Molecular recognition of live methicillin-resistant staphylococcus aureus cells using DNA aptamers

Table 1 Quantitative representation of the different homologous families and Methicillin-resistant Staphylococcus aureus aptamer sequences after Ion Torrent sequencing and alignment

Name of aptamers	Percentage of total sequences	Sequence
DTMRSA1	2.57%	ATCCAGACGTGACGCAGC(N)38TGGACACGGTGGCTTAGTA(N)38 = ATGCGGTTGGTTGCGGTTGGGCATGATGTATTTCTGTG
DTMRSA2	33.74%	ATCCAGAGTGACGCAGCA(N)36TGGACACGGTGGCTTA(N)36 = CGACACGTTAGGTTGGTTAGGTTGGTTAGTTTCTTG
DTMRSA3	10.05%	ATCCAGAGTGACGCAGCA(N)40TGGACACGGTGGCTTAGTA(N)40 = GTAGATGGTTTGGTTGGTGTGGTTTCCTACTGATGTTGGG
DTMRSA4	0.32%	ATCCAGAGTGACGCAGCA(N)39TGTGGACACGGTGGCTTA(N)39 = TTATGGGGTGTGGTGGGGGGTTAATGCGTTGGTTATCCG

The primers used for the selection are presented in bold. Note that some primer sequences changed through the selection process.

Table 2 Relative binding of the selected aptamers to various clinical cell lines

Clinical strains	DTMRSA1	DTMRSA2	DTMRSA3	DTMRSA4
MRSA 2	+++	++++	+++	++++
MRSA 4	+++	+++	+++	++++
MRSA 6	++++	++++	+++	++++
MRSA 7	-	++++	+++	++++
S. aureus 164	-	++++	+	+++
S. aureus 165	-	++++	+	+++
S. aureus 166	-	++++	+	+++
E. faecalis 43	-	++++	+	+++
E. faecalis 44	-	++++	+	++
E. faecalis 45	-	++++	+	+++

This table summarizes the results obtained with the binding assays on clinical strains ofmethicillin-resistant Staphylococcus aureus(MRSA), S. aureusandE. faecalisbacteria. (-) no binding; (+) 0%-25%; (++) 25-50%; (+++) 50%-75%; (++++) 75%-100%. S.aureus: Staphylococcus aureus; E. faecalis: Enterococcusfaecalis.

Table 3 Apparent dissociation constants (Kd) of the four aptamers recognizing methicillin-resistant Staphylococcus aureus bacteria

Name of the aptamer	Kd (nmol/L)
DTMRSA1	1.6 ± 0.5 × 102
DTMRSA2	2.0 ± 0.6 × 102
DTMRSA3	1.3 ± 0.5 × 102
DTMRSA4	9.5 ± 2 × 101