Table 1. Primers Used for PCR-SSCP, REP,... | American Society of Hematology

Table 1.

Primers Used for PCR-SSCP, REP, MSP, BGS, and RT-PCR Analyses

Primer Set	Application and Specificity	Template DNA	Forward Primer (5′ → 3′)	Reverse Primer (5′ → 3′)	Product Size (bp)	Annealing Temperature (°C)
	PCR-SSCP
A	p16 exon 1	G	GGGAGCAGCATGGAGCCG	AGTCGCCCGCCATCCCCT	203	58
B	p16 exon 2A	G	CTGGCTCTGACCATTCTGT	AGCACCACCAGCGTGTCC	171	58
C	p16 exon 2B	G	GACCCCGCCACTCTCACC	AGGTACCGTGCGACATCGC	170	58
D	p16 exon 2C	G	GATGCCTGGGGCCGTCT	CAGGGTACAAATTCTCAGAT	169	55
E	p16 exon 3	G	GTAGGGACGGCAAGAGA	ACCTTCGGTGACTGATG	159	55
F	p14 exon 1	G	GCCTGCGGGGCGGAGAT	GCGGCTGCTGCCCTAGA	316	58
G	p15 exon 1	G	TTCCCAGAAGCAATCCAG	GTTGACTCCGTTGGGATC	384	55
	REP
H	p16 exon 1	G, RE⁺	GGGAGCAGCATGGAGCCG	CTGGATCGGCCTCCGACCGTA	159^*	57
I	p14 exon 1	G, RE⁺	GCCTGCGGGGCGGAGAT	GCGGCTGCTGCCCTAGA	316^†	58
J	p15 exon 1	G, RE⁺	TTCCCAGAAGCAATCCAG	GTTGACTCCGTTGGGATC	384^‡	55
	MSP and BGS
K	p16 exon 1, M	G, Bis⁺	TTATTAGAGGGTGGGGCGGATCGC	GACCCCGAACCGCGACCGTAA	150	65
L	p16 exon 1, M	G, Bis⁺	TTATTAGAGGGTGGGGCGGATCGC	CCACCTAAATCGACCTCCGACCG	234	65
M	p16 exon 1, U	G, Bis⁺	TTATTAGAGGGTGGGGTGGATTGT	CAACCCCAAACCACAACCATAA	151	60
N	p16 exon 1, U	G, Bis⁺	TTATTAGAGGGTGGGGTGGATTGT	CCACCTAAATCAACCTCCAACCA	234	60
	BGS
O	p16 promoter, M/U	G, Bis⁺	GTGATTTTAGGGGTGTTA	TTCCAATTCCCCTACAAA	483	48
P	p14 exon 1, M/U	G, Bis⁺	GGGTTTTAGTTTGTAGTT	CCTCAATAACATCAACAC	255	48
Q	p15 exon 1, M/U	G, Bis⁺	TTTTTTAGGAAGGAGAGA	TAAAACCCCAACTACCTA	285	48
	RT-PCR
R	p16	cDNA	GGTGCGGGCGCTGCTGGA	AGCACCACCAGCGTGTCC	210	58
S	p14	cDNA	GTGGCCCTCGTGCTGATG	AGCACCACCAGCGTGTCC	207	58
T	p15	cDNA	GATCCCAACGGAGTCAAC	AGCACCACCAGCGTGTCC	182	53
U	GAPDH	cDNA	TTGTCAAGCTCATTTCCTG	AGGCCCCTCCCCTCTTC	238	55

Primer Set	Application and Specificity	Template DNA	Forward Primer (5′ → 3′)	Reverse Primer (5′ → 3′)	Product Size (bp)	Annealing Temperature (°C)
	PCR-SSCP
A	p16 exon 1	G	GGGAGCAGCATGGAGCCG	AGTCGCCCGCCATCCCCT	203	58
B	p16 exon 2A	G	CTGGCTCTGACCATTCTGT	AGCACCACCAGCGTGTCC	171	58
C	p16 exon 2B	G	GACCCCGCCACTCTCACC	AGGTACCGTGCGACATCGC	170	58
D	p16 exon 2C	G	GATGCCTGGGGCCGTCT	CAGGGTACAAATTCTCAGAT	169	55
E	p16 exon 3	G	GTAGGGACGGCAAGAGA	ACCTTCGGTGACTGATG	159	55
F	p14 exon 1	G	GCCTGCGGGGCGGAGAT	GCGGCTGCTGCCCTAGA	316	58
G	p15 exon 1	G	TTCCCAGAAGCAATCCAG	GTTGACTCCGTTGGGATC	384	55
	REP
H	p16 exon 1	G, RE⁺	GGGAGCAGCATGGAGCCG	CTGGATCGGCCTCCGACCGTA	159^*	57
I	p14 exon 1	G, RE⁺	GCCTGCGGGGCGGAGAT	GCGGCTGCTGCCCTAGA	316^†	58
J	p15 exon 1	G, RE⁺	TTCCCAGAAGCAATCCAG	GTTGACTCCGTTGGGATC	384^‡	55
	MSP and BGS
K	p16 exon 1, M	G, Bis⁺	TTATTAGAGGGTGGGGCGGATCGC	GACCCCGAACCGCGACCGTAA	150	65
L	p16 exon 1, M	G, Bis⁺	TTATTAGAGGGTGGGGCGGATCGC	CCACCTAAATCGACCTCCGACCG	234	65
M	p16 exon 1, U	G, Bis⁺	TTATTAGAGGGTGGGGTGGATTGT	CAACCCCAAACCACAACCATAA	151	60
N	p16 exon 1, U	G, Bis⁺	TTATTAGAGGGTGGGGTGGATTGT	CCACCTAAATCAACCTCCAACCA	234	60
	BGS
O	p16 promoter, M/U	G, Bis⁺	GTGATTTTAGGGGTGTTA	TTCCAATTCCCCTACAAA	483	48
P	p14 exon 1, M/U	G, Bis⁺	GGGTTTTAGTTTGTAGTT	CCTCAATAACATCAACAC	255	48
Q	p15 exon 1, M/U	G, Bis⁺	TTTTTTAGGAAGGAGAGA	TAAAACCCCAACTACCTA	285	48
	RT-PCR
R	p16	cDNA	GGTGCGGGCGCTGCTGGA	AGCACCACCAGCGTGTCC	210	58
S	p14	cDNA	GTGGCCCTCGTGCTGATG	AGCACCACCAGCGTGTCC	207	58
T	p15	cDNA	GATCCCAACGGAGTCAAC	AGCACCACCAGCGTGTCC	182	53
U	GAPDH	cDNA	TTGTCAAGCTCATTTCCTG	AGGCCCCTCCCCTCTTC	238	55

Abbreviations: M, specific for methylated bisulfite-modified DNA; U, specific for unmethylated bisulfite-modified DNA; G, genomic DNA; RE⁺, restriction enzyme-digested DNA; Bis⁺, bisulfite-treated DNA.

Fragment containing 2 HpaII/MspI and 1 KspI site.

†

Fragment containing 1 HpaII/MspI and 1 KspI site.

‡

Fragment containing 5 HpaII/MspI, 1 KspI, 1NaeI, and 1 EagI site.

View Large

This Feature Is Available To Subscribers Only