Nucleic Acid Extraction and Purification Technologies

Nucleic acid extraction and purification technologies

For research use only. Not for use in diagnostic procedures Extraction and DNA extraction purification solutions chemistries from LGC, Biosearch QuickExtract For DNA screening and genotyping-type Technologies applications, PCR-grade genomic DNA is sufficient, which can be rapidly and efficiently extracted using QuickExtract™ DNA Extraction Biosearch Technologies is unique in the nucleic DNA extraction chemistries Solution. In 3-8 minutes, and using only a single- acid extraction and purification marketplace, QuickExtract 3 tube protocol, PCR-grade genomic DNA from in that we are both a service provider, and almost any sample type can be extracted, without a developer of proprietary chemistries and DNA purification chemistries the use of centrifuges or spin-columns (Figure 1). instrumentation. We develop chemistries and 4-6 PCR-grade purifications – Kleargene instrumentation for customers to use in their NGS-grade purifications – sbeadex (plant, dd saples own laboratories, and it is these same products livestock, blood) QuickExtract Solution has been used to which we use in each of our service laboratories. extract DNA from samples such as hair This allows Biosearch Technologies to be highly DNA/RNA/total nucleic acid follicles, quill-end cells of feathers, tissue- flexible, and offer individual solutions for each of 7 purification chemistries QuickExtract culture cells, buccal cells, zebrafish organs solution our customers. MasterPure and scales, and mouse tail snips. The extracted DNA is suitable for PCR analyses To provide the most efficient and effective Heat at ˚ for inutes 8 Automation and ˚ for inutes (Figure 2), such as genomic, transgenic, extraction or purification method, we offer not or viral DNA screening in animals, or for only a range of different technologies but also the genetic or environmental research and capability to develop tailor-made kit systems for all Purification services screening in humans and other organisms. applications and downstream requirements. 9 DNA purification services Figure 1: Procedure for obtaining PCR-ready RNA purification services PCR-ready DNA using QuickExtract DNA DNA Extraction Solution. Our range of technologies allows delivery of optimised extractions and purifications from an Overview unrivalled array of matrices including: 10 The range of QuickExtract Extraction Solutions for • Plant material (including leaves, seeds, and 11 Order information additional sample types includes: other plant matrices) • Livestock samples (including blood, animal • QuickExtract DNA Extraction Solution tissue, hair follicle, buccal swabs and saliva) • QuickExtract FFPE DNA Extraction Solution • Human samples (including blood, tissue and • QuickExtract Plant DNA Extraction Solution forensic samples) • QuickExtract RNA Extraction Solution • Plasmid preparations • Bacteria, prokaryotes and other Figure 2: Samples extracted with QuickExtract DNA Extraction Solution. PCR was performed using primers to amplify the regions indicated: Lanes microorganisms 1-3, human β-globin; lane 4, transgenic mouse GAPDH; lane 5, E. coli 16S ribosomal RNA gene; lane 6, transgenic SV40 T antigen.

