Monarch® PCR & DNA Cleanup Kit (5 μg)

Description

 
The Monarch PCR & DNA Cleanup Kit rapidly and reliably purifies up to 5 μg of concentrated, high-quality DNA from PCR and other enzymatic reactions. The kit utilizes a bind/wash/elute workflow with minimal incubation and spin times. The columns ensure zero buffer retention and no carryover of contaminants, enabling elution of sample in volumes as low as 6 μl. The buffers provided have been optimized, and do not require monitoring of pH. Eluted DNA is ready for use in restriction digests, DNA sequencing, ligation and other enzymatic manipulations. Designed with sustainability in mind, Monarch kits use significantly less plastic and responsibly-sourced, recyclable packaging. The protocol can also be modified to enable the purification of smaller DNA fragments, including oligonucleotides.

View our videos on protocols, tips, and recycling Monarch.

 
APPLICATIONS
PCR cleanup DNA from PCR reactions can be purified after amplification to remove polymerases, primers, detergents, dNTPs, etc.
Enzymatic reaction cleanup Modifying enzymes such as ligases, kinases, nucleases, phosphatases are efficiently removed allowing efficient desalting and concentration of the DNA sample.
cDNA cleanup DNA/RNA complexes can be purified post-reverse transcription/amplification to enable removal of the RT and polymerase as well as nucleotides.
Labeling cleanup Unincorporated radiolabeled or fluorescently labeled nucleotides can be removed from the DNA substrate
Plasmid cleanup Plasmid preps from unknown sources may contain inhibitors and unwanted contaminants. Purification and concentration can be easily achieved using this kit.
Oligonucleotide cleanup ssDNA oligonucleotides (≥ 18 nt) and dsDNA fragments (≥ 15 bp) can be purified using the Oligonucleotide Cleanup Protocol.


Monarch DNA Cleanup Column Design
Monarch DNA Cleanup Column Design

Monarch columns are designed for performance
Monarch columns are designed for performance. Monarch columns are designed without a frit, which eliminates buffer retention and the risk of carryover contamination, providing fast, worry-free DNA purification.
Monarch columns are designed without a frit, which eliminates buffer retention and the risk of carryover contamination, providing fast, worry-free DNA purification.

 Advantages:
  • Elute in as little as 6 μl
  • Prevent buffer retention and salt carry-over with optimized column design
  • Save time with fast, user-friendly protocols
  • No need to monitor pH
  • Buffers and columns available separately
  • Significantly less plastic used when compared with other kits 
  • Responsibly-sourced and recyclable packaging 

Specifications

DNA Sample Type: DNA from PCR and other enzymatic reactions (e.g., restriction digests, kinase reactions, ligations).*
Binding Capacity: up to 5 μg
DNA Size Range: ~50 bp to 25 kb **
Typical Recovery: DNA (50 bp to 10 kb): 70–90% / DNA (11–23 kb): 50–70%
Elution Volume: ≥ 6 μl
Purity: A260/280 > 1.8 and A260/230 > 1.8
Protocol Time: 5 minutes of spin and incubation time
Compatible Downstream
Applications:
ligation, restriction digestion, labeling and other enzymatic
manipulations, library construction and DNA sequencing.

* ssDNA or dsDNA oligonucleotides from enzymatic reactions can also be purified using the Oligonucleotide Cleanup Protocol .
** DNA ≥ 15 bp to 25 kb (dsDNA) and DNA ≥ 18 nt to 10 kb (ssDNA) can also be purified using the Oligonucleotide Cleanup Protocol.
 

Monarch PCR & DNA Cleanup Kit (5 µg) Protocol 
Monarch PCR & DNA Cleanup Kit (5 µg) Protocol

Monarch PCR & DNA Cleanup Kit (5 μg) performs equivalently to the leading supplier
Monarch PCR & DNA Cleanup Kit (5 μg) performs equivalently to the leading supplier. Preps were performed according to recommended protocols. 1 μg of a 3 kb DNA fragment was incubated with 1 μM primers and OneTaq® Quick-Load® 2X Master Mix (NEB #M0486). DNA was eluted in 20 μl (NEB) and 40 μl (Qiagen) Elution Buffer. Half of the total elution volume was digested with 5 units of DraIII-HF® (NEB #R3510). The digest and the unused portion of the elution were resolved on a 1% w/v agarose gel along with a representative sample of the starting material.
Preps were performed according to recommended protocols. 1 μg of a 3 kb DNA fragment was incubated with 1 μM primers and OneTaq® Quick-Load® 2X Master Mix (NEB #M0486). DNA was eluted in 20 μl (NEB) and 40 μl (Qiagen) Elution Buffer. Half of the total elution volume was digested with 5 units of DraIII-HF® (NEB #R3510). The digest and the unused portion of the elution were resolved on a 1% w/v agarose gel along with a representative sample of the starting material. 
Monarch PCR & DNA Cleanup Kit (5 μg) removes low molecular weight primers from dsDNA samples
Monarch PCR & DNA Cleanup Kit (5 μg) removes low molecular weight primers from dsDNA samples. Three independent amplicons (267 bp, 520 bp, 1003 bp) were spiked with two oligonucleotides (16-mer, 24-mer) to a final concentration of 1 μM. Half of each mix was purified with the Monarch PCR & DNA Cleanup Kit (5 μg) following the included protocol. Equivalent fractions of the original mixture and the eluted material were resolved on a 20% TBE acrylamide gel at 100V for one hour and stained with SYBR Green II.
Three independent amplicons (267 bp, 520 bp, 1003 bp) were spiked with two oligonucleotides (16-mer, 24-mer) to a final concentration of 1 μM. Half of each mix was purified with the Monarch PCR & DNA Cleanup Kit (5 μg) following the included protocol. Equivalent fractions of the original mixture and the eluted material were resolved on a 20% TBE acrylamide gel at 100V for one hour and stained with SYBR Green II.

