Detection of Salmonella enterica subsp. enterica via Quenching of Unincorporated Amplification Signal Reporters in Loop-Mediated Isothermal Amplification

Table 1

Nucleic acid sequences of the generated SopD LAMP primer set. Four types of LAMP primers were designed using Primer Explorer v.5 (Fujitsu Ltd, 2015) based on the following six distinct regions of the target gene: the F3c, F2c, and F1c regions at the 3ʹ side and the B1, B2, and B3 regions at the 5′ side.

Label	Tm (°C)	GC content (%)	Length (bp)	5′ G	3′ G	Sequence (5′ ⟶ 3′)
SopD_S1_F3	59.3	61	18	−5.04	−6.85	CGAAGATGACCTGGCACC
Sop_DS1_B3	59.1	55	20	−5.18	−5.69	GCG​ACT​TCA​CCT​TGT​ACC​TC
SopD_S1_FI						CCT​CTG​CGG​GAC​GCA​TCA​TC
P (F1c + F2)						AAG​TGA​CGG​GAA​ATG​CAC​AA
F1c	64.8	65	20	−5.19	−3.8	CCT​CTG​CGG​GAC​GCA​TCA​TC
F2	60.0	45	20	−4.41	−5.57	AAG​TGA​CGG​GAA​ATG​CAC​AA
SopD_S1_BI						GCT​TGT​CGA​ATG​GCA​GGA​CTC​A
P						—
(B1c + B2)						CGT​AGG​CTC​AAA​GTT​ACC​GG
B1c	64.8	55	22	−5.4	−4.76	GCT​TGT​CGA​ATG​GCA​GGA​CTC​A
B2	59.8	55	20	−5.35	−5.86	CGT​AGG​CTC​AAA​GTT​ACC​GG

Primer sets were evaluated using the Oligo Calculator v. 3.27 (Kibbe WA, https://bpc.facilities.northwestern.edu/OligoCalc) such that hairpin formation and self-dimerization are minimized [22] and were ordered for synthesis from Eurogentec (Belgium).