Nucleic Acid Isolation and Purification, 4th edition - Roche Life

260 Pages·2011·9.76 MB·English

Nucleic Acid Isolation and
Purification
4th edition
Sea Otters
Sea otters are the smallest marine mammals and are adapted to spending almost all of their
lives in the ocean. Although they resemble small seals, sea otters are not actually related to
seals, but rather to weasels, badgers and minks. They belong to the species „Enhydria lutris“,
from the Greek „en hydra“, meaning „in the water“, and the Latin „lutris“, meaning otter.
Sea otters can be found in the Pacific Ocean along the coast of California, up to Alaska,
along the east coast of Russia, and all the way up to the northern tip of Japan. They prefer
coastal waters and only swim out into the deep ocean when travelling between islands and
the mainland.
Unlike other marine mammals such as seals and dolphins, sea otters do not rely on a layer of
fat to insulate their bodies from the cold water. Instead, sea otters depend on their fur to
keep warm. But even with a thick fur coat, the sea otter has to work hard to keep warm,
spending hours each day grooming its fur. Any water needs to be squeezed out and air needs
to be blown into the fur. The air makes the fur waterproof, ensuring that the otter‘s skin
remains warm and dry. That‘s why cleaning is essential. Dirty fur can easily get wet and
place the otter at risk of dying from the cold.
In addition to their thick coats, sea otters have another defense against the cold ocean water.
The otter has a high body temperature (around +38°C), which requires a fast metabolic rate.
As a result, sea otters need to eat a lot, sometimes as much as 25% of their body weight each
day. This is the equivalent of humans eating about 100 hamburgers!
Sea otters eat a variety of foods, including shellfish, sea urchins, fish and many different
types of invertebrate sea life. As they must constantly eat to survive, otters spend a lot of
time diving for food. Otters can dive up to 100 m for several minutes, although they prefer
shallow waters where they can make quicker dives instead.
Capturing their prey is not always an easy task. However, the sea otter is a highly intelligent
animal and perfectly capable of finding ways of capturing hard-to-get prey.
Smaller shellfish clinging to rocks can be prised off by the otter’s strong arms. The sea otter
is fairly strong, but not quite strong enough to defeat the larger abalone, which clings fiercely
to rocks. Using rocks as hammers, the otters are capable of dislodging the abalone with
several firm strikes from the side.
Underground food such as clams can be obtained by digging. Otters can dig with their
forepaws, like dogs, and sometimes use rocks as digging implements. They have a little
pouch under their left armpit in which they can store rocks or food, for example, while
swimming.
Once the otter has found its food, it carries it to the surface to eat. But not all food can be
eaten straightaway. Although sea otters have strong teeth that can bite through crab shells
and some shellfish, other sources of prey, e.g. abalones, have to be cracked open first.
Individual otters seem to have their own preferences as to which method to use to crack
open their prey.
Some otters place a big rock on their chest and then smash their prey on the rock until the
shell breaks open. Other otters reverse this operation, placing their prey on the chest and
then smashing the rock against it. Some otters use numerous short, rapid strikes, while
others administer a few strong blows.
The sea otter’s sense of tidiness can also be observed during eating. Often the otter rolls over
in the water to clear its chest of any waste scraps and avoid soiling its coat.
The curious behavior of sea otters in preparing and eating their food is a perfect illustration
of isolation and purification.
We hope you like this little story about these cute animals.
