DNA Gel Extraction Kit

Cat. No.: A1521384

GRADE & PURITY BioReagent, Suitable for molecular biology

Overview

This kit is based on centrifugal spin column technology and is suitable for recovering DNA fragments from TAE or TBE agarose gels while removing impurities such as proteins, other organic compounds, inorganic salt ions, and oligonucleotide primers. Using this kit, fragments ranging from 100 bp to 15 kb can be recovered with a recovery rate of up to 80%. Each spin column can bind up to 10 μg of DNA. The purified DNA can be directly used for sequencing, ligation, restriction enzyme digestion, PCR, and transformation.

Protocol

Before use, add an appropriate amount of absolute ethanol to Buffer PW2. For 12 mL of Buffer PW2, add 48 mL of absolute ethanol; for 24 mL of Buffer PW2, add 96 mL of absolute ethanol.

1. (Optional) Column Equilibration

Place the KOS spin column into a collection tube. Add 500 μL of Buffer BL to the spin column, centrifuge at 12,000 rpm (13,680 × g) for 30 seconds. Discard the waste liquid and put the spin column back into the collection tube. (Use spin columns processed on the same day.)

Note: Treating spin columns stored at room temperature for a long time with Buffer BL can improve binding yield.

Cut the single target DNA band from the agarose gel (remove as much extra gel as possible) and place it into a clean centrifuge tube. Weigh the gel slice.

Add 3 volumes of Buffer PBD to the gel slice (if the gel weighs 0.1 g, its volume can be considered as 100 μL, then add 300 μL of Buffer PBD). Dissolve the gel at 50°C for 5–10 minutes, gently inverting the tube occasionally to ensure complete dissolution. (If the gel volume is too large, cut it into small pieces beforehand.)

Note: After the gel is completely dissolved, it is best to cool the solution to room temperature before loading onto the column, as the spin column binds DNA more efficiently at room temperature.

Transfer the solution from the previous step to a Spin Column KOS (place the column in a collection tube). Let stand at room temperature for 2 minutes, then centrifuge at 12,000 rpm (13,680 × g) for 30 seconds. Discard the flow-through and place the column back into the collection tube.

Note: The column has a capacity of 700 μL. If the sample volume exceeds 700 μL, load in multiple batches.

Add 580 μL of Buffer PW2 (ensure absolute ethanol has been added before use) to the column. Centrifuge at 12,000 rpm (13,680 × g) for 30 seconds. Discard the flow-through and place the column back into the collection tube.

Note: If the recovered DNA is intended for salt‑sensitive experiments (e.g., blunt‑end ligation or direct sequencing), it is recommended to let the column stand for 2 minutes after adding PW2 before centrifugation.

6. Repeat step 5.

Centrifuge at 12,000 rpm (13,680 × g) for 2 minutes.

Place the column into a clean centrifuge tube and air‑dry it with the lid open at room temperature for 2 minutes to completely evaporate any residual ethanol. Add an appropriate volume of Buffer EB to the center of the membrane (without touching it), let stand for 2 minutes at room temperature, then centrifuge at 12,000 rpm (13,680 × g) for 30 seconds to collect the DNA solution.

Note: The elution volume should not be less than 30 μL, as smaller volumes may reduce recovery efficiency. If the downstream experiment is pH‑sensitive, sterile water can be used for elution. The pH of the elution buffer greatly affects elution efficiency; if using water, ensure its pH is between 7.0 and 8.5 (adjust with NaOH if necessary). A pH below 7.0 results in poor elution. To increase DNA yield, reload the eluate back onto the column and centrifuge again at 12,000 rpm (13,680 × g) for 30 seconds, collecting the DNA solution in the tube.

DNA Concentration and Purity Assessment

The purified DNA fragments can be analyzed by agarose gel electrophoresis and UV spectrophotometry to determine concentration and purity.

DNA concentration is determined by measuring the absorbance at 260 nm (A₂₆₀). If dilution is required, it is recommended to use Buffer EB; diluting with water may lead to inaccurate values. The accurate absorbance at 260 nm should be in the range of 0.1–1.0. An absorbance of 1 unit at 260 nm corresponds to 50 μg/mL for double‑stranded DNA and 40 μg/mL for single‑stranded DNA.