Learn More About Monarch

Kit Components

The following reagents are supplied with this product:

Store at (°C)Concentration
Monarch® DNA Cleanup Binding Buffer251X
Monarch® DNA Wash Buffer255X
Monarch® DNA Elution Buffer251X
Monarch® DNA Cleanup Columns (5 μg)25

Advantages and Features

Features

  • Elute in as little as 6 μl
  • Prevent buffer retention and salt carry-over with optimized column design
  • Save time with fast, user-friendly protocols 
  • No need to monitor pH
  • Buffers and columns available separately
  • Responsibly-sourced and recyclable packaging
  • Significantly less plastic used when compared with other kits

Properties and Usage

Storage Temperature

25°C

Troubleshooting

Troubleshooting


Low DNA Yield

  • Reagents added incorrectly. Check protocol to ensure correct buffer reconstitution, order of addition for buffers, and proper handling of column flow-through and eluents.
  • Incomplete elution during prep. Ensure the DNA Elution Buffer is delivered directly to the center of the column so that the matrix is completely covered and elution is efficient. Larger elution volumes and longer incubation times can increase yield of DNA off the column at the cost of dilution of the sample and increased processing times. For typical fragments below 10 kb, the recommended elution volumes and incubation times should be sufficient, unless the maximal yield is desired. For the purification of larger fragments, heating the DNA Elution Buffer to 50°C prior to eluting and extending the incubation time after buffer addition to 5 minutes can improve yield. Additionally, multiple rounds of elution can be employed to increase the amount of DNA eluted, at the expense of dilution of the sample.
Low DNA Performance
  • Ethanol has been carried-over. Ensure final wash spin time is 1 minute to ensure complete removal of the wash buffer from the column, and be careful when transferring the column to a new tube for elution step to ensure column tip does not contact column flow-through.
  • Trace amounts of salts that produce low OD260/230 ratios can also be carried over during the elution step. Be careful when transferring column to new tube for elution step to ensure the column tip does not contact column flow-through.
View full Troubleshooting Guide for Nucleic Acid Purification

Notes

  1. The kit should be stored at room temperature. Always keep buffer bottles tightly closed and keep columns sealed in the enclosed zip-lock bag. For information regarding the composition of buffers, please consult the Safety Data Sheets. Proper laboratory safety practices should be employed, including the use of lab coats, gloves and eye protection.

FAQs

  1. Can I use water to elute the DNA when using the Monarch Kits?
  2. What is the smallest volume of elution buffer that can be used with the Monarch DNA Cleanup Column?
  3. What is the composition of each buffer provided with the Monarch PCR & DNA Cleanup Kit (5 μg)?
  4. What is the maximum binding capacity of the Monarch DNA Cleanup Column provided with the Monarch PCR & DNA Cleanup Kit (5 μg)?
  5. What factors affect my (A260/A230)?
  6. What size primers can be effectively removed from a PCR reaction?
  7. Can the Monarch PCR & DNA Cleanup Kit (5 μg) be used to purify RNA?
  8. Do you have any recommendations for purification of ssDNA?
  9. Are the columns in the Monarch PCR & DNA Cleanup Kit (5 μg) the same as the ones in the Monarch DNA Gel Extraction Kit?
  10. What size of DNA can be purified with the Monarch DNA Cleanup Columns?
  11. After purification, I see a faint additional band running below the expected size on a gel. What happened?
  12. Are Monarch spin columns compatible with Vacuum Manifolds?
  13. Can I use the Monarch DNA & PCR Cleanup Kit to purify oligonucleotides and other short DNA fragments?

Tech Tips

Monarch PCR & DNA Cleanup Kit protocol
Learn how to isolate DNA from your enzymatic reactions, including PCR, using the Monarch PCR & DNA Cleanup Kit (5 µg).
Tips for using the Monarch PCR & DNA Cleanup Kit
Optimize your DNA isolation from PCR and other enzymatic reactions with our quick tips for using the Monarch PCR & DNA Cleanup Kit.
How to recycle your Monarch Kit components
Learn how you can easily recycle all of the components in your Monarch Kits.

Protocols

  1. Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030)
  2. Quick Protocol for Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)
  3. Oligonucleotide Cleanup Using Monarch® PCR & DNA Cleanup Kit (5 μg) Protocol (NEB #T1030)
  4. Quick Protocol for Oligonucleotide Cleanup Using the Monarch® PCR & DNA Cleanup Kit (5 μg) (NEB #T1030)

Manuals

The Product Manual includes details for how to use the product, as well as details of its formulation and quality controls. The following file naming structure is used to name these document files: manual[Catalog Number].

Troubleshooting Guides

Quality Control

Quality Assurance Statement

  • The product is tested in a RNA capping reaction using the Vaccinia capping enzyme.

Safety Data Sheet

The following is a list of Safety Data Sheet (SDS) that apply to this product to help you use it safely.