Google Sign in options
Remember me
This is not recommended for shared computers

Sign in anonymously
Don't add me to the active users list

Privacy Policy
Sign In
Create Account

Javascript Disabled Detected

You currently have javascript disabled. Several functions may not work. Please re-enable javascript to access full functionality.

Search Articles

Recent Articles

DNA migrate differently in agarose vs PAGE gel

Aug 15 2011 08:59 PM | pcrman in Electrophoresis

Quote

i am currently working a gene in leukemia. The mutant allele has been sequenced to contain 527 base pair. when i run an agarose gel to confirm, it did appear in the position approximately equal to 527 base pair according to the DNA ladder. HOWEVER, when i run a PAGE, it shows up at a different poistion!!(it is at about 600 base pair in PAGE!!!!). Yet the conditions were the same when i run the PAGE and agarose gel (150v, 30 mins)

Many things can affect DNA migration in gel. Check this page "Top 10 Fun Facts for DNA Electrophoresis" to see if there is anything that might have caused the abnormal migration. For example "On a polyacrylamide gel, DNA fragments having AT-rich regions migrate slower than other DNA fragments of the same size."

According to Fermentas troubleshooting, here is a list of things that may affect migration of DNA in gel:

Atypical migration due to different DNA sequence or structure. During high resolution electrophoresis DNA fragments of equal size can migrate differently due to differences
in DNA sequences. AT rich DNA may migrate slower than an equivalent size GC rich DNA fragment. DNA structures such as nicked, supercoiled or dimeric molecules will always show different mobility on gels compared to an equivalent DNA size standard.

Gel shift effect. The presence of DNA binding proteins in the sample, such as ligases, phosphatases or restriction enzymes may alter DNA migration in the gel or cause the DNA to remain in the gel wells. High salt concentration in the sample may also cause gel shift effects.