The A₂₆₀/A₂₈₀ ratio should be between 1.7 and 1.9. If ddH₂O is used instead of Buffer EB for elution, the ratio may be lower due to the influence of pH and ions on absorbance, but this does not indicate low purity.

Specifications

Synonyms

Gel Extraction Kit

Specifications & Purity

BioReagent, Suitable for molecular biology

Grade

BioReagent, Suitable for molecular biology

Application

DNA Extraction

Storage and Shipping

Storage

Room temperature

Shipped In

Normal

Stability And Storage

Store at room temperature long term (15 months).

Contents & Storage

A1521384	Component	50T	100T	Storage
A1521384A	Buffer PBD	50 mL	100 mL	RT.
A1521384B	Buffer PW2	12 mL	24 mL	RT.
A1521384C	Buffer EB	15 mL	15 mL	RT.
A1521384D	Spin Column KOS	1 EA×50	1 EA×100	RT.
A1521384E	2 mL Collection Tube	1 EA×50	1 EA×100	RT.
A1521384F	BL buffer	30 mL	60 mL	RT.

Application Protocols

Item-specific, validated protocols are not provided in the Product Data. The following is a generalized workflow for gel extraction (literature; not item-specific). Adjust steps to the kit’s official instructions and your laboratory’s SOPs.

General spin-column workflow

1. Excise band: Visualize briefly (prefer blue light). Trim away excess agarose; weigh the gel slice.
2. Dissolve: Add ~3 volumes dissolve/binding buffer per 1 volume gel. Incubate 50–60°C with intermittent mixing until fully melted and clear.
3. Promote binding: If required by the kit, add alcohol per protocol and mix.
4. Load: Apply the solution to the spin column; centrifuge as directed to bind DNA. For large volumes, load in multiple passes.
5. Wash: Add wash buffer; centrifuge. Repeat if protocol specifies.
6. Dry spin: Centrifuge 1–3 minutes to remove residual alcohol.
7. Elute: Add 20–50 µL nuclease-free water or Tris buffer to the membrane; incubate 1–5 minutes; centrifuge to collect DNA. Optional second elution to boost yield.

Quality control (general)

• Measure concentration by A260 or fluorometry. Check integrity on an analytical gel. Test a small aliquot in PCR/ligation if the application is critical.

Notes

• For small DNA (<100 bp), reduce elution volume and temperature. For large DNA (>10 kb), extend contact time and consider two elutions.

Biological Roles

This section addresses the biomolecular context of the analyte being purified (DNA) rather than the kit itself.

General background (literature)

• DNA is the hereditary polymer of cells, composed of deoxyribonucleotides linked by phosphodiester bonds forming antiparallel strands in a double helix. Sequence encodes genes and regulatory elements, while physical properties (length, GC content, secondary structure) influence enzymatic manipulation.
• In molecular biology workflows, purified DNA fragments from gels are commonly used for subcloning, mutagenesis, assembly (Gibson/Golden Gate), sequencing library construction, and diagnostic genotyping.

Relevance to gel extraction

• Maintaining DNA integrity is critical: minimizing UV exposure and high-temperature dwell reduces nicks and depurination, preserving high transformation efficiency and accurate sequencing.
• Removal of inhibitors (chaotropes, alcohols, agarose remnants) ensures compatibility with polymerases, ligases, and restriction endonucleases.

Quality indicators (general)

• Spectral ratios: A260/280 ~1.8 for pure dsDNA; A260/230 >2.0 indicates low organic/salt carryover (literature).
• Functional tests: Efficient ligation and PCR amplification of the recovered fragment; robust colony formation after transformation.

Note

• No clinical/diagnostic claims are made. Use is limited to research applications per Product Data.

Buffer Applications

The kit is not itself a stand-alone buffering system; however, elution choices and downstream buffer conditions are central to performance. Item-specific buffer specifications are not provided and remain: Not specified for this item; refer to CoA/Spec Sheet.