2 3 need of a drying stage, and minimising any sbeadex plant contaminating ethanol carryover into the final DNA purification eluate. The switch between binding mechanisms Plant samples are often challenging due to also allows for greater purity of nucleic acids. secondary metabolites, high levels of sugars and polyphenols, or robust cell walls. sbeadex plant chemistries The advantages of sbeadex include: protocols for leaf and/or seed material from a broad range of plant species have been validated and Kleargene has been highly optimised for • High-quality DNA: suitable for all genomic- can be automated on all open platforms, including PCR-grade DNA automation with both 96-well formats (plant and applications (including NGS) the Biosearch Technologies oKtopure. Validated tissue) and 384-well formats (plant), achieving • Compatible with Biosearch Technologies sbeadex purification protocols have been developed purifications higher throughput than comparable purification automated Oktopure platform. for the following plant species (Table 3): technologies. • Automation-friendly: suitable for most popular magnetic-based robotic platforms The advantages of Kleargene include: • Tailor-made lysis conditions according to Plant species with validated sbeadex Kleargene purification protocols customer requirements Aphid, soybean Cucumber Rice, Asian (Oryza Kleargene purification chemistry uses spin- • High throughput DNA purifications (96-well • Quicker results: purification-time optimisation (Aphis glycines) (Cucumis sativus) sativa) plates and a glass-fibre support to purify DNA and 384-well formats) • Flexible batch sizes and kit volumes Aubergine Sunflower Pepper (Capsicum using polar interactions to generate PCR-grade • Semi-automated (via Biosearch Technologies • No organic solvents in final wash buffer: results (Solanum (Helianthus annuum) DNA, applicable with high throughput methods. Genespin platform) in higher purity melongena) annuus) Barley Tomato Protocols have been optimised for both plant and • Manual high throughput purifications (via • No salts in eluates: high OD260/230 Potato (Solanum (Hordeum tuberosum) (Solanum animal purifications, and the Kleargene chemistry centrifugation) vulgare) lycopersicum) can generate yields between 100 ng and 10 µg • Broad range of sample types (plant leaves, sbeadex feature Specification Rapeseed/Canola/ Beet, sugar Oilseed (Brassica DNA from samples ranging from plant leaf tissue plant seeds, animal tissue) Colour Dark brown (Beta vulgaris) Wheat (Triticale) and plant seeds to rodent tails (Figure 4). • High yield of DNA (PCR-grade) napus) Proprietary double-coated Superparamagnetic technology (competitor: single- bead structure Table 3: Examples of plant species, which have validated purification coated) Amount of protocols using sbeadex chemistry. Kit Application areas Expected yield Irregular starting material Size and shape 80% 5-10 µm (diameter); a; <53 µm Amount Kleargene spin Application Expected Faster discovery of new traits resulting >6 leaf punches 5 µg Kit of starting 96-well plates Maximum capacity 2 µg DNA/mg sbeadex particle areas yield Table 1: Scales in faster to market. No laboratory at your material of available Kleargene spin location required 2-3 leaf punches 1.5 µg Binding material and 2-step binding mechanism: first Kleargene kits. 384-well plates technology silica and second DNA adaptor sbeadex mini 20 – 30 mg 2 µg plant Purification format 96 Plant leaves; Plant seeds generation sequencing applications can be met sbeadex KingFisher (lab validated); applicable by Biosearch Technologies portfolio of sbeadex® Automation maxi 80 – 100 mg 10 µg Next-generation with alternative open liquid handlers plant chemistries. All sbeadex kits use surface modified Blood; plant; livestock; forensics; Sample material sequencing-grade superparamagnetic particles that bind nucleic plasmids; other human samples Table 4: Scales of available sbeadex plant kits.

acids via a novel, two-step binding mechanism PCR; KASP®; BHQ® Probe purifications (Figure 3). Firstly, the nucleic acids affix to the Application chemistry; Sanger; NGS; Microarrays beads via polar interactions, and secondly, the nucleic acids are bound via an affinity-driven Storability >12 months sbeadex mediator. This second binding step allows the final Table 2: Features and specification of sbeadex beads. wash steps to be carried out using water-based The requirement to generate high quality and wash solutions, eliminating the quantity DNA for PCR, sequencing and next- sbeadex chemistry can be used for a variety of species, by modifying the lysis conditions. Although

