TABLE 1.

Degenerate primers designed for the amplification of rdpA and sdpA

Peptide or primerSequenceaPositionb
RDP_internal sequence 2 WETLSPTMQATIEGLN 162-177
rdp_r 3′-ACGTYCGNTGNTAICTYCC-5′
RDP_internal sequence 3 NEILDAFHTYQVIYFP 43-58
rdp_fAc 5′-GCITTYCAYACNTAYCAAGT-3′
rdp_fGc 5′-GCITTYCAYACNTAYCAGGT-3′
SDP_N terminus MQTTLQITPTGATLGA 1-16
sdp_fCc 5′-ATGCARACIACICTGCARATCAC-3′
sdp_fTc 5′-ATGCARACIACICTGCARATTAC-3′
SDP_internal sequence 1 LGHVQQAGSAYI 193-204
sdp_rAc 3′-GTACANGTYGTYCGNCC-5′
sdp_rGc 3′-GTACANGTYGTYCGNCC-5′
  • a As described previously (57). IUPAC ambiguity codes: R = A or G, Y = C or T, N = any base, I = inosine.

  • b Alignment is shown in Fig. 2.

  • c To avoid degeneracy near the 3′ end, two pools of primers were designed from some peptides (sequence differences are indicated in boldface).