Table 3.
Primers used in this study.
| Primers used for cloning PCH1 and PCH1 promoter a | ||
|---|---|---|
| Amplified Fragments | Forward primer (5'->3') | Reverse primer (5'->3') |
| PCH1-stop | CACCATGTCTGAACATGTTATGGTTTTGG | CTACCTCAAATCCCTTGCATTCCA |
| PCH1-nonstop | CACCATGTCTGAACATGTTATGGTTTTGG | CCTCAAATCCCTTGCATTCCAAAC |
| PCH1-promoter b | AAGCTTAGTTTCCTCATCATTTGCTATTG | GCGTAAATCCTCACCGGTCTT |
| Primers used to generate yeast two-hybrid constructs, all with a stop codon a | ||
| Amplified fragments | Forward primer (5'->3') | Reverse primer (5'->3') |
| PCH1 | CACCATGTCTGAACATGTTATGGTTTTGG | CTACCTCAAATCCCTTGCATTCCA |
| ELF3 | CACCATGAAGAGAGGGAAAGATGAG | CTAAGGCTTAGAGGAGTCATAGCGTTT |
| ELF4 | CACCATGAAGAGGAACGGCGAGACGA | TTAAGCTCTAGTTCCGGCAGCACC |
| LUX (full length) | CACCATGGGAGAGGAAGTACAAA | TTAATTCTCATTTGCGCTTCCACCT |
| LUX-Nt (amino acids 1-143) | CACCATGGGAGAGGAAGTACAAA | CTATTTAAGTGTTTTCCCAGATAG |
| LUX-Ct (amino acids 144-324) | CACCATGCGACCGCGTTTAGTGTGGACA | TTAATTCTCATTTGCGCTTCCACCT |
| phyA-Ct (amino acids 606-1123) | CACCATGGATCTCAAAATTGATGGTATACAA | CTACTTGTTTGCTGCAGCGAGTTC |
| phyB-Ct (amino acids 640-1173) | CACCATGGCGGGGGAACAGGGGATTGATGAG | CTAATATGGCATCATCAGCATCATGTCA |
| phyC-Ct (amino acids 592-1112) | CACCATGGATAATAGGGTTCAGAAGGTAGAT | TCAAATCAAGGGAAATTCTGTGAGGATCAC |
| phyD-Ct (amino acids 645-1165) | CACCATGGTACAGCAAGGGATGCAG | TCATGAAGAGGGCATCATCATCA |
| phyE-Ct (amino acids 583-1113) | CACCATGAATGGCGTAGCAAGAGATGC | CTACTTTATGCTTGAACTACCCTCTGT |
| COP1 | CACCATGGAAGAGATTTCGACGGA | TCACGCAGCGAGTACCAGAACTTTG |
| TZP | CACCATGGGAGATGGAGATGAGCAA | CTAAAAGCCTAACATTTTTCTCTGCTGA |
| Primers used for qPCR | ||
| Gene | Forward primer (5'->3') | Reverse primer (5'->3') |
| PCH1 set A | CCGGCTCCATTTCTTCGTCA | TCCGGAACAAGAGGTGGTTCT |
| PCH1 set B | GAAGTTATTGTTGTCGCCCT | GGGAAATCCAAAGCGGTATT |
| IPP2 | CTCCCTTGGGACGTATGCTG | TTGAACCTTCACGTCTCGCA |
| APA1 (At1g11910) c | CTCCAGAAGAGTATGTTCTGAAAG | TCCCAAGATCCAGAGAGGTC |
| HFR1 | TAAATTGGCCATTACCACCGTTTA | ACCGTGAAGAGACTGAGGAGAAGA |
| ATHB-2 | GAAGCAGAAGCAAGCATTGG | CGACGGTTCTCTTCCGTTAG |
| PIF4 | GTTGTTGACTTTGCTGTCCCGC | CCAGATCATCTCCGACCGGTTT |
| Primers for genotyping | ||
| Mutant | for wild type PCR (5'->3') | for mutant PCR (5'->3') |
| pch1 (SALK_024229) | TGTCAGGTATTTCGGTCCTTG (LP) and CACTTGCTTGATGCTCATGAG (RP) | AAGAACCGGCAAAGATACCAC (RP) and ATTTTGCCGATTTCGGAAC (LBb 1.3) |
| pif3 (SALK_081927C) | AGTCTGTTGCTTCTGCTACGC (LP) and AAGAACCGGCAAAGATACCAC (RP) | ACATACAGATCTTTACGGTGG (RP)and ATTTTGCCGATTTCGGAAC (LBb 1.3) |
| pif4 (pif4-101) d | CTCGATTTCCGGTTATGG (SL42) and CAGACGGTTGATCATCTG (SL43) | GCATCTGAATTTCATAACCAATC (PD14) and CAGACGGTTGATCATCTG (SL43) |
| pif5 (pif5-1) d | TCGCTCACTCGCTTACTTAC (SL46) and TCTCTACGAGCTTGGCTTTG (SL47) | TCGCTCACTCGCTTACTTAC (SL46) and GGCAATCAGCTGTTGCCCGTCTCACTGGTG (JMLB1) |
| elf3-2 c | TGAGTATTTGTTTCTTCTCGAGC and CATATGGAGGGAAGTAGCCATTAC | TGGTTATTTATTCTCCGCTCTTTC and TTGTTCCATTAGCTGTTCAACCTA |
| elf4-2 c | ATGGGTTTGCTCCCACGGATTA and CAGGTTCCGGGAACCAAATTCT, cut with HpyCH4V. WT has 5 cuts while elf4-2 has 4 cuts to give a unique 689 bp band. | |
| phyB-9 | GTGGAAGAAGCTCGACCAGGCTTTG and GTGTCTGCGTTCTCAAAACG, cut with MnlI, phyB-9 gives 167+18 bp bands, WT gives a 185 bp band. | |
| Primers for making pB7SHHc and pB7YSHHc | ||
| Primer Name | Sequence (5'->3') | |
| pDAN0193 | TGCCCGCCTGATGAATGCTC | |
| pDAN0202 | GCGGGATATCACCACCCTAGGCACCACTTTGTACAAGAAAGCTGA | |
| pDAN201 | TCAGCTTTCTTGTACAAAGTGGTGCCTAGGGTGGTGATATCCCGC | |
| pDAN0223 | ATTCTCATGTATGATAATTCGAGG | |
| pDAN0242 | TACAAAGTGGTGCCTAGGGGTGGAAGCTGGAGCCACCCTC | |
| pDAN0241 | GCGGGATATCACCACCCTAGTGATGGTGATGGTGATGAGCG | |
| pDAN0249 | GCTTTCTTGTACAAAGTGGTGCCTGCTGCTGCTGCC | |
| pDAN0250 | GGTGGCTCCAGCTTCCACCCCCCTTATAGAGCTCGTTC | |
a CACC (underscored) were added to forward primers for cloning into the pENTR/D-TOPO vector.
b a Hind III restriction site (in bold) was added to the forward primer.
c (Nusinow et al., 2011).