General guidance (literature; not item-specific)

• Common eluents:
  • Nuclease-free water: pH approx. neutral; ideal for immediate PCR/ligation.
  • Tris-Cl, 5–10 mM, pH 8.0–8.5: balances DNA stability with enzymatic compatibility.
  • TE buffer, 10 mM Tris, 1 mM EDTA, pH 8.0: improved storage stability; EDTA may inhibit Mg2+-dependent enzymes; dilute or re-purify before such reactions.
• Practical tips:
  • Pre-warm eluent to 50–60°C and allow 1–5 min contact on the membrane for larger fragments.
  • For very small DNA (≤100 bp), elute in minimal volume (e.g., 20–30 µL) and consider lowering temperature to reduce diffusion losses.
• Electrophoresis context:
  • Use low-UV-damage stains (e.g., SYBR Safe equivalents) and run gels in TAE for cloning-grade fragments where lower ionic strength reduces heating and DNA damage; TBE provides sharper bands for small fragments but higher borate can persist; thorough washing mitigates carryover (literature).

Recipes (literature examples; not item-specific)

• 10 mM Tris-Cl, pH 8.5: 1.21 g Tris base to 1 L; adjust pH with HCl. Use nuclease-free water and sterile filter.

Green Alternatives

While this product category is inherently enabling (purification rather than synthesis), greener practices can reduce hazards and waste. The following are general, literature-based alternatives and improvements; they are not item-specific.

Opportunities for greener practice

• Reduce chaotrope usage: Minimize dissolve buffer volumes consistent with full gel solubilization.
• Lower alcohol consumption: Use efficient wash protocols; air-dry just enough to remove residual solvent, avoiding repeat washes.
• Alternative recovery methods:
  • Enzymatic agarose digestion (agarase) to release DNA without chaotropes or silica columns.
  • Electroelution or dialysis-based extraction for larger fragments, avoiding high-salt chemicals.
  • Magnetic bead–based size selection/purification using PEG/NaCl systems; often scalable and amenable to automation with reduced plastic waste.
• Illumination choice: Use blue-light or near-UV transilluminators to lower energy exposure and extend DNA integrity, reducing repeats and waste.

Comparison snapshot (general)

• Silica spin columns: Fast, simple, widely compatible; uses chaotropes/alcohol; generates plastic waste.
• Magnetic beads (PEG/NaCl): Tunable size selection; avoids strong chaotropes; requires magnet and optimization.
• Agarase digestion: Gentle on DNA, few hazardous reagents; longer incubation, enzyme cost.

Waste minimization

• Segregate and neutralize chaotrope-containing waste properly; avoid bleach contact. Consolidate alcohol wastes for recycling where supported by institutional programs.

Pharmaceutical Uses

This is a research-use-only DNA purification kit and is not intended as an excipient or for manufacturing of pharmaceutical products.

• Research use only (per Product Data). No GMP, pharmacopeial monographs, or clinical application claims are made here.
• In pharmaceutical R&D laboratories, analogous kits may be used to prepare DNA constructs for discovery research or analytical characterization, but such use remains non-clinical and outside regulated drug product manufacture unless specifically validated under appropriate quality systems.
• For any regulated use, users must qualify the kit and its procedures under their own quality frameworks; item-specific certifications are Not specified for this item; refer to CoA/Spec Sheet and QA documentation.

Physical Properties

Item-specific quantitative properties (exact buffer compositions, pH, densities, refractive indices, UV cutoffs, etc.) are not provided in the Product Data.

Item-specific status

• Form: Kit containing multiple solutions/consumables (exact list not specified)
• Quantitative specs (pH, salt %, alcohol %, conductivity, etc.): Not specified for this item; refer to CoA/Spec Sheet.

