. Author manuscript; available in PMC: 2011 Oct 10.

Published in final edited form as: Cardiovasc Toxicol. 2010 Jun;10(2):87–99. doi: 10.1007/s12012-010-9065-z

Table 1.

PCR and electrophoresis conditions for amplification and vertical DGGE analysis of the 22 mouse tRNA genes and flanking regions

Target gene(s) and flanking region	Forward and reverse primers^a	PCR conditions			Gradient (%)^b
Target gene(s) and flanking region	Forward and reverse primers^a	MgCl₂ (mM)	Annealing temperature (°C)	PCR cycles	Gradient (%)^b
tRNA 1	MtRNA 1F/1R-PS	2.0	59	32	28–54
tRNA 2	MtRNA 2F-PS/2R	2.2	61	37	36–72
tRNA 3	MtRNA 3F/3R-PS	1.0	63	37	28–54
tRNA 4/5	MtRNA 4F/4R-PS	2.0	59	32	28–54
tRNA 5/6	MtRNA 5F/5R-PS^c	2.2	61	37	28–54
tRNA 7/8/9	MtRNA 6F-PS/6R	1.0	61	40	25–54
tRNA 10/11	MtRNA 7F-PS/7R	2.0	61	32	18–72
tRNA 12/13	MtRNA 8F-PS/8R	2.2	61	32	25–54
tRNA 14	MtRNA 9F-PS/9R	2.0	61	40	25–54
tRNA 15	MtRNA 10F/10R-PS	2.0	61	32	18–72
tRNA 16	MtRNA 11F/11R-PS^d	2.2	61	40	25–54
tRNA 17/18/19	MtRNA 12F-PS/12R	2.0	61	32	18–72
tRNA 20	MtRNA 13F/13R-PS	1.0	61	32	25–54
tRNA 21/22	MtRNA 14F-PS/14R	1.0	61	37	18–72

The oligonucleotide denoted with PS has a psoralen derivative linked to the 5′ end

Hundred percent is defined as 7 M urea plus 40% v/v formamide

Electrophoresis was conducted at 100 V for 17 h for primer set 5, and all others were run at 130 V for 17 h

PCR was carried out with 0.3 μM of each primer for primer set 11, and all other primers were amplified with 0.2 μM of each primer