Endpoint PCR

› Direct and Multiplex PCR

› Thermostable DNA Polymerases

› dNTP Mixes, Bundles & Singles

› Buffer and Enhancer

› Gel, Loading and Staining

ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO
TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCAC-
GAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO

Molecular Biology
2 Introduction Building Blocks of Life

Endpoint PCR from Jena Bioscience

RNA/DNA Preparation
Isolation of genomic DNA/RNA
and plasmid DNA

Endpoint PCR Components & Mixes

Thermostable
3‘ DNA Polymerases
5‘
3‘

5‘
3‘

5‘ Reaction Buffers
dNTPs

3‘
5‘
3‘

Ready-to-use
Mixes

Downstream Restriction
DNA Ladders
Enzymes
Applications
Modifying
DNA Cleanup Kits
Enzymes
www.jenabioscience.com Introduction 3

Building Blocks of Life

Nucleotides & Nucleosides Click Chemistry, Probes & Epigenetics

In our chemistry division, we have Our Probes & Epigenetics as well
hundreds of natural and modified as Click Chemistry sections offer in-
nucleotides in stock. In addition, novative reagents for the function-
with our pre-made building blocks alization, conjugation and labeling
and in-house expertise we manufac- (fluorophores, haptens) of (bio) mol-
ture even the most exotic nucleotide ecules complemented by epigenetic
analog from mg to kg scale. modification analysis tools.

LEXSY Expression Crystallography & Cryo-EM

In the field of recombinant protein For the crystallization of biological
production, Jena Bioscience has devel- macro-molecules – which is often
oped its proprietary LEXSY (Leishmania the bottleneck in determining the
Expression System) technology. It is 3D-structure of proteins – we offer
based on an S1-classified unicellular specialized reagents for protein sta-
organism that combines easy handling bilization, crystal screening, crystal
with a eukaryotic protein folding and optimization, and phasing that can
modification machinery. Besides eve- reduce the time necessary to obtain
rything you need to establish LEXSY in a high resolution protein structure
your lab we also offer custom expres- from several years to a few days.
sion of recombinant proteins.

Molecular Biology & Proteins

For applications in the field of Molecular Biology we offer single
reagents, complete kits and optimized master mixes. This section
includes products for DNA or RNA purification, amplification and
modification with focus on PCR-related techniques.
For your questions regarding Endpoint PCR contact
me directly: [email protected]
4 Building Blocks of Life

Established in 1998 by a team of scientists from

the Max-Planck-Institute of Molecular Physiology
(Dortmund), Jena Bioscience utilizes more than 25
years of academic know-how to develop innova-
tive reagents for clients from both research and
industry in 100+ countries. To date, Jena Bioscience
still remains an owner-operated business.

Imprint:
Design & Layout by timespin - Digital Communication GmbH,
Sophienstr. 1, D-07743 Jena, Germany, www.timespin.de
Copyright: Please contact Jena Bioscience if you want to use
texts and/or images in any format or media.
ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA
CTAUAACTGCCAC www.jenabioscience.com Introduction
ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC 5
AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO

Contents

Thermostable DNA Polymerases ......................................... 6

Which enzyme do I need? .......................................................7

Direct and Multiplex PCR ....................................................... 8

Taq Polymerase Mixes ..............................................................9

Hot Start Taq Polymerase .....................................................10

High Fidelity & Pfu-X Polymerase Mixes .......................... 11

dNTP Mixes ................................................................................12

dNTP Bundles and Singles ..................................................13

Buffer and Enhancer ..............................................................14

Gel, Loading and Staining .....................................................15

6 Thermostable DNA Polymerases Building Blocks of Life

Thermostable DNA Polymerases

Thermostable DNA polymerases are heat-re- upon incorporation of a mismatched base: The
sistant, template-dependent enzymes that add polymerase reverses its direction by one base
free nucleotides to the 3'-end of a newly syn- pair, excises the mismatch, re-inserts the cor-
thesized complementary DNA strand. rect base and continues replication.
They can be divided into proofreading enzymes DNA polymerases are commercialized in various
(with inherent 3’-5’ exonuclease activity) and forms including engineered mutants and blends
non-proofreading enzymes that lack exonu- of polymerases to achieve optimal results in a
clease activity. 3’-5’ exonuclease activity occurs large variety of DNA synthesis reactions (Figure. 1).

