NucleoMag NGS Clean-up and Size Select

Macherey-NagelSKU: MN-744970.500

Size: 500


Clean up and size selection of Next Generation Sequencing library preparation reactions

Versatile magnetic bead clean-up for multiple applications

  • Efficient clean-up of NGS library preparation reactions with tunable size selection
  • Standard DNA or RNA post extraction clean-up
  • Scalable PCR clean-up



Application Clean up and size selection for NGS library preps
Shelf life 24 Months
Target Clean up
CE certified No, research use only
Technology Magnetic bead technology
Brand NucleoMag
Format Magnetic beads
Package unit 5 mL, 50 mL, 500 mL
Handling Magnetic separation
Automated use Yes
Sample material Reaction mixtures from NGS library kits
Sample amount 7.5 pg−5 µg nucleic acids in NGS reaction mixtures
Fragment size 150 bp−approx. 800 bp
Typical recovery ≥ 80 %
Elution volume 10−100 µL
Preparation time 40−120 min/96 preps
Typical downstream application Next Generation Sequencing
Storage temperature 4−8 °C
Shelf life (from production) 24 Months
Hazardous material No


Magnetic bead-based DNA and RNA Clean-up

NucleoMag NGS Clean-up and Size Select

Most sequencing platforms for library preparations require enzymatic reaction Clean-up and fragment size selection. NucleoMag NGS Clean-up and Size Select enables Clean-up reactions, as well as single or double sided size selection, to recover the fragment lengths which are needed in your specific application. Simply dilute the magnetic beads to utilize the tunable size selection feature. Dilution ratios are similar to most other comparable magnetic bead products in the market, allowing for the NucleoMag NGS Clean-up and Size Select kit to be used with your current protocols.

Product at a glance

Technology Magnetic beads
Applications Size selection for next-generation-sequencing workflows
PCR Clean-up
RNA or cDNA Clean-up after purifications or enzymatic
reactions (i. e. IVT or DNA digestion)
Recovery 70 – 100 %
Elution volume 10 – 100 μL
Shelf-life (from production) 24 months
Product sizes 5 mL, 50 mL, 500 mL


Schematic Workflow Overview


1. Add bead suspension to your DNA or RNA solution
2. Incubation of magnetic beads with sample for proper binding
3. Removal of contaminants by ethanol washes
4. Dry magnetic beads to allow evaporation of ethanol traces
5. Elution of DNA or RNA
6. Transfer of the final product to a new plate/tube


One Clean-up kit for all samples! 

Use your current protocol. No changes needed.

Application data – DNA Clean-Up and Size Selection

Size selection of fragment mix

For single sided size selection (left or right), the sample is mixed with the beads in predetermined ratios for the desired exclusion of smaller or larger sized fragments. For the double sided size selection, two binding steps are performed to exclude larger fragments above the cut-off and smaller fragments below the lower cut-off.

Reliable reproducibility in DNA clean-up procedures

To assess reproducibility of DNA clean-up, EcoRI-linearized pcDNA 3.1(+) and Ndel-linearized pGEM inserts were purified with four replicates each. For DNA purification, a sample to NGS clean-up suspension-ratio of 1.0 was used. The parallel Clean-up experiments show high reproducibility and recovery of the target DNA.


Fragment size analysis of prepared NGS libraries

NGS libraries were prepared using Truseq* DNA PCR Free kit from Illumina (red), AMPure* XP (blue) and NucleoMag NGS Clean-up and Size Select (green) for Clean-up and size selection steps. (A) Input DNA, 1 μg sheared E. coli DNA. (B) Size distribution of DNA Fragments after library preparation as input for sequencing with expected fragment size of 650 bp (insert + adapters).

Data kindly provided by TAKARA BIO INC.

Sequencing analysis

In order to compare the sequencing performance after library preparation generation different clean-up and size selection products were tested. Performed tests included the distribution of genome sequence coverage (depth of genome base coverage) and effect on GC content on sequence coverage (A) No significant difference in mapped depth of genome base coverage. The constant depth indicates low bias. (B) Horizontal plot pattern of MN beads compared to AMPure* XP beads. After the summary of aligned read bases within a 0.5 kb genome region, the two samples have been normalized / matched resulting in a horizontally pattern showing the similarity of the two samples.

Data kindly provided by TAKARA BIO INC.

Cited in more than 50 publications

The NucleoMag NGS Clean-up and Size Select has been cited in more than 50 peer-reviewed publications. The kit has been used for PCR Clean-ups as well as in next generation sequencing workflows.

Reference list

Application data – RNA Clean-Up

RNA Clean-Up with reliable recovery rates as well as high purities

A) MACHEREY‑NAGEL’s NucleoMag NGS Clean-up and Size Select beads as well as RNAClean* XP beads from Beckman Coulter (BC) were used for Clean-up of RiboRuler High Range Ladder, resulting in recovery rates of 88.6 ± 7.4 % (MN) and 81.5 ± 5.4 % (BC). B) RNA isolated from HeLa cells were used as input for Clean-up reactions which generated improved purities.

Product ng/μL A260 / A280 A260 / A230
MN Beads 14.4 ± 2.1 2.3 ± 0.1 2.5 ± 0.7
RNAClean* XP 14.4 ± 1.6 2.3 ± 0.1 2.2 ± 0.8

High-integrity RNA after Clean-up with NucleoMag NGS Clean-Up and Size Select kit

RNA samples were cleaned-up using the NucleoMag NGS Clean-up and Size Select kit (MACHEREY‑NAGEL) as well as RNAClean* XP beads (Beckman Coulter). 500 ng RNA was used as starting material. The RNA was eluted in 25 μL and analyzed on Agilent’s Bioanalyzer 2100.  No significant difference in RNA integrity has been observed for used products, as integrity values after clean-up are comparable to the input sample (RIN ≥ 9,4).

NucleoMag NGS Clean-Up and Size Select kit is suitable for Clean-ups of RNA transcripts after in vitro transcription reactions

Riboprobe* System – T7 has been used for in vitro transcription of single-stranded RNA using a pGEM* vector. NucleoMag NGS Clean-up and Size Select and RNAClean* XP were used for Clean-up of IVT reactions.





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