Mr.Vamsi Krishna technically the porosity of the agarose gel is higher than the SDS PAGE. Proteins are smaller molecules compare with nucleic acids. This is the reason why we choose small porosity (acrylamide crosslinkage) for proteins and large porosity (agarose crosslinkage) for DNA or RNA.

Probably you can try SDS PAGE for nucleic acids if it's molecular weight is less than 500 Kda. and the gel percent should be 6 to 8%.

Despite the denaturation method and staining methods are different for both the techniques.

The function of SDS to denature the protein and to give negative charge to it, DNA carry negative charge with phosphate group in both 6.8 and 8.8 pH.

There will be no disulfide bonds to break in DNA so no need of mercapto ethanol.

The running buffe contains glycine pI 5.9 to create two different charge atmosphears it has 6.8 and 8.8 layers in SDS PAGE and its pH 8.3.

In agarose gel Tirs Hcl provide pH 8.5 and buffering condetion.

You need to stain the nuclic acids with ethedium bromide even if you run in SDS PAGE.

good luck

Mr.Vamsi Krishna technically the porosity of the agarose gel is higher than the SDS PAGE. Proteins are smaller molecules compare with nucleic acids. This is the reason why we choose small porosity (acrylamide crosslinkage) for proteins and large porosity (agarose crosslinkage) for DNA or RNA.

Probably you can try SDS PAGE for nucleic acids if it's molecular weight is less than 500 Kda. and the gel percent should be 6 to 8%.

Despite the denaturation method and staining methods are different for both the techniques.

The function of SDS to denature the protein and to give negative charge to it, DNA carry negative charge with phosphate group in both 6.8 and 8.8 pH.

There will be no disulfide bonds to break in DNA so no need of mercapto ethanol.

The running buffe contains glycine pI 5.9 to create two different charge atmosphears it has 6.8 and 8.8 layers in SDS PAGE and its pH 8.3.

In agarose gel Tirs Hcl provide pH 8.5 and buffering condetion.

You need to stain the nuclic acids with ethedium bromide even if you run in SDS PAGE.

good luck

Hi there

yes you can run acrylamide gels to resolve DNA and the advantage is that you get much better resolution than agarose gels; In fact down to single base pair resolution: See the first link for example in terms of commercial sources of such gels which will provide you with some background info 

Be mindful of the fact however that the range of sizes accommodated by agarose gels is much greater than acrylamide gels: If your looking to separate fragments with high sizing accuracy below 1kb then acrylamide gels are fine. Much above that however you could encounter problems: See the second link for guidance on this point

Finally, SDS is used to resolve proteins on acrylamide gels because the SDS provides a charge that effectively ensures that all molecules are separated by sixe alone and not size to charge ratio. This does not apply to DNA/RNA separated by PAGE: In this instance you use TBE buffer and addition of a denaturant like urea to destroy secondary structure and thus ensure that that the DNA/RNA is separated by size alone and not complicated by secondary structure/alternative conformers which would complicate size based separartion

http://www.lifetechnologies.com/order/catalog/en/US/adirect/lt?cmd=catDisplayStyle&catKey=80501&ViewAllCatalog=80501&filterDispName=View%20All&filterType=0&OP=filter&filter=101/75001/80401/80501&_bcs_=H4sIAAAAAAAAAMWSXU%2BDMBSGfw03NlsKOIaXbLjFqLiIemtqOYwmhZK228K%2F9xSC82smXhiT5ny1%0APX2fk058j8YbrYodt4Z4QURy0HvBwfxQr6xtvTDxghWuw%2BEwlaIEC7xqlFRbAWbKVY1bO4MGGjSV%0AqgGd0gXoaWVriV28IHSLxlbvwOV0TtH51MeT8xml%2Fhmma5DYZUlWmnErVMOcIbnVou3rKI3VqGZB%0AbqF%2B0az5hcIwiemoCj1nluHuqPkxR8MKoYFbjKT1whWvCy9Mr57WGR5OhWkl65bMwlbpDpVg8Ro6%0APNHLf89YMmm%2Bh0Qf0%2FMBdqNhsmTGkjRD7VGpmZGIdp8lpJ%2FD%2F4P1Uk%2BAuXppn%2F15D1VicHExcCVc%0Ad5LVogDHQS4lvqxVWykNRvw91hEpt53Ejxi5dIjDNBfNVsIN7EGeJg6iuw0mpZDWvR0NgWuTsdp1%0AOSJ6wQIh0X7GHG89dK274b8VXONxbrOPk%2Fsy51cXA4cZsQMAAA%3D%3D

https://www.idtdna.com/pages/decoded/decoded-articles/pipet-tips/decoded/2011/06/17/running-agarose-and-polyacrylamide-gels