Table 1.
Deduced strong binding sites in vRNA5 of isoenergetic microarray probes.
| Binding sitea,b | Deduced binding sitesc | Probe sequenced | Strength of probe bindinge | Predicted ΔG°37 of probe/ vRNA5 duplex (kcal/mol) for confirmed binding sitesf | RNase H cleavage sites |
|---|---|---|---|---|---|
| 22/184/355/880/883/1251/1280/1300/1429 | 883 1251 1429 |
dDgDdg | S | −9.24 (883, 1251, 1429) |
880–882 (w) 883 (s) 1250–1253 (w) 1254–1260 (s) 1261 (w) 1421–1427 (s) 1428 (w) |
| 256/457/469/546/814/1181 | 469 | dDgDgg | S | −10.03 (469) | 470–484 (s,w) |
| 677 | 677 | DcGgDg | S | −10.81 (677) | 676–684 (s) |
| 275/642/644/790/860/1073/1203/1221/1328/1330 | 1073 1330 |
dGdGdg | S | −10.71 (1073) −12.84 (1330) |
1067–1071 (s) 1073 (s) 1331–1332 (s) 1334 (s) |
| 534/683 | 683 | gUgUgg | S | −9.77 (683) | 676–684 (s) |
| 377/415/562/646/722/862/1205/1450 | 646 | uGdGdg | S | −12.22 (646) | 647 (s) 649–650 (s) |
aPossible complementary binding sites of probes, bsites are denoted by the middle nucleotide of the complementary RNA region; cdeduced binding site for probe by comparison with DNA induced RNase H cleavage results; dnucleotides in capital letter (G, U, D) are 2′-O-methyl-RNA nucleotides, lower case letters (c, g, u, d) are LNA nucleotides, D and d are 2,6 – diaminopurine (2′-O-methyl type or LNA, respectively); ebinding was considered strong (S) when the integrated intensities were ≥1/3 of the strongest intensity. Hybridization condition: buffer 1, 37 °C; fΔG°37 calculated as modified probe/RNA duplex67,68, in parenthesis, the site of binding for which calculation was done; g(s) – strong RNase H cleavage, (w) – weak RNase H cleavage.