Figure 3: Standard work our standard protocols already deliver high quality flow for all sbeadex-based purification chemistry DNA, sbeadex can be customised and optimised according to customer requirements. 4 5 sbeadex livestock The majority of NGS-based genomic analysis DNA/RNA/total technologies (including those working with livestock samples) typically require high-quality DNA preparations which are often challenging nucleic acid purification and labour-intensive to produce. sbeadex livestock is based on one protocol which can be used for all sample types and the oKtopure chemistries can be used for all livestock samples (excluding blood). • Genomic DNA and cDNA cloning MasterPure • PCR, qPCR, RT-PCR and qRT-PCR • Microarray analysis (including CGH and gene Some applications require flexibility of isolating expression profiling) Sample type Animal species sbeadex blood high-molecular weight genomic DNA, total cellular RNA or total nucleic acid from the same The kit uses a scalable salt-precipitation protocol Bovine Blood* Blood samples can often vary considerably in Chicken sample. The MasterPure™ Complete DNA and which eliminates the need for hazardous Hair follicle Dog quality, and this can lead to wide variations in the Saliva RNA Purification Kit allows for isolation of NGS- chemicals (no need for phenol, chloroform or Fish consistency and yield of extracted DNA. sbeadex Semen Goat grade DNA, RNA or total nucleic acid in 30–60 guanidine). Depending on the amount of nucleic Tissue (e.g. ear punch) blood provides high yields of high-molecular Horse minutes using a single kit, and is suitable for many acid required, and size of the sample, different Buccal swab Sheep weight, double-stranded DNA from different FTA cards different sample types. MasterPure kits are available, including: Pig blood preparations including those treated with anticoagulants, including: Applications for the MasterPure kit include: • MasterPure Complete DNA and RNA Table 5: Sample types from different species applicable with the sbeadex • Library preparation for next-generation Purification Kit livestock kit. *Not compatible with the Oktopure. • EDTA blood sequencing of genomic DNA and RNA • MasterPure DNA Purification Kit for Blood • Heparin blood • DNA methylation studies (for example, with use • MasterPure Gram Positive DNA Purification Kit • Citrate blood with the Illumina® Infinium® HumanMethylation • MasterPure Yeast RNA Purification Kit • Buffy coat preparations BeadChips)

Amount Application Expected Kit of starting areas yield material Large volume DNA purifications Whole blood; sbeadex Biobanking and other human research markets offers two cost-effective, easy and rapid methods for buffy coat 100-200 µL 4-12 µg blood preparations require large volume purification technologies which the purification of DNA from large volume samples provide high quality DNA. Biosearch Technologies (Table 9): Table 6: Scales of available sbeadex blood kits. Features Kleargene XL PLUS XL

Detergent-driven cell lysis, followed by DNA cell-components are enriched, and guanidine-based purification with DNA residual proteins are digested away. Technology binding to silica particles. Contaminants are The DNA is subsequently precipitated, removed using organic solvent-based wash washed, dried, and then resuspended. steps, followed by elution.

