How to Choose a DNA and RNA Purification Kit

Looking to assure high-quality DNA and RNA for any downstream application including PCR and Next-Gen Sequencing? With the emergence of new purification technologies, the process has never been easier. Now, advanced purification technologies are suitable for even small input amounts of nucleic acids and low elution volumes, purifying DNA and RNA from gels, enzymatic reactions, and impure or diluted samples. However, with an abundance of options available, it can be tricky to navigate which kit will be the best fit. Explore each kit's top features and what distinguishes them from similar options below.

Selecting the Right Purification Kit

Key Principles:

1. Nucleic Acid Type
2. Fragment Size
3. Contaminants

These three principles dictate which kit is suitable. Protein and salt contamination can be prevalent in any sample. Purification kits are best if looking to remove any unwanted salts, proteins, unincorporated dyes/fluorescence and nucleotides, and phenol.

Alternatively, the OneStep PCR Inhibitor Removal Kits eliminate common contaminants in environmental samples that inhibit downstream applications. The categories for nucleic acid purification and their optimal applications for double-stranded and single-stranded DNA and RNA are listed in Table 1 and Table 2.

Purification Kits Based On Nucleic Acid Type

DNA Purification Kits:

	DNA Clean & Concentrator (DCC)	Genomic DNA Clean & Concentrator (gDCC)	Oligo Clean & Concentrator (OCC)	OneStep PCR Inhibitor Removal Kits	Zymoclean Gel DNA Recovery Kits	Zymoclean Large Fragment DNA Recovery Kit	Select-a-size DNA Clean & Concentrator Kits
Nucleic Acid	dsDNA	dsDNA	dsDNA dsRNA ssRNA cDNA	dsDNA dsRNA ssRNA cDNA	dsDNA	dsDNA	dsDNA
Fragment Size	50 bp — 10 kb	10 kb — 200 kb	16 — 200 nt	Only binds inhibitors	50 bp — 10 kb	10 kb — 200 kb	≥ 50 bp
Format	Column 96-well Magnetic Bead	Column 96-well	Column 96-well	Column 96-well	Column 96-well	Column	Column Magnetic Bead
Common Applications	PCR clean-up	Extracted gDNA clean-up	Small oligo clean-up	Environmental inhibitor removal	DNA size selection from agarose gels	gDNA size selection from agarose gels	DNA & NGS library size selection
Removes	Salts, protein, unincorporated dyes/fluorescence and nucleotides, and phenol			Humic acids, tannins, polyphenolics, melanin	Salts, proteins, and unwanted fragments based on size

DNA Clean & Concentrator (DCC) Kits and Genomic DNA Clean & Concentrator (gDCC) Kits are optimized for dsDNA but are capable of binding single-stranded nucleic acid types. However, the Oligo Clean & Concentrator Kit (OCC) utilizes a binding chemistry more favorable for smaller double-stranded or single-stranded fragments.

Zymo Research’s gel recovery kits and Select-a-Size DNA Clean & Concentrator Kits remove unwanted salts, proteins, and fragments as well as perform size selection. The Zymoclean Recovery Kits provide precise extraction of nucleic acids from agarose gels, while the Select-a-Size DCC Kits purify a desired, tunable range of DNA fragment sizes.

RNA Purification Kits:

	RNA Clean & Concentrator (RCC)	Oligo Clean & Concentrator (OCC)	OneStep PCR Inhibitor Removal Kits	Zymoclean Gel RNA Recovery Kit	ZR Small-RNA PAGE Recovery Kit
Nucleic Acid	dsDNA dsRNA ssRNA cDNA	dsDNA dsRNA ssRNA cDNA	dsDNA dsRNA ssRNA cDNA	dsDNA dsRNA ssRNA cDNA	dsDNA dsRNA ssRNA cDNA
Fragment Size	≥ 17 nt	16 — 200 nt	Only binds inhibitors	≥ 500 nt	≥ 17 nt
Format	Column 96-well Magnetic Bead	Column 96-well	Column 96-well	Column	Column
Common Applications	Extracted or transcribed RNA clean-up	Small oligo clean-up	Environmental inhibitor removal	RNA size selection from agarose gels	Small RNA size selection from PAGE gels
Removes	Salts, protein, unincorporated dyes/fluorescence and nucleotides, and phenol		Humic acids, tannins, polyphenolics, melanin	Salts, proteins, and unwanted fragments based on size

The RNA Clean-Up kits, including RNA Clean & Concentrator (RCC) Kits and Oligo Clean & Concentrator (OCC) Kits are compatible with dsDNA, ssRNA, dsRNA, and ssDNA (including cDNA). The clean and concentrator kits in Table 2 are optimized to elute total RNA and other single-stranded fragments from impure or dilute extractions.

