Introduction

Soil samples contain a large number of microorganisms, the vast majority of which can not be directly cultivated for reproduction and research. Extracting DNA from soil samples is the most effective method for studying soil microorganisms. At present, there are mainly direct and indirect methods for extracting microbial DNA from soil samples. The direct method refers to placing soil samples in the lysis solution, and using effective wall breaking methods to release all microbial DNA into the lysis solution, followed by separation and extraction, such as Zhou’s method. Indirect method refers to placing soil in a buffer, such as Buffer PBS, to separate microorganisms from the soil and then extract DNA. The indirect method can greatly reduce the impact of humic acids and heavy metal salts on DNA extraction in soil, but this method will lose many microorganisms and the resulting DNA is not the entire genome (metagenome) of the soil sample. Currently, few researchers have adopted this method. Extracting DNA directly from soil samples can maximize the likelihood of obtaining the entire genome, but this method faces the following issues:

1. Humic acid pollution. The soil, especially in forests and grasslands, is rich in humic acids. Humic acid is a series of organic molecules, some of which are very similar to nucleic acid molecules and difficult to remove during purification. Trace amounts of humic acid pollution can lead to downstream applications such as PCR and enzyme digestion failure.

2. Lysis method. Soil samples contain various microorganisms, such as bacteria and fungi. Gram positive bacteria and fungi both contain very thick bacterial walls, and effectively breaking down the cell walls of these microorganisms is crucial for extracting high-yield metagenomic DNA. Due to the complexity of soil samples, it is not feasible to use enzymatic methods (such as lysozyme, wall breaking enzyme, snail enzyme) or liquid nitrogen grinding, as the soil contains various metalions or inhibitory factors that inactive the digestive enzymes, or the presence of sand particles in the soil makes liquid nitrogen grinding difficult.

3. The DNA yield is difficult to control. Soil samples would have significant changes in the number and variety of microorganisms due to fertility, inferiority, high moisture content, dryness, or depth of sampling. In a small range of soil samples, the DNA content often varies by thousands of times. In addition, certain chemical components in soil, such as heavy metal salts and clay substances, can cause a decrease in DNA yield.

Magen’s HiPure Soil DNA Kits are currently the most optimized kit for soil DNA extraction. The kit adopts glass bead grinding method and thermal shock chemical wall breaking method, which can be carried out in the point vortex instrument without special bead grinding instrument, and is suitable for a wide range of laboratories. The Absorber Solution in the reagent kit is a humic acid adsorbent exclusively developed by Magen Company, which can efficiently remove various humic acid pollutants. In addition, an alcohol-free silica gel column purification method is also used to efficiently remove various soluble metal salts and other soluble inhibitory factors from the soil. The kit has successfully extracted from the following soil (partially based on customer feedback): soil from forests in nature reserves (30 to 40 years old forest soil with a surface layer of 30-50cm deciduous layer), mangrove soil, grasslands, farmland, seabed mud, sludge, mineral area soil, organic matter contaminated soil, pond mud, garbage mud, air conditioning pipeline deposits, etc.

This product allows rapid and reliable isolation of high-quality genomic DNA from various soil samples. Up to 500 mg soil samples can be processed in 60 minute. The system combines the reversible nucleic acid binding properties of HiPure matrix with the speed and versatilityof spin column technology to eliminate PCR inhibiting compounds such as humic acid from soil samples. Purified DNA is suitable for PCR, restriction digestion, and next-generation sequencing. There are no organic extractions thus reducing plastic waste and hands-on time to allow multiple samples to be processed in parallel.

Details

Specifications

Features	Specifications
Main Functions	Isolation DNA from 200-500mg soil sample
Applications	PCR, southern blot and enzyme digestion, etc.
Purification method	Mini spin column
Purification technology	Silica technology
Process method	Manual (centrifugation or vacuum)
Sample type	Soil
Sample amount	200-500mg
Elution volume	≥30μl
Time per run	≤60 minutes
Liquid carrying volume per column	800μl
Binding yield of column	100μg

Principle

Soil sample is homogenized and then treated in a specially formulated buffer containing detergent to lyse bacteria, yeast, and fungal samples. humic acid,proteins, polysaccharides, and other contaminants are removed using our proprietary Absorber Solution. Binding conditions are then adjusted and the sample is applied to a DNA Mini Column. Two rapid wash steps remove trace contaminants and pure DNA is eluted in low ionic strength buffer. Purified DNA can be directly used in downstream applications without the need for further purification.

