Table 1. Listing of oligonucleotide probe sequences, calculated Tm and ΔG° values, and species to which each probe is specific (single perfect match).
| Probe | Sequence (5′→3′) | Tm (°C) | ΔG° (kcal/mol) | Targeted species (perfect sequence match with test strains) |
|---|---|---|---|---|
| 1 | AAGTCTGAC | 32.03 | –10.49 | B.pumilus |
| 2 | AGTCTGACG | 37.60 | –11.66 | B.pumilus |
| 3 | GGAGCAACG | 42.53 | –12.72 | B.pumilus |
| 4 | GTGAGTGAT | 32.18 | –10.54 | B.pumilus |
| 5 | TGAGTGATG | 32.22 | –10.55 | B.pumilus |
| 6 | GGAGAAGCC | 39.68 | –12.08 | – |
| 7 | GCAGTTACC | 35.95 | –11.27 | P.syringae, P.veronii |
| 8 | CAGTTACCT | 30.93 | –10.31 | P.syringae, P.veronii |
| 9 | CGAGAGTAA | 31.38 | –10.35 | B.pumilus |
| 10 | GAGAGTAAC | 28.35 | –9.62 | B.pumilus |
| 11 | GTAACTGCT | 33.02 | –10.71 | B.pumilus |
| 12 | ATACCTTGC | 32.77 | –10.71 | P.aeruginosa, P.alcaligenes |
| 13 | AACTGCTCG | 39.85 | –12.16 | B.pumilus |
| 14 | TACCTTGCT | 34.42 | –11.11 | P.aeruginosa, P.alcaligenes |
| 15 | TACGTTAGT | 28.85 | –9.93 | P.putida, P.fluorescens |
| 16 | CCTTGCTGT | 39.02 | –11.98 | P.aeruginosa, P.alcaligenes |
| 17 | CGTTAGTGT | 33.56 | –10.80 | P.putida, P.fluorescens |
| 18 | CGTGATTGT | 35.05 | –11.13 | P.syringae, P.veronii |
| 19 | GTTAGTGTT | 27.90 | –9.63 | P.putida, P.fluorescens |
| 20 | GCTGTTTGA | 35.24 | –11.16 | P.aeruginosa, P.alcaligenes |
| 21 | GCTGTTTTG | 34.18 | –10.86 | P.syringae |
| 22 | AGTGTTTCG | 34.90 | –11.08 | P.fluorescens |
| 23 | AGTGTTTTC | 29.30 | –9.91 | P.putida |
| 24 | GTTGGGATG | 35.50 | –11.20 | – |
| 25 | GTGTTTCGA | 35.04 | –11.10 | P.fluorescens |
| 26 | CCTTGACGG | 40.76 | –12.32 | B.pumilus |
| 27 | TTGACGTTA | 31.17 | –10.38 | P.syringae, P.aeruginosa, P.alcaligenes, P.veronii |
| 28 | GTACCTAAC | 28.08 | –9.60 | B.pumilus |
| 29 | GTGGTTCAG | 35.70 | –11.20 | P.aeruginosa, P.alcaligenes |
| 30 | TGGTTCAGC | 39.14 | –12.00 | P.aeruginosa, P.alcaligenes |
| 31 | GGTTCAGCA | 39.14 | –12.00 | P.aeruginosa, P.alcaligenes |
| 32 | GTTCAGCAA | 35.24 | –11.16 | P.aeruginosa, P.alcaligenes |
| 33 | TTCAGCAAG | 34.43 | –11.00 | P.aeruginosa |
| 34 | AGCAAGCTT | 37.74 | –11.77 | P.alcaligenes |
| 35 | AGCAAGTTG | 35.09 | –11.14 | P.aeruginosa |
| 36 | GCAAGCTTG | 39.04 | –11.94 | P.alcaligenes |
| 37 | GCAAGTTGG | 37.95 | –11.70 | P.aeruginosa |
| 38 | CAAGCTTGA | 34.43 | –11.00 | P.aeruginosa |
| 39 | AAGCTTGAT | 31.06 | –10.43 | – |
| 40 | AAGTCCGTT | 36.33 | –11.47 | B.pumilus |
| 41 | AAGTCTGAT | 28.56 | –9.93 | P.aeruginosa |
| 42 | AGCTTGATG | 33.72 | –10.88 | – |
| 43 | AGTCCGTTG | 38.76 | –11.92 | B.pumilus |
| 44 | AGTCTGATG | 31.34 | –10.38 | P.aeruginosa |
| 45 | GCTTGATGT | 34.54 | –11.04 | – |
