Size distributions for starting material and IVT amplified product. Lanes 1–3 each contain 250 ng DNA run on a 2% non-denaturing agarose gel. Lanes 4–5 each contain 500 ng RNA run on a 2% denaturing agarose gel. The denaturing gel is necessary to eliminate RNA secondary structure. Lane 1: 100 bp ladder (NEB). Lane 2: starting material (yeast genomic DNA digested with Alu I and previously gel-purified to a size range of 100–700 bp). Lane 3: amplified product generated by R-PCR from 50 ng starting material. Lane 4: amplified RNA product generated by IVT from 50 ng starting material. Lane 5: 100 bp RNA Ladder (Ambion). The R-PCR amplified product appears to significantly under-represent low molecular weight species. The IVT amplified product may slightly under-represent high molecular weight species. For clarity, the denaturing gel image was rescaled to match the ladder of the non-denaturing gel.