This website uses cookies in order to improve our services. If you proceed visiting this website you accept the usage of cookies. For more info please read our Data Privacy statement.

 

DNA Fragment Size Selection & Quantification Solutions for NGS


Sample Preparation |  Fragmentation  |  Fragment Size Selection  |  Quality Control  |  Library Preparation  |  Template Enrichtment/ Sequencing


After DNA fragmentation you will obtain fragments of different sizes. Depending on the method used for fragmentation the resulting fragment size will vary. For optimal and effective sequencing the fragment size should correspond to the possible read length of the used sequencing platform and sequencing protocols. Furthermore, the size selection step can be used to remove possible inhibitors for further downstream applications such as PCR and sequencing. Magnetic bead and spin column based methods are ideal in order to change the storage or reaction buffer of the DNA fragments.

Different fragment size selection and quantification methods exists. Major protocols are based on gels, magnetic beads or spin columns.

Gel based methods enable a relative precise selection of DNA fragments in the desired length (for example between 150 and 200 base pairs). Gel based purification is more time consuming compared to other methods. For third generation sequencing technologies such as Pacific Biosciences, that enable sequencing of ultra-long reads, gel based fragment size selection and purification instruments such as the PippinHT and the BluePippin are recommended.

Spin columns based methods are easy to handle and very fast. This method enables to select fragments in a relative broad range of sizes, normally it is used to exclude short reads (for example reads with less than 150 base pairs).

Magnetic beads are widely used for fragment size selection. The size of the desired fragments can be influenced by the beads to DNA fragments ratio. This method can be used to remove short or very long fragments.


DNA Fragment Size Selection and Quantification Instruments

Agilent 2100 Bioanalyzer

The Agilent 2100 Bioanalyzer system provides sizing, quantitation and quality control of DNA, RNA, proteins and cells on a single platform, providing high quality digital data.
Source: Agilent

Website

E-Gel® Electrophoresis System

Fast, convenient, and easy electrophoresis of nucleic acids in the 20 bp–10 kb size range. The E-Gel® Electrophoresis System is ideal for analyzing PCR products, restriction digests, and plasmid preparations. With E-Gel® EX gels, you can run the gels in as little as 10 minutes and avoid the messy prep work of pouring hot agarose or making buffers and staining gels.
Source: Thermo Fisher

Website

Fragment Analyzer™

Introducing one powerful instrument to cover the full spectrum of DNA, gDNA and RNA quality control. Fragment Analyzer™ does everything from high-resolution analysis to fast DNA separations, across the widest separation range.
Source: Advanced Analytical

Website

LabChip DS

The LabChip DS complements PerkinElmer's existing LabChip GX and LabChip GXII which provides fluorescent, electrophoretic analysis of fragments of nucleic acids and proteins. In addition, preparation of samples for the LabChip DS platform can be performed on PerkinElmer's liquid handling instruments, including the Sciclone® NGS Workstation, which is a robust, scalable platform that has been specifically customized for next generation sequencing methods, or PerkinElmer's Zephyr® Molecular Biology Workstation, which automates a broad range of standard molecular biology kits.
Source: PerkinElmer

Website

LabChip® GX Touch

LabChip® GX Touch microfluidics technology offers unparalleled electrophoresis separation for High Sensitivity DNA/RNA analysis,DNA smear analysis, and RNA and gDNA integrity analysis on one platform. Even occasional or novice users can start running samples quickly with the simple to use touch screen interface and data visualization capabilities.
Source: PerkinElmer

Website

PippinHT

PippinHT incorporates the company’s highly regarded sizing technology and increases throughput to 24 samples per run, compared to a maximum of five with Pippin Prep or BluePippin. The instrument offers an efficient, automated solution for scientists running busy sequencing labs, core facilities, and other laboratories producing large-scale sequencing data.
Source: SageScience

Website

Ranger Technology

Ranger Technology for Automated Agarose Gel DNA Fragment Selection

Website

ZAG DNA Analyzer™

The ZAG DNA Analyzer holds up to nine 96-well deep plates. Unlike slab gels or microfluidic chips, you can quickly and easily fill the plates with a multi-channel pipetter. ZAG also holds two different separation gels which allows you to set up varying runs ahead of time. Simply set it up and walk away. ZAG will automatically switch to the gel you specified when setting up the run. Both capabilities increase the efficiency of your lab.
Source: Advanced Analytical

Website


DNA Fragment Size Selection Kits

Agencourt AMPure XP™

Agencourt AMPure XP™ Bead PCR Purification protocol

Website

E-Gel® SizeSelect™ gels

The E-Gel® SizeSelect™ gels allow users to separate and recover DNA for short read fragment library construction in just 15 minutes. That's 10 times faster than using conventional gels, and purification kits. E-Gel® SizeSelect™ gels are offered in a 2% agarose concentration, and validated for the recovery of fragments in the 150-200bp size range. Once the DNA is recovered, no additional purification step is required before proceeding to the next step in library construction.
Source: Thermo Fisher

Website

EpiNext™ DNA Size Selection Kit

The EpiNext™ DNA Size Selection Kit is a complete set of optimized reagents for quick removal of DNA fragments of <150 bps for library preparation in next generation sequencing applications. The kit utilizes magnetic bead technology and is suitable for Illumina, Life Technologies (SOLiD), Ion Torrent, and Roche/454 platforms. It can also be used for removing undesired larger DNA fragments by optimizing the bead to DNA volume ratio accordingly. The indicated number of reactions can be performed for a standard 50 µl solution input DNA sample.
Source: Epigentek