| 46 | GTCCGTTGT | 39.53 | –12.08 | B.pumilus |
| 47 | GTCTGATGT | 32.18 | –10.54 | P.aeruginosa |
| 48 | CTTGATGTG | 31.25 | –10.25 | – |
| 49 | TCCGTTGTG | 39.56 | –12.09 | B.pumilus |
| 50 | TCTGATGTG | 32.22 | –10.55 | – |
| 51 | GTGGATACT | 30.35 | –10.21 | P.aeruginosa |
| 52 | AAGCTACTG | 32.18 | –10.55 | P.alcaligenes |
| 53 | AACTACTGA | 27.89 | –9.77 | P.fluorescens, P.veronii |
| 54 | AACTGACTG | 32.75 | –10.64 | P.aeruginosa |
| 55 | AGCTACTGA | 33.22 | –10.85 | P.alcaligenes |
| 56 | ACTACTGAG | 29.78 | –10.05 | P.fluorescens, P.veronii |
| 57 | ACTGACTGA | 33.81 | –10.94 | P.syringae, P.putida |
| 58 | ACTGGCAAG | 39.02 | –11.98 | P.aeruginosa |
| 59 | GCTACTGAG | 34.03 | –10.85 | P.aeruginosa, P.alcaligenes |
| 60 | CTACTGAGC | 34.03 | –10.85 | P.fluorescens, P.veronii |
| 61 | CTGACTGAC | 34.57 | –10.94 | P.syringae, P.putida |
| 62 | CTGGCAAGC | 42.84 | –12.78 | P.aeruginosa, P.alcaligenes |
| 63 | CTACTGAGC | 34.03 | –10.85 | P.fluorescens, P.veronii |
| 64 | CTGACTGAC | 34.57 | –10.94 | – |
| 65 | CTGGATGAC | 34.36 | –10.94 | P.fluorescens, P.veronii |
| 66 | GACTGACTA | 29.96 | –10.07 | P.syringae, P.putida |
| 67 | GGCAAGCTA | 38.60 | –11.91 | P.fluorescens, P.veronii |
| 68 | ACTGACTAG | 29.78 | –10.05 | P.syringae, P.putida |
| 69 | GCAAGCTAG | 36.30 | –11.35 | P.aeruginosa, P.alcaligenes |
| 70 | TGAGCTAGA | 32.52 | –10.71 | P.syringae, P.putida |
| 71 | CAAGCTAGA | 31.51 | –10.41 | – |
| 72 | CTAGAATGT | 25.55 | –9.21 | P.aeruginosa |
| 73 | GTAGAGGTG | 32.85 | –10.61 | P.aeruginosa |
| 74 | TAGAGGTGG | 34.23 | –11.01 | P.aeruginosa |
| 75 | AGAGGTGGT | 38.26 | –11.87 | P.aeruginosa |
| 76 | GAGGTGGTA | 35.07 | –11.17 | P.aeruginosa |
| 77 | AGGTGGTAG | 34.92 | –11.15 | P.aeruginosa |
| 78 | GGTGGTAGA | 35.07 | –11.17 | P.aeruginosa |
| 79 | TGGTAGAAT | 27.55 | –9.77 | P.fluorescens |
| 80 | GTGGTGAAG | 35.70 | –11.20 | B.pumilus |
| 81 | CTCTCTGGT | 35.15 | –11.17 | B.pumilus |
| 82 | TCTCTGGTC | 35.30 | –11.19 | B.pumilus |
| 83 | CTCTGGTCT | 35.15 | –11.17 | – |
| 84 | TGGACCAAC | 38.01 | –11.76 | P.aeruginosa |
| 85 | ACTGTACTG | 31.36 | –10.36 | – |
| 86 | ACCAACATT | 31.39 | –10.50 | P.aeruginosa |
| 87 | CTGTACTGA | 30.68 | –10.22 | – |
| 88 | CATTGACAC | 32.10 | –10.41 | – |
Probes 1–28 were designed for region A and probes 29–90 were designed for region B. Tm values of perfectly matched oligonucleotide duplexes were calculated by the GPD program using formulae of SantaLucia (20), setting [Na+] = 50 mM and [oligonucleotide] = 100 µM. The Tm estimates are intended only to describe the relative stability of different oligonucleotides in a given hybridization reaction, since the absolute values will depend on variables of DNA and ionic concentrations.