2
Contents
Chapter 1 Selection Guide ............................................................................................. 8
Introduction
Product Overview ....................................................................................... 10
Overview of Nucleic Acid Purification and Isolation .................... 14
Methods described in this manual ...................................................... 16
Chapter 2 Overview of Silica Adsorption ............................................................... 18
High Pure Kits and
High Pure PCR Template Preparation Kit .......................................... 21
Silica Adsorption
High Pure PCR Cleanup Micro Kit ...................................................... 34
High Pure PCR Product Purification Kit ............................................. 42
High Pure Plasmid Isolation Kit ........................................................... 49
High Pure RNA Isolation Kit .................................................................. 55
High Pure RNA Tissue Kit ...................................................................... 64
High Pure FFPE RNA Micro Kit ........................................................... 69
High Pure RNA Paraffin Kit .................................................................... 75
High Pure miRNA Isolation Kit ..............................................................84
High Pure Viral RNA Kit .......................................................................... 95
High Pure Viral Nucleic Acid Kit ....................................................... 100
High Pure Viral Nucleic Acid Large Volume Kit ............................ 105
Troubleshooting Procedures for the High Pure Kits .................. 113
Agarose Gel DNA Extraction Kit ....................................................... 122
High Pure 96 UF Cleanup Kit ............................................................. 127
3
Chapter 3 Overview of Ion Exchange Chromatography ................................ 134
Ion Exchange
Genopure Plasmid Midi Kit ................................................................. 136
Chromatography
Genopure Plasmid Maxi Kit ................................................................ 143
Genopure Buffer Set for Low-Copy Number Plasmids ............. 150
Chapter 4 Overview of Solution-based Isolation .............................................. 152
Solution-based Isolation
DNA Isolation Kit for Mammalian Blood ....................................... 154
DNA Isolation Kit for Cells and Tissues ......................................... 162
TriPure Isolation Reagent ..................................................................... 170
Chapter 5 Overview of Affinity Purification ........................................................ 180
Affinity Purification
mRNA Capture Kit .................................................................................. 184
mRNA Isolation Kit ................................................................................. 189
RNA/DNA Stabilization Reagent for Blood/Bone Marrow ..... 197
mRNA Isolation Kit for Blood/Bone Marrow ................................ 198
Chapter 6 Overview of Gel Filtration ..................................................................... 208
Gel Filtration
Quick Spin Columns .............................................................................. 210
mini Quick Spin Columns .................................................................... 214
Chapter 7 MagNA Lyser Instrument ...................................................................... 220
Automated Nucleic Acid
MagNA Pure LC Instrument ................................................................. 222
Isolation
MagNA Pure Compact Instrument .................................................... 223
4
Chapter 8 Introduction ............................................................................................... 226
Premium Performance
PCR Product Selection Guide ............................................................. 227
Products for PCR and
RT-PCR Product Selection Guide ...................................................... 228
RT-PCR
PCR Enzyme dNTPacks ........................................................................ 229
Master Mixes ............................................................................................ 230
Real-Time PCR Instruments ............................................................... 231
Reagents for Real-Time PCR ............................................................. 232
Chapter 9 Tips for Handling Nucleic Acids ........................................................ 234
Appendix
Conversion Tables and Formulas ...................................................... 236
Buffers and Gels for Electrophoresis ............................................... 240
Other Useful Information ..................................................................... 242
Chapter 10 Isolation and Purification of DNA ..................................................... 246
Ordering Guide
Isolation and Purification of RNA ..................................................... 247
MagNA Lyser Instrument and Accessories.................................... 248
Automated Isolation using the MagNA Pure LC Instrument ....248
Automated Isolation using the MagNA Pure Compact
Instrument ....................................................................................................249
Companion Reagents for Isolating Nucleic Acids ........................250
Chapter 11 ......................................................................................................................... 255
Index
5
Disclaimer
* For life science research only. Not for use in diagnostic procedures.
+ For general laboratory use.
# CE/for USA for laboratory use
6
1
Introduction
Selection Guide 8
Product Overview 10
Overview of Nucleic Acid Purification and Isolation 14
Methods described in this manual 16
Selection Guide

Selection Guide
Use this table to select a product according to the type of nucleic acid you wish to purify, then consider the
1
source of the nucleic acid and the scale of the purification.
