TABLE 1.
PCR primers and capture oligonucleotides
| Sequence type and name | Sequence (5′ → 3′) | Positiona | Accession no.b |
|---|---|---|---|
| PCR Primers | |||
| VP7 | |||
| Beg9 | GGC TTT AAA AGA GAG AAT TTC CGT CTG G | 1-28 | M21843 |
| VP7 | ACT GAT CCT GTT GGC CAT CCT TT | 395-373 | M21843 |
| VP4 | |||
| HC5 | GTC TAG ATG GTC CAT ATC AAC C | 200-221 | M32559 |
| HC3 | TTC CTT GTA TTC TGA ATT GGT | 701-681 | M32559 |
| MS2 | |||
| MS25 | CAT GGC TAT CGC TGT AGG TAG C | 79-100 | J02467 |
| MS23 | CGC GAA CGG AGG GGA CGA A | 187-169 | J02467 |
| Capture oligonucleotidesc | |||
| G type | |||
| G*A | GTC TGG CTA GCG GTT AGC TC | 23-42 | M21843 |
| G*A NC | GTC TGG CTA GCG GTT AGC TT | 23-42 | M21843 |
| G*B | TTA TAT TAT CCA ACW GAA GC | 295-314 | M21843 |
| G*B NC | TTA TAT TAT CCA ACW GAA GT | 295-314 | M21843 |
| G1-1 | GTA TTA TCA AAC TGA AGC AAG | 297-317 | M21843 |
| G1-2d | TGA TGG TGA ATG GAA AGA CT | 330-349 | M21843 |
| G1-3d | GTA TTA TCC AAC TGA AGC AA | 297-316 | M21843 |
| G2-1 | TAC TAT CCA GCA GAA GCT AA | 298-317 | U73947 |
| G2-2 | ATA CTA TCC AGC AGA AGC TA | 297-316 | U73947 |
| G2-3 | GAA GCT AAA AAT GAG ATT TC | 310-329 | U73947 |
| G3-1 | GCT GCT TCA GTT GGG TAA TA | 298-317 | D86284 |
| G3-2 | TAA TGG ACT TTA TTA TTT AC | 134-153 | D86284 |
| G3-3 | ATT ATG GAA TAA ATC TTC CG | 203-222 | D86284 |
| G4-1 | GAC ACT GAA TGG AAA GAT A | 331-349 | AF161823 |
| G4-2d | ACA CTG AAT GGA AAG ATA CA | 332-351 | AF161823 |
| G4-3d | ACA GCT GAG ATA GTG TAT CT | 338-357 | AF161823 |
| G9-1 | ATA TTA TCC TAC AGA AGC AT | 297-316 | AF060487 |
| G9-2 | CTT TTA CTT ATT GTT ATT GC | 160-179 | AF060487 |
| G9-3 | ATA TGC AAA TTC ATC ACA GC | 246-265 | AF060487 |
| P type | |||
| P* | CTT GTA TTC TGA ATT GGT GG | 698-679 | M32559 |
| P*NC | CTT GTA TTC TGA ATT GGT GT | 698-679 | M32559 |
| P4-1 | AAT TGA TAT ATT ATT TAA ATC C | 611-590 | M32559 |
| P4-2 | TGA TTT TTG GAC AGC AGT TA | 306-325 | M32559 |
| P4-3 | TGA TTA TTG GCT GCT TAT TAG | 243-263 | M32559 |
| P6-1 | TCA GAT AAA TTT GAA ATT G | 593-578 | U16299 |
| P6-2d | TCA GAC AAG TTT GAA GTT G | 593-578 | U16299 |
| P6-3d | TCA GAT AAG TTT GAA GTT G | 593-578 | U16299 |
| P8-1 | CCT TGG AAT AAT GTA AAA TTC TGA | 636-613 | M96825 |
| P8-2 | CTA TCT ACT GGG TTA ACG TGC | 359-339 | M96825 |
| P8-3 | TGA ACC GCA CGT TAA CCC AGT | 333-353 | M96825 |
| P9-1 | TAA ACC ATT ATT TAT ATA TTG TG | 681-659 | M28349 |
| P9-2 | CGT TGC TGT TAT CAT TGT TTA | 604-584 | M28349 |
| MS2 | |||
| MS2 | GGT ACT AAA AGC TCG CAC AG | 147-128 | J02467 |
a
Nucleotide positions relative to reference sequences.
b
Accession numbers of reference VP4 and VP7 genes and phage MS2.
c
Capture oligonucleotides all have a terminal amino group and 15 T residues at their 5′ ends. The first number in the names of the specific oligonucleotides indicates the genotype with which it is designed to hybridize. The oligonucleotides denoted with an asterisk are generic capture oligonucleotides, and an additional NC (negative control) indicates an intentional mismatch (T) at their 3′ ends. P8-1 is complementary to the sequences of both the P[4] and the P[8] genotypes.
d
Capture oligonucleotides added after the expansion of the array.