PCR wrong size bands?

ccarter25 · #1 (**permalink**) 12-21-2006, 09:29 PM

Hey guys, I'm doing chIP. A lab mate of mine had the particular primers I'm using made about 1.5 years ago. I used them 1 year ago and got the correct size product of 250bp. I'm repeating the same chip with a different antibody and I'm getting a 150bp product in the IP'd and input samples every single time. I've varied the polymerase from PFU to Taq and I've changed temperatures. My question is, could the primers be degraded. Has anyone experienced this phenomenon of constantly getting the same wrong sized band due to that? The sizes for my controls and the primers I created are all correct.

Thanks!

molecule2005 · #2 (**permalink**) 12-25-2006, 12:43 PM

Hey there,

the primers probably are not the problem. Try making new primer batch from the stock although I don't think that would help.

Maybe you are using a different cycling program for PCR than him? Are you using different buffers or salts than him?

Also maybe your DNA is degraded?

Just some ideas! cheers

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