Website

EpiNext DNA Purification HT System

The EpiNext™ DNA Purification HT System (also known as "EpiNext™ beads" or "MQ beads") utilizes magnetic bead technology for high throughput DNA or PCR amplicon purification and DNA size selection. The system can also be used for concentrating DNA and is suitable for selectively and consistently capturing DNA fragments or PCR amplicons that are 100 bps or larger in size.
Source: Epigentek

Website

GeneRead Size Selection Kit

The GeneRead Size Selection Kit enables precise size selection and purification of DNA fragments using a fast and convenient spin-column-based procedure. The kit contains MinElute columns and an optimized binding buffer for the selection of DNA fragments larger than 150 bp.
Source: Qiagen

GET™ AGAROSE DNA method

GET™ AGAROSE DNA method involves release of nucleic acid fragments from gel pieces followed by capture of nucleic acids on the GET™ Spin Columns, washing, and elution of the clean nucleic acid fragments in a suitable buffer. (100-20000 bp fragments)
Source: Gbiosciences

Website

MagJET NGS Cleanup and Size Selection kit

Thermo Scientific MagJET NGS Cleanup and Size Selection kit, sufficient for 1 x 96 preps, is designed for efficient and robust DNA fragment library cleanup and size-selection from a variety of enzymatic reaction mixtures including PCR, ligation, adapter addition and DNA end-repair reaction mixes. The kit utilizes high-capacity MagJET paramagnetic bead technology that ensures efficient recovery of DNA fragment library within a desired fragment length range. The purified DNA fragments are free of any next-generation sequencing workflow inhibiting components, such as sequencing adapters, primer dimers, unincorporated nucleotides, enzymes or salts, and are ready-to-use in downstream NGS applications.
Source: Thermo Fisher

Website

MagSi-NGSPREP

MagSi-NGSPREP provides a convenient tool for ultra-fast and efficient purification and size selection of DNA products. DNA fragments will be bound directly onto the surface of the magnetic beads, leaving unincorporated nucleotides, primers, primer dimers, and other contaminants in solution. Finally, the DNA fragments are eluted with low salt buffer or reagent grade water. The technology for binding of DNA fragments onto the applied magnetic nanoparticle surface does not require use of any hazardous chaotropic buffers. The purification protocols are optimized to provide high yield and purity of the recovered DNA fragments. MagSi-NGSPREP allows either non-selective binding, or size-targeted binding of double-stranded DNA fragments ranging from 80 to 1000 bp with specific reagent volume:sample volume ratio's. By increasing the volume of MagSi-NGSPREP, the efficiency of binding smaller fragments increases. This enables the user to selectively keep or discard undesired fragment sizes.
Source: Magna Medics

Website

Novex® TBE Gels

Novex® TBE Gels provide the highest resolution possible for analyzing restriction digests and PCR products. DNA fragments are clearly resolved into sharp, tight bands. Novex® TBE gels are designed to run on the XCell SureLock® Mini-Cell.
Source: ThermoFisher

Website

Select-a-Size DNA Clean & Concentrator™

The Select-a-Size DNA Clean & Concentrator™Kit (Select-a-Size DCC™) provides the quickest and easiest method for purifying a desired range of DNA fragments sizes from library preps, PCR, endonuclease digestions, ligations, etc. Simply adjust the binding conditions for the desired cutoff, bind, wash, and elute. Selectively recover ≥300 bp, ≥200 bp, ≥150 bp, ≥100 bp, ≥50 bp DNA fragments or perform a double size selection. Unique Zymo-Spin column technology yields high-quality DNA in just minutes that is suitable for next generation sequencing, PCR, and other downstream applications. The entire purification procedure can be performed in as little as 7 minutes for 2 preps or 20 minutes for 24 samples.
Source: Zymo Research

Website

Wizard® SV Gel and PCR Clean-Up System

The Wizard® SV Gel and PCR Clean-Up System is designed to extract and purify DNA fragments of 100bp to 10kb from standard or low-melting agarose gels or to purify products directly from PCR and other common reactions such as restriction digests. Up to 95% recovery is achieved depending upon the DNA fragment size. PCR products are commonly purified to remove excess nucleotides and primers. This membrane-based system, which can bind up to 40μg of DNA, allows recovery of isolated DNA fragments or PCR products in as little as 15 minutes, depending on the number of samples processed. The purified DNA can be used for automated fluorescent DNA sequencing, cloning, labeling, restriction enzyme digestion or in vitro transcription/translation without further manipulation.
Source: Promega

Website


NGS Library Purification Kits

NGS Library Cleanup

NGS Library Cleanup (different magnetic bead based kits for RNA/ DNA extraction and library clean up, normalization, purification

Website

Ion AmpliSeq™ Dynabeads® Cleanup Module

The Ion AmpliSeq™ Dynabeads® Cleanup Module is a magnetic bead-based purification kit used in the construction of RNA libraries for sequencing on the Ion Personal Genome Machine® (PGM™) or Ion Proton™ sequencer. This module is included in the Ion AmpliSeq™ RNA Library Kit, but may be purchased separately if additional modules are needed. For RNA library construction using the Ion AmpliSeq™ RNA Library Kit, the module is used for cleanup after the cDNA synthesis and PCR amplification steps. The module employs Dynabeads® magnetic beads for DNA adsorption and separation, rather than traditional filter columns, for quick and easy processing and simplified automation.
Source: Thermo Fisher

Website


For more information see also Quality Control and Quantification.