Commonly used PCR primers

As in: Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp. 115-175.

27F 5' 		AGA GTT TGA TCM TGG CTC AG 3'	eubacteria
357F 5'		    CTC CTA CGG GAG GCA GCA G 3'  eubacteria
      ANTIgamma 5' CTC CTA CGG GAG GCA GCA GT 3' eubacteria (very similar to 357F)
530F 5' 	GTG CCA GCM GCC GCG G 3' 	eubacteria / archaebacteria
926F 5' 	AAA CTY AAA KGA ATT GAC GG 3'	eubacteria / archaebacteria
1114F 5' 	GCA ACG AGC GCA ACC C 3' 	eubacteria
342R 5' 	CTG CTG CSY CCC GTA G 3' 	eubacteria
519R 5'	 	GWA TTA CCG CGG CKG CTG 3' 	eubacteria / archaebacteria
907R 5'		CCG TCA ATT CMT TTR AGT TT 3' 	eubacteria / archaebacteria
1100R 5' 	GGG TTG CGC TCG TTG 3' 		eubacteria
1492R 5' 	TAC GGY TAC CTT GTT ACG ACT T 3' eubacteria
1525R 5' 	AAG GAG GTG WTC CAR CC 3' 	eubacteria
A8F 5'       TCC GGT TGA TCC TGC C 3'    archaea
A1538R 5'         CGG TTG GAT CAC CTC  3'    archaea

Reverse complement sequence can be used to reverse primer. E.g.:

519R = 5' 	GWA TTA CCG CGG CKG CTG 3' 
519F = 3' 	CWT AAT GGC GCC GKC GAC 5'

bTAG

      GCC TTG CCA GCC CGC TCA GTC

Ayuso-Sacido and O. Genilloud, Microbial Ecology 2004
	A3 	5’-GCSTACSYSATSTACACSTCSGG-3’
	A7R 	5’-SASGTCVCCSGTSCGGTAS-3’

Ayuso-Sacido and O. Genilloud, Microbial Ecology 2004
	K1	5’-TSAAGTCSAACATCGGBCA-3’
	M6R 	5’-CGCAGGTTSCSGTACCAGTA-3’

Ginolhac et al. AEM 70 (9): 5522. (2004)
	KSLF 5’-CCSCAGSAGCGCSTSYTSCTSGA-3’
	KSLR 5’-GTSCCSGTSCCGTGSGYSTCSA-3’

Piel 2002, PNAS
	KSDPQQF 5′-MGNGARGCNNWNSMNATGGAYCCNCARCANMG-3′
	KSHGTGR 5′-GGRTCNCCNARNSWNGTNCCNGTNCCRTG-3′

Courtois et al. AEM 2003 p 49-55
set 1
	sense, 5'-CCSCAGSAGCGCSTSTTSCTSGA-3', 
	antisense, 5'-GTSCCSGTSCCGTGSGTSTCSA-3'; 

set 2
	sense, 5'-CCSCAGSAGCGCSTSCTSCTSGA-3', 
	antisense, 5'-GTSCCSGTSCCGTGSGCCTCSA-3'.

Metsä-Ketelä et al. AEM 68 (9): 4472. (2002)
	F 	5’-TSG CST GCT TGG AYG CSA TC-3’ 
	R 	5’-TGG AANCCG CCG AAB CCG CT-3’

Wawrik et al. 2005
	540F	 5’-GGITGCACSTCIGGIMTSGAC-3’
	1100R	 5’-CCGATSGCICCSAGIGAGTG-3’

Seow et al. AEM 179 (23): 7360. (1997)
	kSALPHA 	 5'-TTC GGC GGX TTC CAG TCX GCC ATG-3'
	ACP		 3'-CCX ATG CTC AGC XAC CGC GAC GAC CT-3'

(Paul et al.)

	Form ID forward :		GAT GAT GAR AAY ATT AAC TC
	Form ID reverse:		ATT TGD CCA CAG TGD ATA CCA
	Form IA/B forward:		TCI GCI TGR AAC TAY GG TCG
	Form IA/B reverse:		GGC ATR TGC CAI ACR TGR AT
	Synechococcus reverse:		CTG AGI GGI AAR AAC TAC GG