Table 3.

The candidate natural aptamer sequences that fold to the target structures

Sequence		Genome	Location	Gene	$\Delta G_{37}^{\text{o}}$ (kcal/mol)	Tm (°C)	$T_{\text{m}}-\Delta G_{37}^{\text{o}}$ test	V	$V-\Delta G_{37}^{\text{o}}$ test
Chloramphenicol
1	5′-TCAGAGCTGA AAAACTGGCC CCGGGTGCAG CTAAAAACTG A	E.coli K12	1 172 203	Mfd	−11.90	78.0	−	1.09	−
2	5′-TCAGAGCTGA AAAACTGGCC CCGAGTGCAG CTAAAAACTG A	E.coli O157:H7	1 532 105	ECs1492
3		E.coli O157:H7 EDL933	1 617 201	Mfd	−10.58	72.6	−	2.40	−
4	5′-GGGAAACGCA AAAATCAGGT ACAGGCAGAC GACGGTGGCG TAAAACTCCC	N.meningitidis Z2491	2 179 300	Non-coding	−9.17	54.4	−	5.28	−
5	5′-GCAACGGAAA AAGCTGCTTT GCCCTTGAAG GCGGGGGGTG ATTCGGAAAA TGC	S.meliloti	493 471	Non-coding	−14.44	48.8	−	6.18	−
Streptomycin
6	5′-GTACCCGGAC GTGCCCTTCC AGGCGTCCAT GGAGGCCTGG CTCGGGGCGG TGC	S.avermitilis	7 323 209	Non-coding	−28.64	111.4	−	0.84	−
ATP
7	5′-GCTGGTCGAA GACACTGGCT GTCGCTGTCG ACGGCGATCA GC	Halobacterium sp. NRC1	pNRC200 92 229	Non-coding
8		Halobacterium sp. NRC1	pNRC100 92 229	Non-coding	−19.43	71.6	+	4.54	+
9	5′-TCTGTCCAAC CAGAGGAAAC TGGCTTCCAA AGTTCTCGGA TGCGGGCTTG ATAGG	M.acetivorans C2A	1 295 025	MA1090	−16.04	71.2	−	6.40	−
10	5′-CAAGGGCTGA AGAAAATGCT GTGGTTATAT CCTACCAGGG TGACGGGGAC CTTG	M.mazei Goe1	3 868 884	vorA	−13.71	69.4	−	8.46	−
11	5′-CTTGCTTTGA AAAAACTGGC AAATTCAACA AGGATTGCGA AGTACG	P.furiosus; DSM 3638	168 991	PF0158	−7.48	63.8	−	9.49	−
Neomycin B
12	5′-TGAGCAGGGG CGAGAAGTTT TTCCTTG	E.coli K12	3 430 475	smf_1	−5.37	67.2	−	8.23	−
13		E.coli K12	1 832 073	Non-coding
14	5′-TGTGTCGGGC GTAGAGTTTT GCGAG	E.coli O157:H7 EDL933	2 508 764	Non-coding	−4.12	59.6	−	3.25	−
15		E.coli CFT073	1 987 894	Non-coding
16	5′-CTGCGGGGGA ACACTTTGGT G	E.coli K12	3 973 740	wecE	−3.54	60.0	−	4.27	−
17	5′-AGTCTGGTGG GCGATATGTT TATTATGAT	E.coli K12	1 324 039	yciQ	−6.10	57.8	+	2.24	−
18		E.coli O157:H7	1 826 735	ECs1840
19		E.coli O157:H7 EDL933	2 260 441	Z2542
20		E.coli CFT073	1 569 619	yciQ
21		E.coli O157:H7	1 373 724	ECs1300
22	5′-ATTCACTGGG CGACATGTTT GATGAAT	E.coli O157:H7 EDL933	1 457 496	Z1560	−5.55	61.4	−	1.41	−
23		E.coli O157:H7 EDL933	1 061 889	Z1121
24		E.coli CFT073	1 130 797	c1166
25		E.coli O157:H7	1 037 740	ECs0954
26	5′-AATGGGCGCA GAGTTTGTT	E.coli O157:H7 EDL933	1 039 400	Z1102	−3.65	60.8	−	1.33	−
27		E.coli CFT073	960 757	c1001
28		E.coli O157:H7	3 148 310	Non-coding
29	5′-CCAGCGGGCG CAGAGTTTAT GGG	E.coli O157:H7 EDL933	3 218 265	Non-coding	−4.98	57.4	−	0.42	−
30		E.coli CFT073	2 704 642	Non-coding
31	5′-TGCGGGCGAA CAGTTTGCA	E.coli O157:H7 EDL933	5 503 670	Non-coding	−7.61	81.0	+	1.12	+
32	5′-TTGAGCAGGG GCGTGAAGTT TTTGCTTTG	E.coli CFT073	3 864 206	Smf	−10.79	83.4	+	1.44	+
33	5′-TTCCTGAAGG GGGACGACTT TGATGGGGA	N.meningitidis MC58	1 221 920	Non-coding	−7.44	65.2	−	8.29	−
34		N.meningitidis Z2491	1 283 084	Non-coding
35	5′-ACGAGGGCGG TAAGTTTTTT T	N.meningitidis MC58	1 468 213	Non-coding	−2.55	51.6	−	1.22	−
36		N.meningitidis Z2491	1 553 595	Non-coding
37	5′-GCAGGTGGGC GCAGAGTTTG CCATT	C.trachtomatis	604 373	yjeE	−9.07	83.0	−	0.76	−

The physical properties, energetic test results, and location(s) of each candidate sequence are reported. $\Delta G_{37}^{\text{o}}$, T_m, and V denote the free energy, melting temperature and Valley index, respectively. The $T_{\text{m}}-\Delta G_{37}^{\text{o}}$ and $V-\Delta G_{37}^{\text{o}}$ test results (+ or −) at 90% confidence level are calculated using the thermodynamic scatter plots (see text and Figure 4). Location refers to the position of the start site of a candidate sequence (by nucleotide number) and Gene refers to the gene's name (GenBank annotations) or non-coding region containing the candidate sequence. The locations of sequences 7 and 8 are in the associated species' plasmids. The most promising candidates are numbered in bold.