Thermostable DNA
Polymerases
5’→ 3’ polymerization

Proofreading
Non-proof-reading Blends
3’→ 5’ exonuclease

Wild Type Engineered Wild Type Wild Type Engineered

■
Taq Polymerase ■
Sequencing ■
High Fidelity ■
Pfu Polymerase ■
Pfu-X
■
Taq Hot Start Polymerase Polymerase ■
Pfu Hot Start Polymerase
Polymerase (Taq Δ1-272, ■
High Fidelity Polymerase (increased
■
Tth Polymerase F667Y) Hot Start ■
Pwo fidelity and
■
Taq 5’→3’ exo- Polymerase Polymerase processivity)
Polymerase ■
Tli Polymerase
(Klentaq)

Taq: Thermus aquaticus, Tth: Thermus thermophilus, Pwo: Pyrococcus woesei, Pfu: Pyrococcus furiosus,
Tli: Thermococcus litoralis.
Enzymes available from Jena Bioscience

Figure 1
Proofreading and non-proofreading enzymes are marketed as wild type, engineered mutants, and blends
thereof covering a very broad range of applications.
 www.jenabioscience.com Which enzyme do I need? 7

Which enzyme do I need?

The available portfolio of our polymerases (Fig. 1) allows choosing the most appropriate enzyme for
a particular application. In most cases it is desired that a PCR yields large amounts of DNA with high
specificity (no by-product DNA) and high fidelity (minimum number of mutations).
Since these requirements sometimes may be contradictory – and also depend on the buffer system
and the cycling regime – Jena Bioscience offers the polymerases Taq Pol, Taq Hot Start, High Fidelity,
High Fidelity Hot Start, Hot Start, Pfu-X and Sequencing Pol that cover the entire range of applications
(see Table).

Fidelity /
Efficiency /
Enzyme Specificity Error rate Application
Yield
[1], [2]

■
Standard PCR / optimized for
minimal by-product formation
Taq Polymerase ++ ++ 10-5 ■
Routine and plate based PCR,
automated pipetting

■
High specificity PCR / high sensitivity
Taq Hot Start
++ +++ 10-5 PCR
Polymerase ■
Diagnostic PCR

■
High fidelity PCR / long range PCR
High Fidelity ( > 30 kb)
+++ ++ 2 × 10-6
Polymerase ■
Amplification of GC-rich and other
difficult templates

■
High fidelity PCR with highest
specificity and sensitivity
High Fidelity Hot
+++ +++ 2 × 10-6 Long range PCR, amplification of
Start Polymerase
■

difficult templates and of small

template amounts

■
Amplification with highest fidelity
Pfu-X Polymerase +++ +++ 2 × 10-7 ■
High speed amplification of difficult
and long templates

■
Incorporation of ddNTPs (Sanger
Sequencing
++ ++ NA Sequencing)
Polymerase ■
SNP genotyping

References:
[1] The error rate of a polymerase is calculated as number of mutations per number of base pairs per DNA doublings (PCR cycles).
ER = MF / (bp · d)
ER: Error rate MF: number of mutations (mutation frequency)
bp: number of base pairs (fragment length) d: DNA doublings (number of PCR cycles)
[2] Jena Bioscience, 2011
8 Direct and Multiplex PCR Building Blocks of Life

Direct and Multiplex PCR

Direct PCR Master is designed for PCR amplification directly from whole blood, animal tissues and
plant tissues without the need of prior DNA purification processes.

Multiplex PCR Master is specially designed for the set-up of multiplex PCR reactions. It contains an
optimized composition of polymerase, nucleotides, MgCl2 and stabilizing components in a specifically
developed buffer system allowing the parallel amplification of a multitude of fragments in a single
PCR assay.

