Introduction

This product provides an easy-to-use workflow for selective isolation of bacterial DNA from samples that are intrinsically rich in host DNA, such as body fluids or swabs. The method is specific for the identification of intact bacteria so it prevents false results due to nucleic acids from dead bacteria. The Kit allows isolation of enriched bacterial DNA suitable for a variety of applications, including qPCR and whole metagenome or 16S rRNA gene sequencing.

Details

Specifications

Features	Specifications
Main Functions	Isolation gDNA from biological sample and remove host DNA
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	Culture medium, swab, parasitic blood, tissue, sputum, etc.
Sample amount	Blood sample, homogenate, plasma, brain effusion, swab immersion solution, centrifuged concentrated liquid, etc.:0.5-1ml
Elution volume	≥50μl
Time per run	≤60 minutes
Liquid carrying volume per column	800μl
Binding yield of column	100μg

Principle

This product is based on silica Column purification. This product efficiently depletes human and animal host DNA and yields enriched bacterial DNA. An optimized combination of mechanical and chemical lysis allows efficient disruption of bacterial cells. Target DNA is adsorbed on the membrane, while protein is not adsorbed and is removed with filtration. After washing proteins and other impurities, nucleic acid was finally eluted with low-salt buffer (10mm Tris, pH9.0, 0.5mm EDTA).

Advantages

• High concentration – the host DNA is digested by dnase, without contamination of host DNA
• High recovery – DNA can be recovered at the level of PG
• Good repeatability – silica technology can obtain ideal results every time
• Wide applicability – it can be used in blood, tissue, intestinal contents and other samples

Kit Contents

Contents	D314802	D314803
Purification Times	50 Preps	250 Preps
Hipure DNA Mini Columns I	50	2 x 125
2ml Collection Tubes	50	2 x 125
2ml beads Tubes	50	250
Buffer DRB	15 ml	60 ml
Buffer ES	6 ml	30 ml
Reagent DX	0.5 ml	1 ml
Buffer DL	30 ml	120 ml
Buffer GW1	22 ml	110 ml
Buffer GW2	12 ml	50 ml
DNase I (Powder)	6 mg	30 mg
Proteinase K	24 mg	120 mg
Protease Dissolve Buffer	5 ml	15 ml
Buffer AE	15 ml	60 ml

Storage and Stability

DNase I and Proteinase K should be stored at 2–8°C upon arrival. However, short-term storage (up to 12 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. The entire kit can be stored at 2–8°C, but in this case buffers should be redissolved before use. Make sure that all buffers are at room temperature when used.

This product provides an easy-to-use workflow for selective isolation of bacterial DNA from samples that are intrinsically rich in host DNA, such as body fluids or swabs. The method is specific for the identification of intact bacteria so it prevents false results due to nucleic acids from dead bacteria. The Kit allows isolation of enriched bacterial DNA suitable for a variety of applications, including qPCR and whole metagenome or 16S rRNA gene sequencing.

Introduction

Free-circulating nucleic acids, such as tumor-specific extracellular DNA fragments and mRNAs in the blood or fetal nucleic acids in maternal blood, are present in serum or plasma usually as short fragments, <1000bp (DNA). HiPure Circulating DNA Midi Kit enables efficient purification of these circulating nucleic acids from human plasma, serum, or urine. The extracted products can be used for clinical in vitro detection.

Details

Specifications

Features	Specifications
Main Functions	Isolation circulating DNA from 1-5ml plasma, serum, body fluids using vacuum protocol
Applications	qPCR, liquid or solid chip analysis, hybridization and SNP detection, etc.
Purification method	Mini spin column
Purification technology	Silica technology
Process method	Manual (vacuum)
Sample type	Serum, plasma and other cell-free fluid samples
Sample amount	1-5ml
Elution volume	≥50μl
Time per run	≤60 minutes
Liquid carrying volume per column	4ml
Binding yield of column	1mg

Principle

This product is based on silica Column purification. The sample is lysed and digested with lysate and protease, DNA is released into the lysate. Transfer to an adsorption column. Nucleic acid is adsorbed on the membrane, while protein is not adsorbed and is removed with filtration. After washing proteins and other impurities, Nucleic acid was finally eluted with low-salt buffer.

