For more than five years now, I have used MetaPhor agarose to help me genotype my transgenic mice. MetaPhor agarose is an intermediate melting temperature agarose (75°C) that provides one of the finest resolutions for DNA fragments from PCR or RT-PCR reactions.
Using a 2 – 4% gel (made in either TAE or TBE) it is possible to resolve fragments that are anywhere from 20 – 800 bp in length. With this agarose I have been able to differentiate a 99bp fragment from a 110 bp fragment on a 3% gel (running the gels at 120V at room temperature). Because the resolution is so good, I also use this agarose for resolving my PCR products on a routine basis.
In addition to being able to resolve DNA fragments between 20-800bp and working well for more routine PCR product analysis, it is possible to recover DNA fragments from MetaPhor agarose easily. Like any other agarose, lower percentage gels are delicate for handling, while the higher concentrations play with your patience during critical preparation time.
Besides being expensive, one might fuss about the preparation time involved, which includes, soaking the agarose in cold buffer for about 10-15 minutes before heating it in the microwave, so as to prevent it from foaming. Secondly, once the molten gel has solidified after having being poured into a cast, it should be kept at 4°C for 20 minutes before use to obtain a good resolution and for easier handling of the gel.
Overall, Metaphor is an excellent agarose and can be used in place of 2-4% polyacrylamide gels for resolving small DNA fragments. I would suggest that one should consider accepting the latency of its preparation time, rather than compromise on resolution efficiency. Once again remember, this gel not watched boils over!
Katholieke Universiteit Leuven
MetaPhor Agarose from Lonza
Can resolve small DNA fragments, works well with routine PCR products and can isolate DNA fragments from this agarose as easily as with standard agarose
There is a pre-soaking step that should be followed as well as a 20 minute 4<sup>°</sup>C incubation after the gel has solidified
The Bottom Line
Works well for resolving small differences in DNA fragments without having to resort to polyacrylamide gels