qPCR – Repeat Phage Portal Primer Specificity Check

Due to the odd (and poor) results from the first qPCR to look at this phage portal gene, I’m repeating the qPCR exactly, but have made fresh 1:1000 dilutions of the two RLOv+ samples (08:3-15, 08:3-16) with TE.

See the earlier qPCR run for master mix calcs.

All samples were run in duplicate.

See the qPCR Report (see Results below) for plate layout, cycling params, etc.


qPCR Report (PDF): Sam_2016-03-17 10-42-54_CC009827.pdf
qPCR Data File (CFX): Sam_2016-03-17 10-42-54_CC009827.pcrd

Firstly, the fresh dilutions resolved the issue with the poor amplification previously seen with the RLOv DNA helicase assay; they look perfect in this run.

Quick summary for the phage portal qPCR:

  • Amplification in all 4 samples (RLOv- & RLOv+).
  • Much, much earlier amplification in RLOv+ samples.
  • Good, single peaks in melt curves
  • RLOv+ and RLOv- samples show different temps for peaks in melt curves

If the phage portal gene was present in the RLOv, then we would expect the amplification (i.e. the Cq values) of DNA helicase and the phage portal gene to be extremely close. However, in the RLOv+ samples, there’s a ~1000-fold difference in DNA helicase/phage portal levels.

If the phage portal gene was present in just the RLO, then we would expect similar amplification (i.e. Cq values) in both RLOv+/- samples. However, we see an EXTREME difference in phage portal gene levels between RLOv+ samples and the RLO- samples (~10,000-fold difference in levels). If the phage portal gene was present in both RLOv+/- samples, then that could possibly help explain this difference, due to the massive phage load in the RLOv+ samples (based on DNA helicase data). However, this doesn’t seem to be the case…

We see two distinct melt curve peak temps between the RLOv+/- samples. If the phage portal gene was present in both sample types, then the RLOv+ samples should exhibit a dual peak in the melt curves. However, this is not the case. This is difficult to explain since the RLOv+ samples also contain RLOv- (i.e. the RLO bacteria) DNA. If the PCR product generated in the RLOv- samples is indeed distinct from that produced in the RLOv+ samples, then we should see that product in the melt curve of the RLOv+ samples, but we don’t.

I will repeat this qPCR using undiluted, source DNA from the RLOv- samples. This should shift their amplification ~10 Cq (a 10-fold difference in amplification equates to ~3.32 Cqs) earlier. This, in turn, will allow their signal to generate higher levels of fluorescence and, hopefully, increase the melt curve peak for a more accurate assessment of melt temp(s); just to make sure the melt temp is accurate.


qPCR Amplification Plots (DNA helicase in green; Phage portal gene in blue)

qPCR Amplification Plots of Phage Portal Gene

qPCR Melt Curves of Phage Portal Gene

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