How to Choose a DNA and RNA 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.

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.

Table 2: RNA compatible purification kits and their suggested applications.

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.

In contrast, 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.

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.

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 > 200 kb.

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 (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.