Advantages

• High yield – most optimal process, free DNA (>50bp) can be obtained to the maximum extent
• High concentration – low elution volume, ensuring high nucleic acid concentration
• High purity – low alcohol binding method, completely removing inhibitor and protein pollution
• High recovery – DNA can be recovered at thelevel of PG by silica gel column purification

Kit Contents

Contents	IVD3182
Purification Times	50
Buffer ACL	250 ml
Buffer ACB*	300 ml
Buffer DCW1*	22 ml
Buffer DCW2*	10 ml
Proteinase K	540 mg
Protease Dissolve Buffer	30 ml
Carrier RNA	110 μg
Nuclease Free Water	20 ml
HiPure CFDNA Mini Columns	50
2 ml Collection Tubes	100
Extender Tube	50
Vac-Connector	50

Storage and Stability

Proteinase K, Carrier RNA should be stored at 2-8°C upon arrival. However, short-term storage (up to 12 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. The entire kit can be stored at 2-8°C, but in this case buffers should be redissolved before use. Make sure that all buffers are at room temperature when used.

Experiment Data

Free-circulating nucleic acids, such as tumor-specific extracellular DNA fragments and mRNAs in the blood or fetal nucleic acids in maternal blood, are present in serum or plasma usually as short fragments,

Endonucleases Non-Specific, HL-SAN

OverView

HL-SAN efficiently removes nucleic acids from buffers typically used in protein purification. Due to its high salt tolerance, it is the obvious choice for host-cell DNA removal in settings where salt is added to reduce aggregation. Especially efficient for removing nucleic acids from proteins with high affinity for DNA and RNA. Proven performance during lysis and early stages of protein purification processes, as well as high-salt eluates. Cold-adapted enzyme with excellent performance also at ambient temperatures and during over-night digestion at 4°C.

Recommended applications:

Complete removal of DNA 

Viscosity reduction

Key advantages with this Salt Active Nuclease:

• Non specific endonuclease
• Optimum activity at high salt concentration (0.5 M NaCl)
• Active at low temperatures (20% at 6ºC)
• Easily inactivated
• Broad pH range
• Temperature stable

Figures

Figure 1. Optimum activity in solutions with high salinity

HL-SAN has optimum activity at ∼0.5 M NaCl, but operates at a broad range of [NaCl] and [KCl]. The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer, pH 8.5, 5 mM MgCl₂ with varying [NaCl] or [KCl]. The maximum activity was set to 100%.

Figure 2. Temperature and activity

HL-SAN has optimum activity at ~35°C, but works over a broad temperature range (20% activity at 10°C and 50°C). The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer, pH 8.5 containing 5 mM MgCl₂ and 0.5 M NaCl.

Fig 3. The effect of MgCl₂ and MnCl₂ concentration on the HL-SAN activity.

The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer, pH 8.5, 0.5 M NaCl and with varying concentrations of MgCl₂ or MnCl₂. The activity of the sample containing 5 mM MgCl₂ was set to 100%.

Figure 4. HL-SAN activity vs pH/[NaCl]

The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer with different pHs and different concentrations of NaCl. All buffers contained 5 mM MgCl₂. The nature of the buffer was pH-dependent, but generally the NaCl-optimum was the same in all buffers/pHs. The exception was etanolaminbuffer at pH 9 and pH 9.5 in which the NaCl-optimum was shifted to the left (not shown).

Figure 5. Buffer composition affects substrate preference

Without NaCl, the specificity towards ssDNA and dsDNA is similar. At 0.5 M NaCl, the activity towards dsDNA increases, while the activity towards ssDNA is unaffected.

Figure 6. HL-SAN digests ssDNA to ~5-13 nt, and dsDNA to ~5-7 nt

The size of the end products from ssDNA varies from ~5-13 nt, while dsDNA is digested to around ~5-7 nt. The size of the end products seems to depend on the DNA sequence. Substrates 1 and 2 were ssDNA with different sequences and substrates 3 and 4 were dsDNA with similar sequences but with a FAM-label at different ends. Substrate 5 was dsDNA with the same sequence as substrate 3 and 4 but with a FAM-label at both ends.

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Figure 7. HL-SAN activity decreases with increasing concentrations of glycerol

The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer, pH 8.5, 5 mM MgCl₂, 0.5 M NaCl and with increasing concentrations of glycerol. The activity of the control not containing glycerol was set to 100%.

Figure 8. The activity of HL-SAN at different concentrations of imidazole

The activity of HL-SAN was tested in a 25 mM Tris-HCl buffer, pH 8.5, 5 mM MgCl₂, 0.5 M NaCl and with varying concentrations of imidazole. The activity of the control not containing imidazole was set to 100%.

HL-SAN efficiently removes nucleic acids from buffers typically used in protein purification. Due to its high salt tolerance, it is the obvious choice for host-cell DNA removal in settings where salt is added to reduce aggregation. Especially efficient for removing nucleic acids from proteins with high affinity for DNA and RNA. Proven performance during lysis and early stages of protein purification processes, as well as high-salt eluates. Cold-adapted enzyme with excellent performance also at ambient temperatures and during over-night digestion at 4°C.