Looking to assure high-quality DNA and RNA for any downstream application, including PCR and Next-Generation Sequencing? With the emergence of new purification technologies, the process has never been easier. Today, advanced purification kits can handle even small input amounts of nucleic acids and low elution volumes, enabling purification from gels, enzymatic reactions, and impure or diluted samples. They are also suitable for single stranded DNA purification and other specialised workflows.
However, with an abundance of options available, it can be tricky to decide which kit is the best fit. Below, we outline each kit's main features and what distinguishes them from similar options.
Selecting the right purification kit
Key principles:
Nucleic acid type
Fragment size
Contaminants
These three principles determine which kit is most suitable. Protein and salt contamination can be prevalent in any sample. Purification kits are essential for removing unwanted salts, proteins, unincorporated dyes/fluorescence and nucleotides, as well as phenol.
Alternatively, the OneStep PCR Inhibitor Removal Kits eliminate common contaminants in environmental samples that can inhibit downstream applications. The categories for nucleic acid purification and their optimal applications for double-stranded and single stranded DNA and RNA are summarised 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, cDNA, dsRNA, ssRNA | Only binds inhibitors | dsDNA | dsDNA | dsDNA |
| Fragment size | 50 bp – 10 kb | 10 kb – 200 kb | 16 – 200 nt | – | 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 | 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, phenol | Humic acids, tannins, polyphenolics, melanin | Salts, proteins, unwanted fragments based on size |
DNA Clean & Concentrator (DCC) Kits and Genomic DNA Clean & Concentrator (gDCC) Kits are optimised for dsDNA but can also bind single-stranded nucleic acid types with modified protocols. The Oligo Clean & Concentrator Kit (OCC) is designed for smaller double-stranded or single stranded DNA fragments.
Zymo Research’s gel recovery kits and Select-a-Size DNA Clean & Concentrator Kits remove unwanted salts, proteins, and fragments while allowing for precise size selection. The Zymoclean Recovery Kits extract nucleic acids from agarose gels, while Select-a-Size DCC Kits purify a 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, cDNA, dsRNA, ssRNA | dsDNA, cDNA, dsRNA, ssRNA | dsDNA, cDNA, dsRNA, ssRNA | dsDNA, cDNA, dsRNA, ssRNA | dsDNA, cDNA, dsRNA, ssRNA |
| Fragment size | ≥ 17 nt | 16 – 200 nt | – | ≥ 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, phenol | Humic acids, tannins, polyphenolics, melanin | Salts, proteins, unwanted fragments based on size |
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 optimised for total RNA and other single-stranded fragments from impure or dilute extractions.
The RNA recovery kits provide precise size-selection of double-stranded and single-stranded nucleic acids, removing 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 are notable for binding only PCR inhibitors, not nucleic acids. These kits offer a fast, one-step process for cleaning impure samples prior to PCR, sequencing, and reverse transcription (RT), with a 50 – 90% recovery rate. The column matrices remove contaminants such as humic acids, tannins, polyphenolics, and melanin – inhibitors commonly found in environmental samples like soil, plants, seeds, and faeces.
Choosing between similar kits
DNA Clean & Concentrator vs. Genomic DNA Clean & Concentrator Kit
If the DNA fragment is < 10 kb, the DCC kit is optimal, recovering 50 bp – 10 kb fragments with a 70 – 90% yield.
If the fragment is > 10 kb, the gDCC kit provides the highest recovery (70 – 95%).
Both are scalable, but the DCC kit also offers automation with an optional magnetic bead format.
Zymoclean Gel DNA Recovery vs. Select-a-Size DNA Clean & Concentrator Kit
For precise size selection of dsDNA fragments from agarose gels, Zymoclean Gel DNA Recovery Kits are best.
Select-a-Size Kits enable size selection DNA kits functionality without gel excision, with adjustable cut-offs for ≥ 50 bp dsDNA and automation readiness.
RNA Clean & Concentrator vs. Oligo Clean & Concentrator Kit
The OCC kit is suited for short oligonucleotides, while the RCC kit is optimal for total RNA and can handle larger inputs. Both provide > 90% recovery.
Zymoclean Gel RNA Recovery vs. ZR Small-RNA PAGE Recovery Kit
The Zymoclean Gel RNA Recovery Kit is best for fragments ≥ 500 nt from agarose gels, while the ZR Small-RNA PAGE Recovery Kit isolates 17 – 200 nt fragments from polyacrylamide gels, with ≥ 50% recovery for the smallest sizes.
This article is based on an original post by Zymo Research. You can read the original here.
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Zymo Research
Zymo Research is a leader in molecular biology, offering a comprehensive range of products for DNA, RNA, and epigenetics research. Established in California in 1994, the company is renowned for its high-quality nucleic acid purification technologies, including kits and reagents for DNA and RNA clean-up, isolation, and sequencing. Zymo is also a pioneer in epigenetics, with products for DNA methylation analysis, chromatin analysis, and NGS library preparation. Each product is designed to be simple to use, reliable, and available at competitive prices, making them ideal for both academic and biopharmaceutical research.