DNA Cleanup Kits for DNA Purification and Concentration

DNA cleanup kits purify and concentrate DNA from enzymatic reactions, phenol-chloroform extractions, and dilute solutions by removing enzymes, salts, organic solvents, unincorporated nucleotides, and RNA using silica-membrane spin columns.

MBP supplies Zymo Research DNA Clean & Concentrator to registered vendors at Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center. Request a quote for DNA cleanup kits designed for DNA purification, concentration, reaction cleanup, and preparation of high-quality DNA for downstream molecular biology applications by contacting customerservice@mbpinc.net.

DNA Cleanup Kits

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What are DNA Cleanup Kits?

DNA cleanup kits purify and concentrate pre-extracted or pre-amplified DNA by removing enzymes, salts, organic solvents (phenol, chloroform), unincorporated nucleotides, RNA, detergents, and other contaminants from DNA solutions using silica-membrane spin columns with a bind-wash-elute protocol. Unlike PCR cleanup kits that are specifically optimized to remove primers and dNTPs from PCR reactions, DNA cleanup kits accept broader input chemistries - including post-phenol-chloroform extraction DNA, genomic DNA in high-salt lysis buffers, restriction digest reactions, and dilute DNA solutions requiring concentration - and elute DNA in minimal volumes (as little as 6 ul) for immediate use in downstream applications. Use a DNA cleanup kit whenever your DNA preparation contains inhibitors incompatible with downstream enzymatic reactions, when residual phenol must be removed, or when dilute DNA must be concentrated into a small volume.

What you will find:

DNA Clean & Concentrator™ (DCC): Efficient spin-column systems (5, 25, 100, 500 preps) created to concentrate low-concentration DNA into ultra-pure, transfection-quality volumes.
Genomic DNA Clean & Concentrator: Tailored procedures for extracting large templates while maintaining genomic integrity for long-read sequencing uses.
Select-a-Size DNA Clean & Concentrator™: Tailored systems for the recovery of size-specific fragments, efficiently eliminating adapter dimers and non-target amplicons.
ZR-96 DNA Cleanup Systems: Scalable 96-well and MagBead configurations designed for high-throughput, automated processes while ensuring reproducibility-validated outcomes.

How to Choose a DNA Cleanup Kit

Capacity and Input Volume

Zymo DNA Clean & Concentrator kits are available in formats matched to DNA input mass: DCC-5 (<=5 ug input, elute >=6 ul), DCC-25 (<=25 ug input, elute >=25 ul), DCC-100 (<=100 ug input, elute >=25 ul). Choose the format whose maximum capacity exceeds your expected DNA input by at least 2-fold to avoid column overloading, which reduces yield and purity. For genomic DNA preparations from tissue (typically 5-30 ug), DCC-25 or DCC-100 is appropriate.

Minimum Elution Volume and Concentration

For maximum DNA concentration, Zymo DCC-5 elutes in 6 ul - the industry minimum for standard silica columns. If the input volume is 500 ul (1 ng/ul) and the elution is 6 ul, the final concentration reaches approximately 80 ng/ul (assuming 95% recovery), a concentration suitable for transfection, electroporation, and microinjection.

Size Selectivity

Standard DNA cleanup kits retain all DNA >=100 bp. If size selection is also required, use gel extraction (for specific band isolation) or AMPure XP beads (for size-range selection by bead: volume ratio adjustment) rather than a standard cleanup kit.

Post-Phenol-Chloroform Cleanup

For DNA recovered from phenol-chloroform extraction, add 5 volumes of binding buffer and 2 volumes of 100% ethanol to the aqueous phase before column loading. The organic solvent in residual phenol or chloroform does not significantly impair column binding at these dilutions. Multiple column reloads allow processing of large aqueous-phase volumes through a single column.

RNase A Treatment for DNA-Only Preparations

For gDNA preparations that must be RNA-free for optical mapping or certain long-read sequencing library kits, add RNase A (100 ug/ml) to the DNA solution, incubate at 37 degrees C for 10 minutes, then proceed directly to DCC cleanup. The RNase digestion products are removed during the wash steps.

Specifications Context

Zymo DNA Clean & Concentrator kits use a single-buffer system with Zymo-Spin column technology and recover DNA from PCR, enzymatic reactions, phenol-chloroform extractions, and dilute solutions. DNA is eluted in volumes as small as 6 ul, providing up to 80-fold concentration from 500 ul inputs. The kits remove enzymes, proteins, salts, organic solvents, dyes, unincorporated nucleotides, primers, and other small molecules, delivering DNA ready for restriction digestion, ligation, sequencing, Southern blotting, transfection, and long-read library preparation. DNA cleanup and concentration are standard workflow steps in genomics laboratories at Howard Hughes Medical Institute, Vanderbilt University, and MD Anderson Cancer Center, where removing trace inhibitors from gDNA before library preparation significantly improves NGS library complexity and uniformity.

