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Table 1 Sequences of oligonucleotide primers

From: microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.)

Cleavage site mappinga
OsABP 1st PCR 5′-ATCAAAATCATATCCCCTCCGC-3′ 258 bp
Nested PCR 5′-TCCTCCCTCCATACGAAAATTCTG-3′ 144 bp
OsDBH 1st PCR 5′-GAAAAGGGGAACAGTGCTAG-3′ 150 bp
Nested PCR 5′-AACCAGTTCAGCTTTGGCTGCT-3′ 100 bp
OsDSHCT 1st PCR 5′-GGCAGGTGGCAGGAAGATTATA-3′ 490 bp
Nested PCR 5′-ACATCGCCGGTCATCAATCCGACAT-3′ 310 bp
QRT-PCR for gene amplification
OsABP Forward 5′-GGGGGAGGATGGTGAGTAAT-3′ 211 bp
Reverse 5′-CCACCACCATCATCATCAAA-3′
OsDBH Forward 5′-ACGATGGCACCTCAGAGAAT-3′ 177 bp
Reverse 5′-TGGACCAAGTGACAGATGGA-3′
OsDSHCT Forward 5′-GAGGAGGTGGAGAACACGAG-3′ 237 bp
Reverse 5′-GTAGGCCTTGGCCATCTC-3′
α-Tubulin Forward 5′-GGTGGAGGTGATGATGCTTT-3′ 200 bp
Reverse 5′-ACCACGGGCAAAGTTGTTAG-3′
QRT-PCR for miRNA amplification b
osa-MIR414 Forward 5′-TCATCCTCATCATCATCGTCC-3′ 100 bp
osa-MIR164e Forward 5′-GGGAGTTCTGTGATTGGAGAG-3′ 100 bp
osa-MIR408 Forward 5′-TGGAGAAGCAGGGCACGTGA-3′ 100 bp
U6 Forward 5′-CGATAAAATTGGAACGATACAGA-3′ 150 bp
Reverse 5′-ATTTGGACCATTTCTCGATTTGT-3′
  1. a Gene-specific reverse primers used in combination with the FirstChoise RLM-RACE Kit (Ambion, Invitrogen) forward and nested primers.
  2. b Specific reverse primers for miRNAs, used in combination with the Universal qPCR forward primer provided in the NCode VILO kit (Invitrogen).