General properties of typical DNA gel extraction systems (literature; not item-specific)

• Binding/dissolve buffer: aqueous, high ionic strength with chaotropic agents (e.g., guanidinium salts) to disrupt water structure and promote DNA–silica adsorption; sometimes orange dye indicators to signal pH.
• Wash buffer: aqueous alcohol (ethanol or isopropanol) with low salt to remove proteins, agarose residues, and chaotrope carryover.
• Elution buffer: nuclease-free water or 5–10 mM Tris-Cl, pH ~8.0–8.5 (no EDTA if downstream enzymology is sensitive).
• Temperature effects: elevated temperatures (37–60°C, literature) can accelerate gel dissolution and improve elution efficiency for larger DNA fragments.
• DNA solubility: high in low-ionic-strength aqueous buffers; decreased in high alcohol/chaotrope conditions which favor adsorption to silica.

Notes for practitioners

• Aggressive heating can increase depurination of DNA; balance dissolution rate with integrity (minimize time >60°C).
• For accurate spectrophotometry, ensure complete removal of chaotropes and alcohols; their residual absorbance at 230 nm and 260 nm can bias A260/280 and A260/230 ratios.

Quality & Grades

Item-specific facts

• Grade: BioReagent, Suitable for molecular biology (per Product Data)
• What this typically implies: Components manufactured and handled to minimize nuclease (DNase/RNase) and protease contamination; low bioburden and low trace organics that could inhibit polymerases and ligases.

How to interpret this grade (general guidance)

• Molecular biology suitability focuses on enzymatic compatibility rather than analytical UV transparency or trace metal content. Buffers are prepared using nuclease-free water and cleanroom/aseptic workflows where applicable.
• Each lot should support downstream enzymatic reactions (PCR, restriction digestion, ligation) without measurable inhibition when used as directed.

Verification and documentation

• Certificates of Analysis typically include functional QC (e.g., recovery of a control DNA fragment, absence of DNase activity) and may report pH targets for buffers. For this specific item, any such values are Not specified for this item; refer to CoA/Spec Sheet.

Stabilizers and preservatives

• Not specified for this item; refer to CoA/Spec Sheet. In general, elution buffers for DNA purification avoid EDTA if immediate downstream enzymology is anticipated; some kits may optionally provide TE for long-term DNA stability.

User expectations

• Expect reproducible recovery, low salt/alcohol carryover after recommended spins/dries, and DNA suitable for cloning and sequencing when best practices are followed.

Reaction & Applications

Item-specific applications from the catalog are not listed; below are standard laboratory uses and best practices for DNA gel extraction kits (literature; not item-specific).

Primary application

• Recovery and purification of DNA fragments from agarose gels after electrophoretic separation, yielding DNA compatible with cloning, PCR, restriction digestion, ligation, sequencing, qPCR, and library preparation.

Workflow highlights

• Excise bands under blue light if possible to minimize UV-induced nicking and thymine dimer formation; if UV is used, limit exposure time and wavelength (e.g., 302 nm, short exposure) to reduce damage.
• Gel dissolution: Cut gel to minimal size. Typical dissolve buffer volumes scale with gel mass (literature: ~3 volumes buffer per 1 volume gel). Gentle mixing at 50–60°C accelerates dissolution.
• DNA binding: High-salt/chaotrope conditions and, often, added alcohol promote adsorption to silica matrices.
• Washing: Alcoholic washes remove chaotropes and agarose; ensure complete removal by a final dry spin to prevent carryover.
• Elution: Use low-ionic-strength buffer or water; pre-warm and incubate on the membrane for 1–5 minutes before centrifugation to maximize recovery. A second elution can raise total yield at the expense of concentration.

Performance considerations (general)

• Fragment size: Very small DNA (<70–100 bp) and very large DNA (>10–15 kb) may show reduced recovery; optimize gel percentage, dissolve temperature, and elution conditions accordingly.
• Downstream compatibility: Proper washing/drying ensures minimal inhibition in ligation and PCR. Assess DNA integrity via A260/280 and test PCR if critical.

Reaction Conditions

No item-specific procedural parameters are provided. The following are general, literature-based conditions commonly used with DNA gel extraction kits (not item-specific):

Gel and visualization

• Agarose concentration: 0.8–1.0% for 0.5–10 kb; 1.5–2.0% for 100–1000 bp. Use blue light where possible to reduce DNA damage.

