Which characteristic makes polyacrylamide better than agarose for resolving smaller DNA fragments?
Polyacrylamide gels are formed by crosslinking acrylamide with N,N'-methylenebisacrylamide, yielding highly uniform pores of 3 to 5 nm diameter depending on total concentration (T%) and crosslinker (C%). This pore size is an order of magnitude smaller than agarose gels, which have pores of 50 to 200 nm. Small pores provide stronger molecular sieving, allowing resolution of DNA differing by single nucleotides in 5 to 500 bp range. Agarose cannot resolve fragments below 50 bp effectively. Thus smaller pore size confers superior resolving power for small nucleic acids.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.