Enhance your capabilities—reach out to the MBP Inc. team now to obtain a quote for your DNA concentration requirements.

FAQ

DNA cleanup kits (also called DNA clean and concentrators or DNA purification kits) purify and concentrate pre-extracted or pre-amplified DNA by removing enzymes, salts, organic solvents, phenol, chloroform, unincorporated nucleotides, RNA, and other contaminants from DNA solutions using silica-membrane spin columns and a bind-wash-elute protocol. Unlike PCR cleanup kits that specifically remove primers and dNTPs from PCR reactions, DNA cleanup kits are used to purify DNA from any aqueous solution where the goal is inhibitor removal and/or concentration into a minimal volume.

Use a DNA cleanup kit when: (1) purifying genomic DNA after extraction when the eluate contains residual lysis salts or guanidinium; (2) removing phenol and chloroform from phenol-chloroform DNA extractions before enzymatic reactions; (3) concentrating dilute DNA from large volumes into a small elution volume; (4) removing RNA from a DNA preparation after RNase A treatment; (5) cleaning up genomic DNA after restriction digest before Southern blotting; or (6) removing EDTA, organic solvents, or detergents from DNA before enzymatic reactions. PCR cleanup kits can substitute in most of these applications, but DNA cleanup kits are validated for broader input chemistries.

Zymo DNA Clean & Concentrator kits retain DNA from 100 bp upwards with full recovery; for fragments ≥50 bp, adjust the ethanol ratio. For a size-selective application retaining only large DNA (>300 bp) while removing primers and small fragments, adjust the binding conditions. QIAGEN QIAquick PCR & Reaction Cleanup Kit retains DNA from 100 bp to 10 kb. For recovery of intact genomic DNA >50 kb without shearing, use a DNA cleanup approach without vortexing — resuspend gently and avoid forceful pipetting.

Zymo DNA Clean & Concentrator-5 kits elute in as little as 6 µl of water or TE buffer, concentrating DNA from a 25–500 µl input into a 6 µl eluate — representing up to an 80-fold concentration. For applications requiring highly concentrated DNA inputs (transfection, electroporation, microinjection), the 6 µl elution provides maximum DNA concentration. QIAGEN MinElute PCR Purification Kit elutes in 10 µl minimum. Warm elution buffer to 65–70°C before applying to the column membrane to maximize elution efficiency.

Yes. Silica-membrane DNA cleanup kits effectively bind DNA in the presence of residual phenol and chloroform at standard chaotropic binding conditions, then wash away the organic solvents during the wash step. For DNA precipitated from phenol-chloroform extractions, resuspend the pellet in TE buffer, add 5 volumes of binding buffer, and proceed with standard column cleanup. Zymo DNA Clean & Concentrator kits are specifically validated for post-phenol-chloroform cleanup of genomic DNA.

Standard DNA cleanup kits do not degrade or selectively exclude RNA — both DNA and RNA bind the silica membrane under standard chaotropic conditions. For DNA preparations that must be RNA-free, add RNase A (100 µg/ml final) to the input solution and incubate at room temperature for 5 minutes before adding binding buffer and loading the column. The RNA degradation products (short oligoribonucleotides) will be washed away during the column wash steps, and the eluate will contain only DNA. Alternatively, select a genomic DNA extraction kit that includes an on-column RNase A treatment step.

Yes — DNA cleanup and concentration is a primary application. Dilute DNA in binding buffer (5:1 or 6:1 binding buffer:DNA volume), add 2 volumes of absolute ethanol, load onto the Zymo-Spin column, wash, and elute in 6–25 µl. This concentrates DNA from input volumes up to 500 µl into as little as 6 µl. For very dilute DNA solutions below 10 ng/ml, carrier DNA (1–5 ng non-specific salmon sperm or poly-dA) can be added to improve recovery by providing a minimum nucleic acid mass for efficient column binding.

DNA cleanup is required or recommended before: transfection of mammalian cells (residual phenol, ethanol, or detergent reduces transfection efficiency); restriction enzyme digestion (EDTA from TE buffer inhibits MgCl₂-dependent restriction enzymes); ligation reactions (residual salt inhibits T4 DNA ligase); electroporation (high-salt DNA preparations cause electrical arcing); Southern blotting (requires highly pure gDNA free of RNA and organic contamination); and NGS library preparation quality assessment (residual RNA inflates NanoDrop DNA concentration estimates, misleading library input normalization).

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