Nucleic Subtype Origin/Source Scale Recommended Product see
Acid Page
Type
tissue, cultured cells, bacteria, yeast, blood,
 High Pure PCR Template Preparation Kit 21
dried blood spots
tissue, cultured cells, bacteria, yeast, mouse   DNA Isolation Kit for Cells and Tissues 162
Genomic tail
human blood, dried blood spots  High Pure PCR Template Preparation Kit 21
mammalian/human blood   DNA Isolation Kit for Mammalian Blood 154
propagated in E. coli  High Pure Plasmid Isolation Kit 49
Plasmid propagated in E. coli  Genopure Plasmid Midi Kit 136
propagated in E. coli  Genopure Plasmid Maxi Kit 143
serum, plasma, blood, other body fluids,  High Pure Viral Nucleic Acid Kit 100
supernatant from cell cultures
Viral
serum, plasma, whole blood   High Pure Viral Nucleic Acid Large 105
Volume Kit
DNA PCR mixture  High Pure PCR Product Purification Kit 42
• High Pure PCR Cleanup Micro Kit 34
 High Pure 96 UF Cleanup Kit 127
restriction enzyme digests, labeling and  High Pure PCR Product Purification Kit 42
modifying reaction mixture
• High Pure PCR Cleanup Micro Kit 34
DNA
radiolabeled DNA  Quick Spin Columns 210
fragments
radiolabeled DNA, removal of excess  mini Quick Spin Columns 214
fluorescent-labeled terminators
agarose gel slices   Agarose Gel DNA Extraction Kit 122
 High Pure PCR Product Purification Kit 42
• High Pure PCR Cleanup Micro Kit 34
ss DNA, ds DNA, PCR products, cRNA • High Pure PCR Cleanup Micro Kit 34


Scale: • 
micro mini midi maxi
8 Nucleic Acid Isolation and Purification Manual
Selection Guide

Selection Guide,
continued
1
Nucleic Subtype Origin/Source Scale Recommended Product see
Acid Page
Type
cultured cells, tissues, total RNA   mRNA Isolation Kit 189
•  mRNA Capture Kit 184
mRNA
whole blood/bone marrow    mRNA Isolation Kit for Blood/Bone 198
Marrow
cultured cells, bacteria, yeast, blood  High Pure RNA Isolation Kit 55
tissue  High Pure RNA Tissue Kit 64
cultured cells, tissues, bacteria, yeast, blood,    TriPure Isolation Reagent 170
Total plant cells
RNA
RNA formalin-fixed, paraffin-embedded tissue • High Pure FFPE RNA Micro Kit 69
formalin-fixed, paraffin-embedded tissue,  High Pure RNA Paraffin Kit 75
fresh-frozen tissue
animal tissue, stabilized animal tissue,  High Pure miRNA Isolation Kit 84
animal cell culture, formalin-fixed,
paraffin-embedded tissue
serum, plasma, other body fluids, supernatant  High Pure Viral RNA Kit 95
Viral RNA
from cell cultures
radiolabeled RNA  Quick Spin Columns 210
RNA
fragments
 mini Quick Spin Columns 214


Scale: • 
micro mini midi maxi
Introduction 9
Product Overview Product Overview
Detailed Product Characteristics Recommended Uses
Product Overview
Detailed Product Characteristics
Purification method/Product Starting material and quantity Yield/recovery Time required PCR/ RT-PCR DD-RT- cDNA RE Southern Labeling Northern RNase CloningSequen- in vitro in Trans- Micro -
1 long PCR Synthesis/ digestion blotting modifying blotting protection cing trans- vitro fection array 1
PCR primer reactions assays cription trans- Spotting
extension lation
Ultrafiltration
High Pure 96 UF Cleanup Kit PCR products (100 bp to > 10 kb), 25 µl (150 bp, 40%; 1500 bp, < 20 min     
