Optimized PCR conditions minimizing the formation of chimeric DNA molecules from MPRA plasmid libraries

BMC Genomics

Table 1 Occurrence of chimeric BC–ROI combinations under different ePCR conditions for the two-plasmid template system

Round #2 ePCR conditions	Total read count				Reads with chimeric BC–ROI combinations, %
	R#1		R#2		BC1–ROI2		BC2–ROI1		Average
	BC1	BC2	BC1	BC2	R#1	R#2	R#1	R#2	R#1	R#2
0.5 μl of round #1 ePCR products, 20 cycles	134,011	134,779	47,072	46,333	1.579	1.651	1.465	1.347	1.522	1.499
0.3 μl of round #1 ePCR products, 20 cycles	43,782	44,788	10,327	10,452	0.831	0.629	0.737	0.440	0.784	0.535
0.5 μl of round #1 ePCR products, 18 cycles	21,042	21,733	166,862	170,934	0.200	0.225	0.230	0.211	0.215	0.218

The settings of the round #1 ePCR were the same for all samples: 15 amplification cycles starting with ~ 2 × 10⁶ template DNA molecules
R#1 and R#2 stand for replicate 1 and replicate 2, respectively

ISSN: 1471-2164