RNA isolation / purification Bacteria - Gram negative Klebsiella pneumoniae

Generally isolating RNA from Gram-negative bacteria is easy, however keeping your working environment clean and RNase free (use RNase inhibitor) is essential. Some common points to keep in mind: a) Use fresh samples for isolation or store them by freezing in RNA stabilizing buffer until use. b) Choose the bacterial input amounts carefully, to ensure buffer volumes are adequate and not to overload the columns.

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4 years ago

4 years ago by Paul G. Macon United States

Some help with RNA isolation using Trizol

Hello! I used Trizol to extract total RNA from in-vitro cultured bacteria (1 X 10^8 cells). After phase separation, I mixed ~0.4 ml of the upper phase which contains RNA with 0.5 mL cold isopropanol. However, the amount of RNA when measured in Nanodrop was very low. In addition, the ratio between 260 and 230 was around 0.1 to 0.5. Is there a chance that my sample was contaminated by the Trizol reagent? When I collected the aqueous phase I made sure to not touch the lower phase. What should I do?

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Found 2 matching solutions for this experiment

mirVana™ miRNA Isolation Kit, with phenol

Thermo Fisher Scientific

Upstream tips	Protocol tips	Downstream tips
	"For RNA to dissolve better and to yield high levels, preheat elution buffer at 95C. Addition of β-mercaptoethanol in lysis buffer can be skipped because the phenol will do the job of nuclease inactivation. To capture a higher amount of mRNA, modify the amount of lysis buffer :ethanol (from 1:1 to 1:1.5) during the binding step. Do vortex for 2-plus minutes. This will facilitate the removal of tightly bound proteins typically associated with RNA."

Protocol tips
"For RNA to dissolve better and to yield high levels, preheat elution buffer at 95C. Addition of β-mercaptoethanol in lysis buffer can be skipped because the phenol will do the job of nuclease inactivation. To capture a higher amount of mRNA, modify the amount of lysis buffer :ethanol (from 1:1 to 1:1.5) during the binding step. Do vortex for 2-plus minutes. This will facilitate the removal of tightly bound proteins typically associated with RNA."

Protocol tips

"For RNA to dissolve better and to yield high levels, preheat elution buffer at 95C.
Addition of β-mercaptoethanol in lysis buffer can be skipped because the phenol will do the job of nuclease inactivation.
To capture a higher amount of mRNA, modify the amount of lysis buffer :ethanol (from 1:1 to 1:1.5) during the binding step.
Do vortex for 2-plus minutes. This will facilitate the removal of tightly bound proteins typically associated with RNA."

Manufacturer protocol Publication protocol 1 Relevant paper

SV Total RNA Isolation System

Promega

Upstream tips	Protocol tips	Downstream tips
	Do not freeze-thaw the DNase more than three times after rehydration. After adding ethanol to the RNA wash solution, label the bottle so that you fellow researchers don't add any extra.	For better lysis, pipet the RNA Lysis Buffer over the bottom of the well.

Protocol tips
Do not freeze-thaw the DNase more than three times after rehydration. After adding ethanol to the RNA wash solution, label the bottle so that you fellow researchers don't add any extra.
Downstream tips
For better lysis, pipet the RNA Lysis Buffer over the bottom of the well.

Manufacturer protocol Publication protocol 1 Relevant paper

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