20-300 µl 90%; 4500 bp, 90%, 8000 bp,
80%)
Silica Adsorption
High Pure PCR Template Preparation Kit* blood, 200 – 300 µl 3 – 9 µg 20 min    
cultured cells, 104 – 108 15 – 20 µg 20 min
thymus tissue, 25 – 50 mg 5 – 20 µg 80 min, incl. lysis
mouse tail, 25 – 50 mg 5 – 10 µg 200 min, incl. lysis
yeast, 108 cells 10 – 13 µg 50 min, incl. lyticase digest
bacteria, 109 cells 1 – 3 µg 35 min, incl. lysozyme digest
dried blood spots 9 mm punch-out 80 min, incl. lysis
High Pure PCR Product Purification Kit PCR, modifying, labeling, restriction >80% recovery of 5 – 25 µg DNA 10 min      
digestion reaction, 100 µl; agarose gel >100 bp
slices
High Pure PCR Cleanup Micro Kit PCR, modifying, labeling, restriction >80% recovery of 5 – 25 µg DNA 10 min      
digestion reaction, agarose gel slices
High Pure Plasmid Isolation Kit* E. coli XL1 blue, pUC 19 (2 ml) 12 µg 30 min       
E. coli HB 101, pUC 19 (2 ml) 6 µg 30 min
E. coli DH5, pUC 19 (2 ml) 3.5 µg 30 min
High Pure RNA Isolation Kit* blood, 200 – 500 µl sufficient for 10 RT-PCR reactions 50 min, incl. RBC lysis      
cultured cells, 106 20 µg 25 min
yeast, 108 cells 20 µg 45 min, incl. lyticase digest
bacteria, 109 cells 35 – 50 µg 90 min, incl. lysozyme digest
High Pure RNA Tissue Kit solid tissue, 1 – 10 mg 0.5 – 3.0 µg/mg 30 min      
High Pure miRNA Isolation Kit tissue, stabilized tissue, cell culture, depending on miRNA 30 min   
FFPE tissue sections
High Pure Viral RNA Kit serum, plasma, urine, supernatant from product detectable by RT-PCR 10 min 
cell culture,
200 – 600 µl
High Pure Viral Nucleic Acid Kit* serum, plasma, blood, supernatant from product detectable by PCR or 20 min  
cell culture, RT-PCR
200 – 600 µl
High Pure 16 System Viral Nucleic Acid serum, plasma, supernatant from cell product detectable by PCR or 30 min  
Kit culture, 200 µl RT-PCR
High Pure Viral Nucleic Acid Large serum, plasma, whole blood 1 – 2.5 ml 25 min  
Volume Kit
High Pure RNA Paraffin Kit fresh-frozen or formalin-fixed paraffin- 0.3-1.5 µg/5 µm section, 2 h without overnight   
embedded tissue 2-6 µg/20 mg incubation
fresh-frozen tissue
High Pure FFPE RNA Micro Kit 1-10 µm FFPE tissue sections 1.5-3.5 µg/5 µm 60 min without 3h   
incubation
Agarose Gel DNA Extraction Kit agarose gel slices, 100-200 mg 80% recovery of fragments 60 min     
(0.4-9.5 kb)
Ion Exchange Chromatography
Genopure Plasmid Midi Kit E.coli DH5, pBS (30 ml) >85 µg 60 min      
Genopure Plasmid Maxi Kit E.coli DH5, pBS (150 ml) >420 µg 75 min      
Affinity Purification
mRNA Isolation Kit for Blood/ blood, bone marrow aspirate, 50 – 200 ng/ml blood 90 min     
Bone Marrow* 1.5 – 5 ml
mRNA Isolation Kit* tissue, 50 mg – 1 g 7 – 14 µg/100 mg tissue 60 min     
cells, 2 x 105 – 108 0.3 – 25 µg/107 cells 40 min
total RNA, 250 µg – 2.5 mg 1 – 5 µg/100 µg total RNA 30 min
mRNA Capture Kit tissue, up to 20 mg product detectable by RT-PCR 60 min 
cells, up to 5 x 105 product detectable by RT-PCR 40 min
total RNA, up to 40 µg product detectable by RT-PCR 30 min
10 Nucleic Acid Isolation and Purification Manual Introduction 11