Agarose gels are best for separating larger DNA fragments and are easy to use, non-toxic, and flexible regarding pore size.

Polyacrylamide gels provide high-resolution separation of small molecules like proteins or small DNA fragments but require careful handling due to toxicity and more complex preparation.

Agarose gels are used for seperation of DNA bands with 10bp or more differences. but in polyacrlamide gels even 1bp DNA bands can be seperated.

FOR ISSR MARKERS-1.5% agarose gels are used

FOR SSR MARKERS -POLYACRLAMIDE GELS ARE USED

Key differences are the pore size which result in different separation range and buffer composition which result in non-denaturing approach for agarose and in denaturing for acrilammide using SDS-page

in the following links you can found more details about both:

SDS-page:

https://www.blogger.com/video.g?token=AD6v5dyp2LLPNQObE-O7xpUxV02oGcx4RQ0mfxIRjK1x1YHBCYw3Av9JZTXdeO6JXLu6wl6Cd2omOIASqXY7BDpDcvlzrJ8fQSoqXnMyd5Fqcc3vRe-1JCCyISDv7Y-UACmOPKhEV6M

agarose gel:

https://www.blogger.com/video.g?token=AD6v5dxB5wweSgHEks3TU3bm1QoGEYZU6GT8788soF0i7SEVvaQwM2AgHXmDY62fIzukFrMMDbFQEFOPMfSyV4GwvJHPY9U__KiUhmaCsx6NAwneL2yJYbaSu_DV-H4_to6BznMtlE59

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Manuele

Agarose gel is typically used to determine the size of DNA or to separate a DNA mixture (for example, for the R&D of transformed plasmid with vector). The pore size of agarose is larger compared to polyacrylamide.

Polyacrylamide is used to separate protein bands from a mixture, but it can also be used for DNA as well when the difference between two DNA bands is less than 50bp (typically). For instance, if a solution contains two DNA sizes (550bp and 590bp), these two DNAs cannot be perfectly separated using agarose gel; instead, polyacrylamide gel is needed.