Whereas the RNA recovery kits provide precise size-selection of double-stranded and single-stranded nucleic acids. These kits remove unwanted salt, protein, and fragments from either agarose or PAGE isolated samples.

PCR Inhibitor Removal Kits:

OneStep PCR Inhibitor Removal Kits yield high-quality DNA or RNA and stand out for their ability to only bind PCR inhibitors and not nucleic acids. These kits consist of a fast, one-step procedure for cleaning impure samples prior to PCR, sequencing and reverse transcription (RT), with a 50 – 90% recovery rate. The column matrices efficiently remove contaminants that can inhibit downstream applications such as humic acids, tannins, polyphenolics, and melanin. These inhibitors are common in environmental samples like feces, soil, plants, and seeds.

Choosing Between Similar Kits

DNA Clean & Concentrator vs. Genomic DNA Clean & Concentrator Kit

DNA Clean & Concentrator (DCC) Kits and Genomic DNA Clean & Concentrator (gDCC) Kits are both optimized for dsDNA samples, but they can also bind single-stranded or cDNA fragments with protocol modifications.

If the DNA fragment is < 10 kb, then DCC is optimal. DCC provides better DNA recovery of smaller fragments, 50 bp – 10 kb, at a 70 – 90% yield

If the DNA fragment is > 10 kb, then gDCC is the best kit to achieve the greatest sample recovery. The gDCC provides optimal recovery of larger DNA fragments, > 10 kb, at 70 – 95%.

Although both kits are scalable to increase the sample processed per prep, the DCC kit also has automation capabilities with an optional magnetic bead format.

Zymoclean Gel DNA Recovery vs. Select-a-Size DNA Clean & Concentrator Kit

When it comes to recovering precise size selection dsDNA fragments from agarose gels the Zymoclean DNA Kits are best. The Zymoclean gel DNA Recovery Kit optimally recovers the desired dsDNA isolated fragment from 50 bp – 10 kb with a typical recovery of 70 – 90%, while the Zymoclean Large Fragment DNA Recovery Kit best recovers isolated samples from 10 kb up to > 200kb.

On the other hand, Select-a-Size DNA Clean and Concentrator Kits are optimized for size selection over a broad range of dsDNA fragments without the need for gel excisions. Manipulating titration cutoffs allows customization for selectively isolating the fragment range of interest. This kit can manipulate a size selection range cutoff for ≥ 50 bp dsDNA and is automation ready with a magnetic bead format available.

RNA Clean & Concentrator vs. Oligo Clean & Concentrator Kit

RNA Clean & Concentrator (RCC) Kits and Oligo Clean & Concentrator (OCC) Kits are both shown to work with all nucleic acids. However, the OCC kit is best suited for DNA and short RNA oligonucleotides. Whereas the RCC kit is optimal for total RNA, cDNA, and other single-stranded fragments and can be scaled to process larger sample inputs per prep; it is also automation ready with a magnetic bead format available.

When it comes to yield, the OCC kit will yield ssDNA/RNA or dsDNA ≥ 16 nucleotides, while the RCC kit will yield total RNA ≥ 17 nucleotides. Both kits provide a yield with > 90% recovery, respectively.

Zymoclean Gel RNA Recovery vs. ZR Small-RNA Page Recovery Kit

The Zymoclean Gel RNA Recovery Kit is optimal for larger fragments that are effectively isolated in agarose gels with high resolution. While the ZR Small-RNA PAGE Recovery Kit purifies RNA from polyacrylamide gels. Whereas Zymoclean Gel RNA Recovery Kit extracts RNA resolved in TAE, TBE, and MOPS buffered agarose gels and provides ≥ 80% recovery for fragments ≥ 500 nucleotides.

On the contrary, the ZR Small-RNA PAGE Recovery Kit allows for the recovery of small RNA (and DNA) fragments, 17 - 200 nucleotides, from up to 20% (w/v) polyacrylamide gels stained with ethidium bromide or ssRNA-specific dyes (native or denatured). Additionally, this kit can bind small fragments, 17 - 28 nucleotides, with ≥ 50% recovery.

Fragment size and isolation effectiveness per gel composition are two key factors to consider when deciding between these gel recovery kits.