Automation Manual purifications only Manual purifications only

Applications NGS-grade NGS-grade

Starting volume Scalable: Up to 10 mL Scalable: Up to 10 mL

Whole blood; Saliva (including Oragene Whole blood; Saliva (including Oragene Sample types collection tubes); Tissue; collection tubes); Tissue; Table 7: Key features of large volume DNA Typical DNA yields 10-800 µg 10-800 µg purification chemistries. 6 7 One example for the need of high throughput molecular biology-based technologies is for plant Automation and livestock breeders to accelerate their breeding Purification services programmes. Throughput, DNA quality, downstream application requirements, required labour We at Biosearch Technologies have developed and running costs are the main drivers and deciding Feature Customer benefit factors when selecting high throughput automation purification for both DNA and RNA protocols from Flexible high-throughput platforms. Biosearch Technologies can offer both a wide range of starting materials and volumes laboratories utilising our Applicable for any project the oKtopure™ and Genespin™ to meet these which enable the delivery of services for most oKtopure and Genespin size and sample type. systems. requirements, which allows for standardised, (semi) applications or custom solutions utilising our automated, high throughput DNA purifications unique range of in-house technologies. High quality nucleic acid with optimal yield from Efficient purification of The power of next generation sequencing (Table 8). column-based methods and high quality DNA with the superior purity of nucleic acid highest quantity of DNA (NGS) has transformed how we interrogate using magnetic bead-based possible. geneticKey features information; it deliversoKtopure information Genespin Table 8: Key features DNA purification methods. on an unprecedented scale and provides an of both oKtopure and Grade of automation Fully automated Semi-automated Genespin automated 16+ years of experience Trustworthy, robust, opportunity to conquer challenges unresolved platforms, compatible with services in DNA extraction and reproducible and reliable Throughput Up to 5,000 samples/day Up to 20,000 samples/day sbeadex and Kleargene genotyping. data. by previous technologies. However, outstanding chemistries, respectively. achievementsFormat are seldom96-well realised in isolation. 96- and 384-well We have developed highly-optimised DNA Turnaround times Standard and rapid sample ranging from 2-8 weeks Plant leaf; Plant seed; Livestock Plant leaf; Plant seed; Rodent purification service protocols, starting from a wide Applications turnaround time options. depending on the project (ear punch, tissue) tails variety of sample types, including: needs DNA quality Very high (NGS-grade) High (PCR-grade) Convenient services like All genomics-based applications, PCR-based technologies, • Plant (including roots, leaves and seeds) sample management, sample Additional customisable Downstream applications including NGS including KASP, BHQ • Blood (human; animal, FTA cards) storage, quantification and services to suit your normalisation, dispensing, and needs. Replicator functions 96-well 96- and 384-well • Tissue (hair, saliva, liver, skin) more. • Tissue culture cell preparations Dimensions (cm) 170 x 68.5 x 65 170 x 68.5 x 65 • Plasmid preparations from Table 9: Key feature of Biosearch Technologies purification services. Laboratory requirements Air pressure Centrifuge with plate adaptors bacterial growth cultures Consumables Tip wash option Tip wash option RNA purification services

Our RNA service laboratories in Germany can purify high quality RNA for specialised downstream processing applications. Typical sample types include:

• Blood and tissue • RNAlater® preserved tissue • Plant (including leaves and seeds) • Samples collected in PAXgene® blood tubes

8 9 Overview Order information

QuickExtract Kleargene sbeadex MasterPure DNA Extraction- QuickExtract Superparamagnetic beads – sbeadex

