For the detection of hup transcripts the RNA was extracted from c

For the www.selleckchem.com/products/ABT-737.html detection of hup transcripts the RNA was extracted from cells grown under N2-fixing conditions (BG110) and collected in the transition between the light and the dark phase. Reverse transcription (RT) reactions were performed with 1 μg of total RNA, following the protocol of the ThermoScript™ RT-PCR System (Invitrogen Corporation, Carlsbad, CA), and using LmhoxHR, GWhoxW1R or LmhupW2R as hoxH-, hoxW-, or

hupW-specific antisense primers, respectively. The three different cDNAs produced were used as templates in PCR amplifications for the detection of the cotranscription of hoxEF, hoxF-hcp, hoxUY, hoxYH (cDNA generated using LmhoxHR), ORF16-hoxW (cDNA generated using GWhoxW1R), and hupSL and hupL-W (cDNA generated using LmhupW2R). The cDNAs produced were used in PCR amplifications performed with the primer pairs RThoxE1F-GWhox8R, Wortmannin cell line RThoxF1F-LmHCPR, LMhoxUF1-GW5Lmhox2R, LmhoxYF-LmhoxHR, LmhoxWorfF1-LmhoxWR2, LMS3′A-LMH2B, and LMH5A-GW3LmhupWR1, for hoxEF, hoxF-hcp, hoxUY, hoxYH, ORF16-hoxW, hupSL, and hupL-W detection, respectively (Table 2).

The PCR program profiles were as follows: 94°C for 2 BV-6 min followed by 35 cycles of 45 s at 94°C, 45 s at 50°C (hox), 55°C (hupSL) or 64°C (hupL-W) and 1 to 2 min at 72°C, concluding with a 7 min extension at 72°C. Negative controls included the omission of reverse transcriptase in the RT reaction prior to the PCR, and a PCR to which no template was added. Genomic DNA was used as a positive control. Generated PCR products were analyzed on a 1% (w/v) agarose gel. Identification of transcription start points (tsp) by Rapid Amplification of cDNA Ends (5′-RACE) The RNA used to establish the localization of the transcription start points was extracted from cells grown in the same conditions and collected

at the same time points as for the cotranscription experiments (see above). 5′-RACE was carried out using the FirstChoice® RLM-RACE Kit (Ambion, Inc., Austin, TX) following the instructions of the manufacturer. Celecoxib For the identification of the tsp upstream hoxE, hoxW and hupW the gene-specific antisense primers RChoxE1R, RChoxE2R, RChoxE3R, and RChoxE4R (hoxE), LmxisHR4, LmxisHR3, LmxisHR2, and LmxisHR1 (xisH), or LmhupW3R, LmhupW2R, LmhupW1R, and GW3LmhupWR1 (hupW) (Table 2) were used together with the kit adaptor-specific primers. PCR amplifications were carried out with the following profiles: 94°C for 3 min followed by 35 cycles of 30 s at 94°C, 30 s at 55°C (hoxE and xisH) or 58°C (hupW), and 1 min at 72°C, and concluding with 7 min extension at 72°C. The obtained PCR products were cloned into the pGEM®-T Easy vector (Promega, Madison, WI), and subsequently sequenced at STAB Vida (Lisbon).

Comments are closed.