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Table 1 Primers used for PCR amplification.

From: Rice black-streaked dwarf virus P6 self-interacts to form punctate, viroplasm-like structures in the cytoplasm and recruits viroplasm-associated protein P9-1

Primer

Sequence (5′→3′) a

Locations b and modifications

PGFP-F

ggtacc ATGGGTAAAGGAGAAGAAC

1aa;Kpn I

PGFP-R

gagctc TTATTTGTATAGTTCATC

full-length reverse primer with stop codon; Sac I

PS6-1-F

CG ggatcc ATGTCTGCCC

1aa; Bam HI

PS6-4-F

CTAG ccatgg GA ATGTCTGCCCACCTGACCAATTTAG

1aa; Nco I

PS6-5-R

CG ggatcc TTACTCAGAGCTTAGTTGCCAGAGG

full-length reverse primer with stop codon; Bam HI

PS6-6-R

CCG ctcgag CTCAGAGCTTAGTTGCC

full-length reverse primer without stop codon; Xho I

PS6-8-R

CCG ctcgag ATCAGCTACTTCGTCAG

449aa; Xho I

PS6-9-F

CG ggatcc AC ATGTCTGCCCACCTG

1aa; Bam HI

PS6-10-F

CCG ctcgag ccatgg AAGCTTCTGATGTCCAG

274aa; Xho I, Nco I

PS6-11-F

CCG ctcgag ccatgg ACTTGATTAATCATGCC

395aa; Xho I, Nco I

PS6-12-R

CG ggatcc ggtacc ATCTCCAAAGTTAGCATCTAC

703aa; Bam HI, Kpn I

PS6-15-R

CG ggatcc ggtacc CGTTTCATTAGCAGATGTTTTG

659aa; Bam HI, Kpn I

PS6-16-R

TCC cccggg GAACAGATCGGCATGATTAATC

403aa; Sma I

PS6-17-F

TCC cccggg GTGAATGATTTAACTGACGAAG

440aa; Sma I

PS6-18-R

CATG gggccc GTCTTTCTCTTTTAGTAAAGAACAG

615aa; Apa I

PS6-19-F

CATG gggccc TCTGCTAATGAAACGAATGATG

655aa; Apa I

PS6-20-R

CATG gggccc GGCAATCTGTTCTTTAGCTTGTC

580aa; Apa I

PS6-21-F

CATG gggccc GAGAACGAAATGTTGAAGGAACAG

620aa; Apa I

PS6-24-F

GC tctaga ccatgg ACGTACTCAACCTGTCCAA

98aa; Xba I, Nco I

PS6-25-F

GC tctaga ccatgg AAGCTTCTGATGTCCAGTC

274aa; Xba I, Nco I

PS6-26-R

CCG ctcgag ggtacc CTCAGAGCTTAGTTGCCAGAG

full-length reverse primer without stop codon; Xho I Kpn I

PS9-5-F

CTAG ccatgg GA ATGGCAGACCAAGAGCG

1aa; Nco I

PS9-6-R

CG ggatcc AACGTCCAATTTCAAGG

full-length reverse primer without stop codon; Bam HI

PS9-9-F

CG ggatcc ATGGCAGACC AAGAGCG

1aa; Bam HI

PS9-10-R

CCG ctcgag AACGTCCAATTTCAAGG

full-length reverse primer without stop codon; Xho I

PS9-11-F

CCG gaattc TCTCATCTCCCTAACC

76aa; Eco RI

PS9-12-R

CG ggatcc CAAATACATTAAAAAGCC

207aa; Bam HI

PS9-13-F

CCG gaattc GGTGAAAATCCAAACTC

208aa; Eco RI

PS9-14-R

CG ggatcc GTGATTAACTTCTTTATTTG

248aa; Bam HI

PS9-15-F

CCG ctcgag CT ATGGCAGACCAAGAGCG

1aa; Xho I

PS9-16-R

ggtacc ggatcc TCAAACGT CCAATTTCAAG

full-length reverse primer, Kpn I, Bam HI

PS9-17-F

gaattc gtcgac ATGGCAGACCAAGAGC

1aa, Eco RI, Sal I

PS9-18-F

gaattc gtcgac ATGTCGTTGTTGCCAAT

167aa, Eco RI, Sal I

PS9-19-F

gaattc gtcgac ATGTATATAAAAGGCTT

198aa, Eco RI, Sal I

  1. a Introduced restriction endonuclease sites are in lower case. Two extra nucleotides (italicized) were added to allow in-frame expression of fusion proteins of interest.
  2. b Numbered according to P6 amino acid sequence. The F or R designation in the primer names denotes whether the primer is a forward (5′) or reverse (3′) primer, respectively.
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Virology Journal

ISSN: 1743-422X