---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2011-04-07 21:37:29+00:00
layout: post
slug: 53-race-pcrs-nested-pcrs-for-cox2-sequence
title: 5'/3' RACE PCRs - Nested PCRs for COX2 Sequence
categories:
  - 2011
  - Miscellaneous
tags:
  - cDNA
  - COX
  - COX2
  - Crassostrea gigas
  - cyclooxygenase
  - gel
  - gel extraction
  - Pacific oyster
  - PCR
  - PGS
  - PGS2
  - prostaglandin synthase
  - RACE
  - SMART RACE
  - Ultrafree-DA
---

Due to the failure of the primary PCR on both 5' and 3' RACE cDNA libraries (from 20080619) yesterday, will perform nested PCR using a nested GSP designed by Steven (CgPGSRACEsrNGSP1; SR ID:1209). The 5uL of PCR reactions that were set aside yesterday were diluted to 250uL with tricine-EDTA (supplied with the Clontech SMARTer RACE cDNA Amplification Kit) as instructed in the Clontech manual. The master mix and tube layouts were exactly the same as yesterday's, but instead of using 2.5uL of RACE cDNA library as template, I used 5uL of the diluted PCR reaction. Additionally, Universal Nested Primers were used instead of the Universal Primer Mix (both supplied in the kit). Cycling parameters followed "Program 2" from the Clontech manual for 25 cycles.

Entire PCR rxns were run on a 1.2% gel, as instructed by the Clontech manual.

Results:

![](https://eagle.fish.washington.edu/Arabidopsis/20110407-01.jpg)

So..... What we see here is a melted gel!

But! We also see a successful PCR! The first three lanes (excluding the Hyperladder I) are 5' RACE rxn, followed by two different negative controls (the negative control in the last lane is the one we're really concerned with and it's totally clean). The next three lanes are the 3' RACE rxn, followed by two different negative controls (the negative control in the last lane is the one we're really concerned with and it's totally clean). As hoped/expected, we got a nice, clear product in the 5' RACE rxn.

The bright band (~1500bp) in the 5' RACE rxn PCR was excised and purified using Millipore Ultrafree DA columns according to protocol. Will clone and sequence this product.