Product Cat.-No. Amount

Direct PCR Master PCR-111S 2 × 1,25 ml (2 × conc.)
PCR-111L 10 × 1,25 ml (2 × conc.)
Multiplex PCR Master PCR-110S 2 × 1,25 ml (2 × conc.)
PCR-110L 10 × 1,25 ml (2 × conc.)
 www.jenabioscience.com Taq Polymerase Mixes 9

Taq Polymerase Mixes

Taq Polymerase is the enzyme of choice for

most routine PCR applications.
To allow choosing between convenience and
flexibility, Jena Bioscience offers Taq polymer-
ase in various types of formulations ranging
from complete master mixes over core kits
containing all required components in one box
to individual enzyme packs.

Product Cat.-No. Amount

Ruby Taq Master (2 ×) PCR-164S 4 × 1,25 ml (2 × conc.)

ready-to-use, for direct gel loading PCR-164L 20 × 1,25 ml (2 × conc.)
PCR-164XL 100 ml (2 × conc.)

Crystal Taq Master (2 ×) PCR-166S 4 × 1,25 ml (2 × conc.)

ready-to-use, for routine PCR applications PCR-166L 20 × 1,25 ml (2 × conc.)
PCR-166XL 100 ml (2 × conc.)

Red Load Taq Master (5 ×) PCR-108S 1 ml (5 × conc.)

ready-to-use, for direct gel loading PCR-108L 5 × 1 ml (5 × conc.)
PCR-214S 200 units
Taq Core Kit
Kit of thermostable DNA polymerase, PCR-214L 1000 units
dNTPs and reaction buffer
PCR-214XL 5000 units

Taq Polymerase PCR-211S 200 units

thermostable, recombinant PCR-211L 1000 units
PCR-211XL 5000 units

Taq Polymerase / Labeling Buffer PCR-201S 200 units

thermostable, recombinant PCR-201L 1000 units
Sequencing Polymerase PCR-206S 200 units
Taq Polymerase mutant for incorporation of ddNTPs PCR-206L 1000 units
10 Hot Start Taq Polymerase Building Blocks of Life

Hot Start Taq Polymerase

Hot Start PCR technique reduces non-specific amplifications and offers a convenient reaction set-up
at room temperature. The polymerase is recommended for routine & diagnostic PCR applications,
high throughput PCR or genotyping and provides an improved specificity and sensitivity when ampli-
fying low-copy-number targets or working with complex backgrounds.

Product Cat.-No. Amount

Ruby Hot Start Master (2 ×) PCR-165S 4 × 1,25 ml (2 × conc.)

ready-to-use, for direct gel loading PCR-165L 20 × 1,25 ml (2 × conc.)
PCR-165XL 100 ml (2 × conc.)
PCR-167S 4 × 1,25 ml (2 × conc.)
Crystal Hot Start Master (2 ×)
ready-to-use, for highly sensitive and specific PCR-167L 20 × 1,25 ml (2 × conc.)
PCR applications
PCR-167XL 100 ml (2 × conc.)
PCR-215S 200 units
Hot Start Core Kit
Kit of aptamer-inhibited hot start pol for PCR-215L 1000 units
high specificity, dNTPs & reaction buffer
PCR-215XL 5000 units
PCR-216S 200 units
Hot Start Core Kit Ab+
Kit of antibody-blocked hot start DNA polymerase, PCR-216L 1000 units
dNTPs and reaction buffer
PCR-216XL 5000 units
PCR-212S 200 units
Hot Start Polymerase
Heat-activatable DNA polymerase for high specificity, PCR-212L 1000 units
aptamer-inhibited
PCR-212XL 5000 units
PCR-213S 200 units
Hot Start Polymerase Ab+
Heat-activatable DNA polymerase for high specificity, PCR-213L 1000 units
antibody-blocked
PCR-213XL 5000 units

Good to know: Why Hot Start Polymerase?