Advantages

• Fast – several samples can be extracted in 40 minutes (after digestion)
• High purity – purified DNA can be directly used in various downstream applications
• Good repeatability – silica technology can obtain ideal results every time
• High recovery – DNA can be recovered at the level of PG

Kit Contents

Contents	D314202	D314203
Purification Times	50 Preps	250 Preps
Hipure DNA Mini Columns II	50	250
2ml Collection Tubes	50	250
2ml Bead Tubes	50	250
Buffer SOL	60 ml	250 ml
Buffer SDS	5 ml	20 ml
Buffer PS	10 ml	50 ml
Absorber Solution	10 ml	50 ml
Buffer GWP	40 ml	220  ml
Buffer DW1	30 ml	150  ml
Buffer GW2*	20 ml	2 x 50  ml
Buffer AE	15 ml	30 ml

Storage and Stability

Absorber Solution should be stored at 2-8°C upon arrival. However, short-term storage (up to 24 weeks) at room temperature (15-25°C) does not affect their performance. The remaining kit components can be stored dry at room temperature (15-25°C) and are stable for at least 18 months under these conditions.

Experiment Data

Soil samples contain a large number of microorganisms, the vast majority of which can not be directly cultivated for reproduction and research. Extracting DNA from soil samples is the most effective method for studying soil microorganisms. At present, there are mainly direct and indirect methods for extracting microbial DNA from soil samples. The direct method refers to placing soil samples in the lysis solution, and using effective wall breaking methods to release all microbial DNA into the lysis solution, followed by separation and extraction, such as Zhou’s method. Indirect method refers to placing soil in a buffer, such as Buffer PBS, to separate microorganisms from the soil and then extract DNA. The indirect method can greatly reduce the impact of humic acids and heavy metal salts on DNA extraction in soil, but this method will lose many microorganisms and the resulting DNA is not the entire genome (metagenome) of the soil sample. Currently, few researchers have adopted this method. Extracting DNA directly from soil samples can maximize the likelihood of obtaining the entire genome, but this method faces the following issues:

Description

Nucleic acid testing (NAT) is the method of choice for detection and quantification of a wide range of micro organisms. Primerdesign manufactures and supplies high quality quantitative real-time PCR kits for the detection and simultaneous quantification of numerous significant pathogens . A copy number standard curve is provided for quantification and an the internal extraction template (DNA or RNA), controls for the quality of the nucleic acid extraction and eliminates false negative results.

The kit is designed with the broadest possible detection profile to ensure that all clinically relevant strains and subtypes are detected. Target sequences are selected by working with data from key opinion leaders in the field. Multiple sequence alignments and unprecedented real-time PCR expertise in design and validation ensure the best possible kit.

Details of the target and priming specificity are included in the individual handbooks above.

Packaged, optimised and ready to use. Expect Better Data.

Exceptional value for money
Rapid detection of all clinically relevant subtypes
Positive copy number standard curve for quantification
Highly specific detection profile
High priming efficiency
Broad dynamic detection range (>6 logs)
Sensitive to < 100 copies of target Accurate controls to confirm findings

The PCR-free NGS DNA Library Prep Kit was developed for construction of DNA libraries for next generation sequencing (illumina platform). The kit adds 3′-dT-tailed library adapters to both ends of DNA fragments efficiently. The kit uses double strand DNA fragments (blunt and/or sticky) as input DNA for NGS library construction, and is compatible with DNA fragments generated from both enzymatic methods (BioDynami DNA fragmentation enzymes etc.) and physical methods (sonication, nebulization etc.).

PCR-Free NGS DNA Library Prep Kit Workflow

PCR amplification is a standard step for library preparation of Next-Generation Sequencing. The PCR is used to amplify fully ligated DNA fragments and to add index information to the libraries. The indexing is for the pooling of the library samples in an effort to reduce the sequencing cost.

However, PCR introduces uneven amplification of DNA in some DNA regions with extreme GC-contents and secondary structures. This bias can cause very low sequencing coverage in such regions. DNA sequencing in these regions is still a huge challenge.

PCR-free library prep can reduce library bias and minimize sequencing gaps. The sequencing data from PCR-free library samples have even genomic coverage with few gaps and better depth in GC-rich regions. Our PCR-free NGS kit offers optimal coverage in the regions that are traditionally difficult, such as high-GC content regions, low-GC content regions, and repetitive sequence regions.

Two index types are available for the kit:

Non-index: Libraries do not have index.

Index: Each library contains one i5 index and one i7 index.  Library multiplexing up to 96 samples is possible. List of indexes can be downloaded Here.

Kit advantages:

• • • Total time: 1 hr
    • Hands-on time: 5 min
    • Easy procedure: Ready-to-use master mix & Less reaction components
    • Input DNA amount from 100 ng to 1 ug

The PCR-free NGS DNA Library Prep Kit was developed for construction of DNA libraries for next generation sequencing (illumina platform). The kit adds 3′-dT-tailed library adapters to both ends of DNA fragments efficiently. The kit uses double strand DNA fragments (blunt and/or sticky) as input DNA for NGS library construction, and is compatible with DNA fragments generated from both enzymatic methods (BioDynami DNA fragmentation enzymes etc.) and physical methods (sonication, nebulization etc.).