Nucleic Acid Purification Kit

April 13, 2018

Albert Einstein College of Medicine
Microbiology and Immunology
MD/PhD Doctoral Candidate

Overall

Quality of Results

Ease-of-Optimization

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Company:

Zymo Research

Product Name:

Direct-zol RNA MiniPrep Plus

Catalog Number:

R2072

I picked this kit to purify RNA for both RNA-seq and microarray experiments. It seemed nice because it allows for on-column DNase I treatment, and shortened my processing time by a couple hours. However, while the kit produced enough usable RNA for some of my less sensitive experiments, it consistently produced low-yields and had poor A260/230 and A260/280 ratios.

Experimental Design and Results Summary

Application

RNA purification

Starting Material

Total RNA extracted in TRIzol

Protocol Overview

Total RNA in TRIzol is added directly to the provided column. Then like most nucleic acid purification kits, you simply wash several times with various buffers and then elute the "purified" product in water.

Tips

The kit has two buffers (RNA wash buffer and RNA pre-wash buffer), and they are not used in the order you would anticipate. So double check you are using the right one at the right step.

Results Summary

I have used this kit at least 5 times in the course of preparing RNA for both RNA-seq and microarray experiments. It was nice because it allows for on-column DNase I treatment, and shortened process time by a couple hours. However, everytime I get low yields (between 600 and 1.5 µg), A260/A230 ratios below 1, and A260/A280 ratios no higher than 1.5. Worse yet, when looking at the scanning spectrograms the RNA peak sits closer to 270 nm, than it does to 260 nm, which is confusing to say the least. In the past this has provided enough usable RNA for my experiments, but just enough. Also, they have two buffers (RNA wash buffer and RNA pre-wash buffer), and they are not used in the order you would anticipate. Recently, I needed much larger amount of RNA and so went back to the tried and true TRIzol-chloroform extraction. I had consistent yields of 9 µg or more, no peak at 230 nm, and an A260/280 of between 1.7-1.9.

DOI or PMID #

N/A

Additional Notes

N/A

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Summary

The Good

Quick processing time and on-column DNAse I treatment option

The Bad

While usable, the RNA yields are low and contain organic and protein contaminants

The Bottom Line

Stick with TRIzol-chloroform extraction and separate DNase I treatment. It may take a little longer, but the results will be well worth it, especially with expensive and sensitive experiments like RNA-seq.

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