Dissolution and binding

• Slice size: Minimize volume around the band to reduce reagent use.
• Dissolve buffer: ~3 volumes per 1 volume gel (by weight/volume approximation), incubate 50–60°C with occasional mixing until fully liquefied.
• Optional alcohol addition: Some protocols require adding ethanol/isopropanol before loading to promote binding (check kit-specific instructions).

Washing and drying

• Wash buffer: Alcoholic wash(s) per protocol; centrifuge as directed.
• Dry spin: 1–3 minutes to remove residual alcohol completely; longer for large columns.

Elution

• Volume: 20–50 µL typical; smaller volumes increase concentration. Pre-warm eluent to 50–60°C and incubate 1–5 minutes on matrix.
• Repeat elution: A second elution can raise total yield by 5–20% (literature) but reduces concentration.

Expected outcomes (literature)

• Recovery: Often 50–90% depending on fragment size (higher for 200 bp–5 kb; lower for very small/very large DNA).
• Purity: A260/280 ~1.8; A260/230 >2.0 when washes/drying are complete.

Always follow the kit’s IFU/SOP for lot-specific parameters.

Safety & Handling

Item-specific hazard classification is not provided in the Product Data. Always consult the product’s SDS for authoritative information.

Item-specific facts

• GHS classification, pictograms, H-statements: Not specified for this item; refer to SDS.
• Storage: Room temperature (per Product Data). Shipments under normal conditions.

General safety considerations for DNA gel extraction kits (literature; not item-specific)

• Likely hazards: Chaotropic salts (e.g., guanidinium thiocyanate/hydrochloride) are harmful if swallowed, cause skin/eye irritation; alcohol-containing wash buffers are flammable; buffers may be irritants. Some kits include indicators or surfactants with additional hazards.
• Incompatibilities: Avoid mixing guanidinium-containing waste with bleach (risks formation of toxic gases such as cyanogen chloride; literature). Keep alcohol-containing solutions away from ignition sources. Store tightly capped to prevent evaporation of alcohol and pH drift.
• PPE: Laboratory coat, safety glasses or face shield, and appropriate chemical-resistant gloves (e.g., nitrile). Use in a fume hood when heating chaotrope solutions or handling volatile alcohols.
• First aid (overview; defer to SDS): Rinse eyes/skin with water for at least 15 minutes; remove contaminated clothing; if inhaled, move to fresh air; if ingested, seek medical attention.
• Waste: Collect guanidinium- and alcohol-containing liquids separately from halogenated and oxidizing wastes; label according to local regulations.

UV precautions (gel work)

• Minimize UV exposure to prevent DNA damage and personal eye/skin injury. Prefer blue-light transilluminators and wear appropriate PPE shields.

Solvent Selection

This product is a purification kit rather than a solvent. Solvent choice arises when selecting elution medium and during downstream use of the purified DNA.

Item-specific facts

• Exact elution buffer composition is not provided. Any numeric specifications are Not specified for this item; refer to CoA/Spec Sheet.

General guidance (literature; not item-specific)

• Elution options:
  • Nuclease-free water: maximizes compatibility with immediate downstream enzymatic reactions; slightly lower long-term stability versus buffered eluent.
  • Low-salt Tris (e.g., 5–10 mM, pH 8.0–8.5): improves DNA stability without significantly inhibiting most enzymes.
  • TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0): enhances storage stability but EDTA can chelate Mg2+ and inhibit polymerases; dilute or repurify before sensitive enzymology.
• Elution temperature and volume: Warmer eluent (37–60°C) and smaller volumes increase concentration; multiple elutions trade concentration for total yield (literature).
• Wash solvents: Alcohol content aids desalting; ensure complete removal (air-dry spin) to avoid inhibition in PCR/ligation.

Comparison snapshot (general)

• Water: highest enzymatic compatibility; least buffering.
• Tris buffer: balanced compatibility/stability.
• TE: best stability; may require additional cleanup for Mg2+-dependent enzymes.

Tip

• Pre-warm eluent and allow 1–5 minutes of static contact on the matrix before centrifugation to improve recovery of larger fragments.