Key features 3-8 minute quick Highest throughput Magnetic beads with DNA and RNA Part number Volume Description Part number Preparations Description and easy extraction purification flexible protocols and no purification from QuickExtract DNA QE09050 50 mL NAP41301 96 sbeadex plasmid technology for PCR- by 384 spin plate chaotrophic salts/alcohol in same workflow Extraction solution NAP41310 960 sbeadex plasmid grade DNA format final wash buffer QuickExtract Plant QEP70750 50 mL DNA Extraction solution NAP41405 96 sbeadex tissue Mechanism of Quick and easy Glass fibre solid Surface-modified Salt-precipitation QuickExtract RNA NAP41450 960 sbeadex tissue action extraction and direct support inserted into superparamagnetic based chemistry QER090150 50 mL Extraction solution usage a microtiter plate particlessuperparamagnetic NAP41501 96 sbeadex forensic QuickExtract FFPE particles QEF81050 50 mL DNA Extraction solution NAP41510 960 sbeadex forensic NAP41601 96 sbeadex mini plant Products QuickExtract DNA Kleargene plant spin sbeadex plant MasterPure Table 11: Order information for QuickExtract products. Extraction Solution Complete DNA and NAP41610 960 sbeadex mini plant Kleargene tissue sbeadex livestock RNA Purification Kit High Volume Preparations - Kleargene and PLUS XL NAP41602 96 sbeadex maxi plant QuickExtract FFPE spin NAP41620 960 sbeadex maxi plant DNA Extraction sbeadex blood MasterPure DNA Part number Preparations Description Solution Purification Kit for NAP44701 96 sbeadex livestock trial NAP40801 10 PLUS XL (up to 10 mL) sbeadex tissue Blood NAP44702 960 sbeadex livestock QuickExtract Plant NAP40810 50 PLUS XL (up to 10 mL) sbeadex maxi plant DNA Extraction sbeadex forensic MasterPure Gram Kleargene blood NAP41640 960 KBS-1012-005 8 (oKtopure) Solution Positive DNA (up to 10 mL) sbeadex mini plant sbeadex plasmid Purification Kit Kleargene blood NAP41607 960 KBS-1012-006 32 (oKtopure) QuickExtract RNA (up to 10 mL) NAP41606 96 sbeadex mini plant trial Extraction Solution MasterPure Yeast Kleargene blood KBS-1012-007 160 RNA Purification Kit (up to 10 mL) Table 15: Order information for sbeadex products. Automation Semi-automated Semi-automated Fully automated (excluding Semi-automated Table 12: Order information for Kleargene products for high volume blood samples. potential (heating required) (centrifugation lysis) (centrifugation Genespin required) required) Precipitation- MasterPure Complete DNA Part number Description and RNA Purification Kit Corresponding Liquid handler Genespin oKtopure Liquid handler 96 Head Genespin high-throughput Biosearch KBS-0010-001 Part number Description Kleargene prep robot Technologies MC85200 100 RNA or 200 DNA purifications 384 Head Genespin high-throughput instrument KBS-0010-002 MC 89010 5 RNA or 10 DNA purifications Kleargene prep robot Scalability 96-well format 96- or 384-well Customised kits adapted in 96-well format KBS-0900-023 On-site fully inclusive service contract format 96-well format Table 13: Order information for MasterPure products. Table 16: Order information for Genespin products. Options for Adaption volume Adaption of buffer Adaption to any sample Adaption volume Spin plates – Kleargene customisation composition material (lysis) Part number Preparations Description oKtopure Table 10: Overview of extraction and purification chemistries from Biosearch Technologies. KBS-1012-201 1 x 96 Kleargene plant Part number Description KBS-1012-202 4 x 96 Kleargene plant oKtopure high-throughput KBS-0009-001 KBS-1012-210 16 x 96 Kleargene plant DNA extraction robot oKtowash™, concentrated wash KBS-1012-211 64 x 96 Kleargene plant KBS-0009-002 buffer (500 mL) KBS-1012-204 1 x 384 Kleargene plant KBS-0009-003 oKtopure offline tip wash option KBS-1012-205 4 x 384 Kleargene plant oKtopure mix plates (Thermo KBS-0009-004 KBS-1012-212 16 x 384 Kleargene plant 1.2 mL deep well plate) KBS-1012-213 80 x 384 Kleargene plant KBS-0009-005 Wash buffer bulk reservoirs (pack of 4) KBS-1012-400 1 x 96 Kleargene tissue Extended on-site fully inclusive KBS-0009-999 KBS-1012-401 4 x 96 Kleargene tissue service contract KBS-1012-442 16 x 96 Kleargene tissue KBS-0010-003 oKtopure tips KBS-1012-443 64 x 96 Kleargene tissue KBS-6212-027 Magnetic plate

Table 14: Order information for Kleargene spin plates products. Table 17: Order information for oKtopure products. 10 11 Products and services

Products Services

DNA extraction products (sbeadex®, mag™ and DNA and RNA extraction services Kleargene™ kits) Sample management and project support services oKtopure™ and Genespin DNA extraction systems KASP® SNP and InDel genotyping BHQ® Probes (Dual-labeled, BHQplus®, BHQnova™) All-inclusive genotyping services Enzymes and PCR reagents (KlearKall™, KlearTaq™, KlearTaq™ HiFi) Sanger sequencing

Whole Genome Amplification (WGA) kits SSR to KASP SNP marker conversion service

IntelliQube® qPCR and end-point PCR system Next generation sequencing services

SNPline™ high-throughput SNP genotyping system Genotyping by Sequencing (GBS) services

Nexar® ultra-high-throughput SNP genotyping system Whole Genome Amplification (WGA)

DNA fragment library prep kits (NxSeq® AmpFREE SeqSNP targeted GBS service and UltraLow Library Kits)

NGS enzymes (NxGen® T4 DNA Ligase, T4 PNK, T4 DNA Polymerase, Taq98 DNA Polymerase)

For research use only. Not for use in diagnostic procedures

Integrated tools. Accelerated science.

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