arbitrary primer for this?
The aptamer amplifying PCR primers are complementary to the primer binding sequences flanking the random sequence of aptamer. So these are designed and synthesized based on the sequence of primer binding sequences of aptamer. All aptamers in a library have same set of primer binding sequences at the 3'and 5'end of aptamer.
@Shripal. I do know that the primers are complementary to the primer binding sequences but while designing the library can we take any primer binding sequence?
Yeah! it may be arbitrary but we have to keep some thing in mind. Like if we want the transcription of the aptamer, then we use T7 promoter sequence as primer binding sequences. We should also keep in mind that is should be as much shorter to avoid non-specific binding. So based on our purpose we decide the primer sequence....we can also put restriction sites or any tagging sequence in primer binding sequence...
@ Simon. Thanx for the help,even I was thinking of going for a published sequence to avoid any problems.
@ Shripal. Thanx for your advice. Since I will be opting for ssDNA aptamers so will not require the other modifications but yes for separation purposes I'll be using tagged primers.
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