The series of DNA Size Selection Kits (Magnetic Beads) were developed for DNA size selection using magnetic beads. A total of 11 kits are available, with different selection ranges spanning from 50 bp to over 10 kb. The kits provide a simple and quick approach for the enrichment of a specific range of DNA fragments. The kit workflow allows double-sided or single-sided size selection for specific size cutoffs.

Gel images of different ranges of size selection. Sheared human genomic DNA was used as input.

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DNA size selection is a selective capture of DNA fragments of a specific range of size for next-generation sequencing (NGS) library preparations, PCR, ChIP assay, DNA ligations, endonuclease digestions, adapter removal, and other genomics and molecular biology applications. DNA size selection is preferred after NGS library prep in most of the cases. The NGS library preparation is related to the quality of the sequencing data. Precise NGS library size selection can increase sequencing efficiency, improve data quality, and reduce costs.

There are two types of sequencing technologies: short-read sequencing and long-read sequencing. Short-read sequencing uses DNA libraries that contain small insert DNA fragments of similar sizes, usually several hundred base pairs. The sequencing efficiency can be improved if the DNA size selection is in the right range. Cat.# 20104S and 20104L are the best kits for NGS library size selection of illumina paired-end 100 (PE100) sequencing with 100-200 bp library inserts; Cat.# 20105S and 20105L are the best kits for NGS library size selection of illumina paired-end 150 (PE150) sequencing with 150-300 bp library inserts; and Cat.# 20106S and 20106L are the best kits for NGS library size selection of illumina paired-end 300 (PE300) sequencing with 300-600 bp library inserts.

Long-read sequencing uses a large DNA fragment as input and makes very long reads. Usually, library size selection is preferred to remove smaller fragments. Cat.# 20110S and 20110L are the best kits for long-read sequencing size selection with DNA sizes >5 kb, and Cat.# 20111S and 20111L are the best kits for long-read sequencing size selection with DNA sizes >10 kb.

The magnetic beads technology uses paramagnetic particles, also known as SPRI (Solid Phase Reversible Immobilization) beads, to bind DNA reversibly and selectively. DNA fragments can be size-selected and purified by changing the properties of the magnetic beads or SPRI beads. The magnetic beads can easily separate the beads-binding DNA from the contaminants and unwanted components in the samples. The samples after DNA size selection are free of contaminants such as buffer components, enzymes, proteins, salts, dNTPs, primers, and adapters. Our proprietary magnetic beads reagents improve yield, selectivity, and reproducibility.

Specific DNA fragments at a certain length range can be purified simply using magnetic separation with different beads components, avoiding tedious and time-consuming gel extraction and column-based purification. The magnetic beads method is popular for common DNA size selection, including library size selection. The first beads-binding step, referred to as the right-side clean-up, removes large DNA fragments. The large DNA fragments are bound to the beads and are discarded. The desired DNA fragments in the supernatant are transferred to a new well, and new beads are added to the supernatant for the second beads-binding, referred to as the left-side clean-up. The double-size selected DNA fragments are eluted after ethanol rinsing.

DNA size selection with dual clean-ups.

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A single clean-up is needed for DNA size selection with large fragments. In this case, only the large DNA fragments are bound to the beads. The selected larger DNA fragments are eluted after ethanol rinsing.

DNA size selection with single clean-up for >5 kb and >10 kb DNA.

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Features of DNA size selection and library size selection

• • • High specificity and high recovery of size selection
    • 11 selection ranges are available, including 5 ranges for NGS library size selection
      • • 50-100 bp
        • 100-200 bp
        • 200-500 bp
        • 250-350 bp: ideal for illumina PE100 sequencing
        • 300-450 bp: ideal for illumina PE150 sequencing
        • 450-750 bp: ideal for illumina PE300 sequencing
        • 500-1000 bp
        • 1-3 kb
        • 1-5 kb
        • >5 kb: ideal for long-read sequencing
        • >10 kb: ideal for long-read sequencing
    • Fast and simple
      • • 20-min protocol
        • No gel purification required
        • No columns required
        • No centrifugation required
    • Efficient removal of contaminants and unwanted components

Introduction

This kit provides fast purification of high-quality RNA from cells, tissues, and yeast using silica-membrane spin columns with a binding capacity of 100μg RNA. There is no need for phenol/chloroform extractions and time-consuming steps such as CsCl gradient ultracentrifugation or isopropanol precipitation. RNA purified using the HiPure Total RNA Purification System can be used for applications such as RT-PCR, Northern blotting, poly A+ RNA (mRNA) purification, nuclease protection, and in vitro translation.