Storage & Reconstitution

Item-specific facts (from Product Data)

• Storage conditions: Room temperature
• Shipping: Normal
• Appearance/composition details: Not specified for this item; refer to CoA/Spec Sheet.

General guidance for kit components (literature; not item-specific)

• Stability: Most chaotrope and buffer solutions are stable at ambient temperature when tightly sealed. Alcohol-containing washes can evaporate; keep caps closed firmly.
• Precipitates: Some buffers may form salt precipitates at lower temperatures; redissolve by warming to room temperature (or up to ~37–50°C) and mixing before use.
• Nuclease control: Avoid introducing nucleases; use clean tips/tubes and avoid touching column membranes with gloves or tips.
• Reconstitution: If any component ships as a concentrate or requires alcohol addition, follow the product’s IFU. For this specific item, any such requirements are Not specified for this item; refer to CoA/Spec Sheet.
• Shelf life: Not specified for this item; refer to CoA/Spec Sheet.

Storage tips

• Store in a dry location away from strong oxidizers. Do not mix chaotrope-containing waste with bleach. Protect from excessive heat to prevent buffer degradation and evaporation.

Use limitation

• For research use only (per Product Data).

Structure & Identity

Item-specific identifiers (CAS, InChIKey, SMILES, molecular formula/weight) are not applicable to this kit-format product.

Item-specific facts (from Product Data)

• Product type: DNA Gel Extraction Kit (kit of reagents/consumables for nucleic acid purification)
• Grade: BioReagent, Suitable for molecular biology
• Storage: Room temperature; shipped under normal conditions
• Research use note: For research use only

General description (literature/typical kits; not item-specific)

• Typical components: a chaotrope-containing gel-dissolve/binding buffer, silica spin columns or equivalent solid-phase, an alcohol-containing wash buffer, and a nuclease-free elution buffer (water or low-salt Tris).
• Underlying chemistry: DNA binds to silica in the presence of chaotropic salts and alcohol; contaminants are removed by washing; DNA is eluted in low-ionic-strength buffer or water.
• Target material: double-stranded DNA fragments excised from agarose gels (commonly 70 bp to ~10–15 kb, depending on matrix and protocol; literature).

Structural features (general)

• Purified analyte: linear duplex DNA with 3′- and 5′-hydroxyl termini preserved for ligation, PCR, sequencing, etc. No single small-molecule structure applies.

Traceability

• Lot-specific CoA/Spec Sheet will define exact compositions and any stabilizers if present. Values not provided in Product Data should be treated as: Not specified for this item; refer to CoA/Spec Sheet.

Synthetic Utility

As a purification kit, this product is not a chemical reagent for organic synthesis. Its “synthetic utility” pertains to enabling DNA construct assembly and molecular cloning workflows (literature; not item-specific).

Enabling roles

• Fragment isolation: Provides clean, size-defined DNA fragments from agarose gels for downstream assembly (e.g., Gibson Assembly, Golden Gate/Type IIS cloning, ligation-based cloning).
• Quality enhancement: Removal of agarose, salts, and stains reduces inhibition in restriction digests and polymerase reactions, improving assembly yields.

Workflow integration (general)

• After PCR and gel purification, fragments with compatible overlaps/cohesive ends are joined enzymatically. Clean DNA reduces off-target ligation and improves colony counts after transformation.
• For synthetic biology, gel-purified parts lower background from nonspecific amplicons or primer-dimers.

Best practices

• Use low-UV exposure to preserve ends for ligation.
• Thoroughly dry columns after wash steps to remove residual alcohol that would inhibit ligases and polymerases.
• Choose elution buffer compatible with the next enzymatic step (water or low Tris for most assemblies; avoid EDTA before ligation or PCR).

Target Specificity

Not applicable. This product is not an affinity reagent or antibody and has no antigen/epitope specificity. It is a general nucleic acid purification kit designed to recover DNA fragments from agarose gels irrespective of sequence.

Item-specific fields (clone, isotype, host, species reactivity): Not applicable.