Time Nick Message 00:04 xp_prg anyone know a way to tell if primer3 primers have hairpins in them? 00:05 rbuels hmmmmm 00:05 rbuels don't think hairpins in primer pairs are usually a problem, because of the temps they run PCRs at 00:06 xp_prg so you don't know a way to do it? 00:06 rbuels but having never actually done any wet lab work myself, i'm probably full of it 00:06 rbuels xp_prg: didn't say that. 00:06 rbuels lol 00:06 rbuels probably if you aligned the primer against a reverse complement of itself? 00:06 rbuels and looked for strong matches? 00:07 rbuels you could use BLAST (apt-get install blastall), probably 00:08 xp_prg ok cool 00:08 rbuels to get a reverse complement you can use the revcom() method on a Bio::Seq 00:08 xp_prg I don't understand how having a reverse compliment helps me with this problem 00:08 rbuels oh wait...not the reverse compliment 00:08 rbuels just the reverse 00:09 xp_prg don't understand how the reverse helps either 00:09 rbuels xp_prg: well a hairpin can form when a molecule sticks to itself right? 00:10 rbuels so...... 00:10 rbuels wait it's not the reverse either.. 00:10 * rbuels thinks a little more 00:11 xp_prg no a hairpin is usually a cell receptor and has hydrophobic molecules and is shaped like a hairpin 00:11 xp_prg if a primer is a hairpin it will disrupt the transcription of the protein 00:12 rbuels never heard of that kind of hairpin 00:12 rbuels well...actually yeah that makes sense.... 00:12 rbuels the hairpin conformation would screw up transcription 00:13 rbuels but the hairpin forms because of certain properties that primer's nucleotides have in relation to eachother, right? 00:13 xp_prg don't know what else to tell you that I have told you 00:14 rbuels yeah.....so to detect possible hairpin conformations you would find where one part of the primer would be the reverse complement of itself... 00:15 rbuels i think. 00:16 xp_prg its an actual melecular strucure 00:16 xp_prg with hydrophobic probperties, dong what you said doesn't address that in any way I think 00:17 rbuels this is what you're talking about right? http://en.wikipedia.org/wiki/Stem-loop 00:18 rbuels cause that's what i was talking about 00:19 xp_prg http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html 00:19 xp_prg it talks about it here 00:21 rbuels yeah those are the same thing. intramolecular interaction of the primer with itself forming stem loops. 00:22 rbuels i don't know how to measure the delta-G of a given loop though 00:22 xp_prg oh cool, forgive me, I am not as versed as you :> 00:23 rbuels i would think that primer design programs would take all this stuff into account...... 00:23 rbuels but i don't really know, since i've never done any primer design 00:24 rbuels yeah....looks like primer3 does anyway 00:27 rbuels xp_prg: if you're running a debian-based system, apt-get install primer3 00:27 rbuels zless /usr/share/doc/primer3/README.txt.gz 00:27 rbuels search for string PRIMER_SELF_ANY 00:28 rbuels that's the primer3 input arg that tweaks some of the checking it does for this kind of thing 00:33 xp_prg thanks rbuels 00:34 rbuels xp_prg: no prob. as you can tell, primer design is not by forte ;-) 00:34 rbuels s/by/my/ 00:34 xp_prg well always good to learn new things :> 00:34 xp_prg I am still confused what a primer does :> 00:36 rbuels http://upload.wikimedia.org/wikipedia/commons/8/87/PCR.svg 00:36 rbuels in the diagram, the primers are the red lines 00:37 rbuels little piece of dna that sticks to the other pieces, and provides a start for polymerase to build more dna 00:41 xp_prg hmm... interesting 14:35 deafferret ooo! ooo! I know about primers! :D