Which chemical is NOT used in denaturing buffers for agarose gels?
Denaturing buffers for agarose electrophoresis of RNA employ agents that disrupt secondary structures and prevent renaturation during migration. Glyoxal and dimethyl sulfoxide (DMSO) covalently and non-covalently modify guanine residues, preventing base pairing and maintaining linear conformation. Formaldehyde at alkaline pH and formamide perform similar denaturing functions by disrupting hydrogen bonds. EDTA, while not a denaturant, chelates magnesium to inhibit RNases. TEMED, N,N,N',N'-tetramethylethylenediamine, is exclusively a catalyst for polyacrylamide polymerization, accelerating free radical formation from persulfate. It has no role in agarose chemistry or RNA denaturation.
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.