Details

Specifications

Features	Specifications
Main Functions	Isolation total RNA (not include miRNA) from 20mg tissue, 150mg plant, 5 x 106 cell using two columns (gDNA removed column)
Applications	RT-PCR, qRT-PCR, Northern hybridization, second generation sequencing
Purification method	Mini spin column
Purification technology	Silica technology, DNA filtration technology
Process method	Manual (centrifugation or vacuum)
Sample type	Animal soft tissue, cultured cells, lymphocytes, simple plant tissue
Sample amount	Cells:≤1 x 107 Animal tissue sample: 1-20 mgPlant tissue: 50-150 mg
Yield	2-100μg
Elution volume	≥50μl
Time per run	≤25 minutes（1-24 samples）
Liquid carrying volume per column	800µl
Binding yield of column	100µg

Principle

The Kit isolates total RNA from up to 10⁷ cells or 20 mg tissue. A short workflow enables RNA isolation with genomic DNA removal in less than 25 mins. Samples are first lysed and homogenized. The lysate is passed through a DNA Mini column, ethanol is added to the flow-through, and the sample is applied to a RNA column. RNA binds to the membrane and contaminants are washed away. High-quality RNA is eluted in as little as 30µl water using the Kit.

Advantages

• Efficient removal of DNA – unique genomic DNA removal column without DNase treatment
• High quality – high purity total RNA can be directly used in various sensitive downstream applications
• Fast – several samples can be extracted in 25 minutes by column method
• Safe – no phenol chloroform extraction required
• Sensitive – RNA can be recovered at the level of PG

Kit Contents

Contents	R411102	D411103
Purification Times	50 Preps	250 Preps
HiPure DNA Mini Columns	50	250
HiPure RNA Mini Columns	50	250
2ml Collection Tubes	100	2 x 250
Buffer RLC	50 ml	200 ml
Buffer RW1	50 ml	200 ml
Buffer RW2*	12 ml	2 x 50 ml
RNase Free Water	10 ml	30 ml

Storage and Stability

HiPureKit can be stored dry at room temperature (15-25°C) and are stable for at least18 months under these conditions. During shipment, crystals or precipitationmay form in the Buffer RLC. Dissolve by warming buffer to 37°C.

This kit provides fast purification of high-quality RNA from cells, tissues, and yeast using silica-membrane spin columns with a binding capacity of 100μg RNA. There is no need for phenol/chloroform extractions and time-consuming steps such as CsCl gradient ultracentrifugation or isopropanol precipitation. RNA purified using the HiPure Total RNA Purification System can be used for applications such as RT-PCR, Northern blotting, poly A+ RNA (mRNA) purification, nuclease protection, and in vitro translation.

Permagen’s most universal bar magnet plate. From PCR plates to almost any microplate including deep well, flat bottom, pyramid bottom, round bottom, full-skirt PCR, and 1/2 skirt PCR the MSPU650 has you covered

SBS SLAS Footprint (127.75mm x 85.50mm) to fit into any automated liquid handling robot 

Features include solid aluminum alloy construction and hard coat anodized finish for years of trouble-free use, and compatible with any magnetic bead

SKU #

MSPU650

Features

• SBS/ SLAS footprint
• Solid Aluminum alloy design
• Precision manufactured for more consistent results
• Fast magnetic bead separations
• Integrated corner brackets to help keep microplate in place
• Made in USA 
• For Research use only

Compatibility

• Round bottom plates 
• Pyramid bottom plates 
• Flat Bottom plates
• Deep well plates
• PCR Plates (Full-skirt)
• Any magnetic beads
• Any common liquid handlers i.e. Tecan®, Opentrons®, Hamilton®, Agilent®, Beckman®, etc

Volumes

Minimum – 30 µL (PCR Plate)

Maximum – 2 mL (Deep Well Plate)

Permagen’s most universal bar magnet plate. From PCR plates to almost any microplate including deep well, flat bottom, pyramid bottom, round bottom, full-skirt PCR, and 1/2 skirt PCR the MSPU650 has you covered