---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2011-02-09 04:36:01+00:00
layout: post
slug: pcr-new-c-gigas-cox-primers-for-sequencing-of-isoforms
title: PCR - New C. gigas COX Primers for Sequencing of Isoforms
categories:
  - 2011
  - Miscellaneous
tags:
  - COX
  - Crassostrea gigas
  - cyclooxygenase
  - gel
  - gel extraction
  - Hyperladder I
  - isoforms
  - Pacific oyster
  - PCR
  - PGS
  - prostaglandin synthase
  - 'SR ID: 1146'
  - 'SR ID: 1151'
  - 'SR ID: 1190'
  - 'SR ID: 1191'
  - 'SR ID: 1192'
  - 'SR ID: 1193'
  - Ultrafree-DA
---

Used new primers for obtaining bands for additional sequencing of both COX isoforms in C. gigas. [Master mix calcs are here](https://eagle.fish.washington.edu/Arabidopsis/Notebook%20Workup%20Files/20110208-01.jpg). Master mix shorthand (MM##) is described below:

MM07 - Cg_COX_416_F (SR ID: 1193) + Cg_COX1_qPCR_R (SR ID: 1191) Expected band size (if no intron) = ~1540bp

MM08 - Cg_COX_416_F (SR ID: 1193) + Cg_COX2_454align1_R (SR ID: 1190) Expected band size (if no intron) = ~1540bp

MM09 - Cg_COX1/2_qPCR_F (SR ID: 1192) + Cg_COX1_qPCR_R (SR ID: 1191) Expected band size (if no intron) = ~225bp

MM10 - Cg_COX1/2_qPCR_F (SR ID: 1192) + Cg_COX2_454align1_R (SR ID: 1190) Expected band size (if no intron) = ~225bp

MM11 - Cg_COX_1519_F (SR ID: 1146) + Cg_COX2_454align1_R (SR ID: 1190) Expected band size (if no intron) = ~275bp

MM12 - Cg_COX_982_F (SR ID: 1151) + Cg_COX2_454align1_R (SR ID: 1190) Expected band size (if no intron) = ~812bp

Results:

![](https://eagle.fish.washington.edu/Arabidopsis/20110208.jpg)

Ladder is Hyperladder I from Bioline.

Master mixes are indicated underneath each group by the labels MM##. The order within each MM group (from left to right) is: template, NTC, NTC.

All bands boxed with green were purified using Millipore's Ultrafree-DA spin columns. Samples were stored @ -20C in "Sam's Misc. -20C Box".

MM07 - Fails to produce any bands of any size. Suggests the presence of intron(s) causing the size of the potential amplicon to exceed the capabilities of the polymerase under these cycling conditions.

MM08 - Produces a band of ~400bp which is well below the expected 1540bp (if no introns) size. Due to the faintness of the band, the band was not excised. Will consult with Steven to see if he thinks it worth repeating to produce sufficient product for sequencing.

MM09 - Produce a ~500bp band. The band was excised. This band size is ~275bp larger than the expected size of 225bp. This implies the presence of an intron in this region. This band size differs from that produced by MM10, which suggests that this primer set can be used for qPCR AND distinguish between the COX1 and COX2 isoforms.

MM10 - Produced a ~700bp band. The band was excised. This band size is ~475bp larger than the expected size of 225bp. This implies the presence of an intron in this region. This band size differs from that produced by MM09, which suggests that this primer set can be used for qPCR AND distinguish between the COX1 and COX2 isoforms.

MM11 - Produced multiple bands, of which two were excised; a ~3000bp band and a ~600bp band. These bands were excised solely based on their intensity and their immediate useability for sequencing. Will discuss with Steven on whether or not this should be repeated and the other bands excised for sequencing purposes. Both bands that were excised exceed the expected band size of ~275bp, suggesting the presence of multiple introns. Additionally, the presence of so many products suggests that the primers are not very specific, in regards to their target.

MM12 - An extremely faint band of ~350bp can be seen, however, due to it's faintness and it's small size (expected size was ~812bp), the band was not excised. Will discuss with Steven to see if this warrants repeating to accumulate sufficient product for sequencing purposes. No amplification of any larger products suggests the presence of introns, causing the size of the potential amplicon to exceed the capabilities of the polymerase under these cycling conditions. This is also confirmed by the MM11 PCR results in which a 3000bp band was produced. Since the primer set in MM12 has an additional 600bp at the 5' end, this has already exceeded the abilities of the polymerase, even if this addtional 600bp does NOT include an additional intron. However, it is curious that the MM12 primer set does not produce smaller, spurious PCR products as is seen in the MM11 primer set (these two primer sets both use the same forward primer).