Standard thermostable polymerases (e.g. Taq) show optimal performance around 70°C.
Nevertheless, a remaining enzymatic activity at room temperature may lead to unspecific
products.
If using Hot Start Technology, the polymerase activity is blocked by an aptamer or antibody
(Ab+) at ambient temperature and switched on automatically at the onset of the initial
denaturation. The thermal activation prevents the extension of nonspecifically annealed
primers and primer-dimer formation at low temperatures during PCR setup.
 www.jenabioscience.com High Fidelity & Pfu-X Polymerase Mixes 11

High Fidelity & Pfu-X Polymerase Mixes

High Fidelity Polymerase is based on a blend Pfu-X Polymerase is the ideal choice for ap-
of Taq DNA polymerase and a proofreading plications where efficient amplification of
enzyme specially designed for highly accurate DNA with highest fidelity is required. This en-
and efficient amplification. It shows excellent gineered enzyme has a proofreading function
results with extremely long (up to 30 kb), GC- that reduces error rates by a factor of 200 com-
rich or other difficult templates. pared to Taq Polymerase.

Product Cat.-No. Amount

High Fidelity Core Kit PCR-234S 100 units
Kit of thermostable pol for high accuracy,
dNTPs & reaction buffer PCR-234L 500 units
High Fidelity Hot Start Core Kit PCR-235S 100 units
Kit of heat-activatable pol for high accuracy,
dNTPs & react. buffer PCR-235L 500 units
Pfu-X Core Kit PCR-237S 100 units
Kit of proofreading DNA polymerase for highest
accuracy, dNTPs and reaction buffer PCR-237L 500 units

High Fidelity Polymerase PCR-204S 100 units

Thermostable DNA polymerase for high accuracy PCR-204L 500 units
High Fidelity Hot Start Polymerase PCR-205S 100 units
Heat-activatable DNA polymerase for
high accuracy & specificity PCR-205L 500 units

Pfu-X Polymerase PCR-207S 100 units

Proofreading DNA polymerase for highest accuracy PCR-207L 500 units
12 dNTP Mixes Building Blocks of Life

dNTP Mixes

Molecular biology grade dNTP Mixes are specified

for use in all molecular biology applications
including real-time PCR, high-fidelity PCR,
long-range PCR, LAMP, cDNA synthesis, reverse
transcription, DNA labeling or sequencing. Jena
Bioscience guarantees purities greater 99  %
(confirmed by RP-HPLC) combined with highest
long term stability.

Product Cat.-No. Amount

dNTP Mix NU-1006S 400 μl

Equimolar Mix of 10 mM dATP, dCTP, dGTP and dTTP NU-1006L 2 × 1 ml

dNTP Mix NU-1023S 200 μl

Equimolar Mix of 25 mM dATP, dCTP, dGTP and dTTP NU-1023L 1 ml

dNTP Mix dUTP NU-1020S 200 μl

Premix of 10 mM dATP, dCTP, dGTP and 20 mM dUTP NU-1020L 1 ml
 dNTP Bundles and Singles 13

dNTP Bundles and Singles

Jena Bioscience is a primary manufac-

turer of premium quality dNTPs. Our
dNTPs are synthesized using enzymatic
technologies followed by chromato-
graphic purification cascades. dNTPs are
manufactured in a single step from their
corresponding Ribo-NTPs.

Each lot is tested functionally by a set of PCR, RT-PCR and Klenow reactions. All dNTPs are screened for
remains of bacterial/human DNA, DNases, RNases, nicking enzymes or proteases.

Product Cat.-No. Amount

dNTP Bundle NU-1005S 4 × 200 μl (4 × 20 μmol)

4 × 100 mM (dATP, dCTP, dGTP, dTTP) NU-1005L 4 × 1 ml (4 × 100 μmol)
dATP-Solution – 100 mM Sodium salt solution NU-1001L 1 ml
dCTP-Solution – 100 mM Sodium salt solution NU-1002L 1 ml
dGTP-Solution – 100 mM Sodium salt solution NU-1003L 1 ml
dTTP-Solution – 100 mM Sodium salt solution NU-1004L 1 ml
dUTP-Solution – 100 mM Sodium salt solution NU-1008L 1 ml
dITP-Solution – 100 mM Sodium salt solution NU-1007L 1 ml

Jena Bioscience’s annual manufacturing capacity of several hundred liters of 100 mM dNTP solutions.
On request, Jena Bioscience provides bulk amounts at significant discounts, custom formulations,
packaging & labeling.

All dNTPs and PCR Mixes are available as solids.

Learn more in our Lyophilisation brochure or get in touch
([email protected]).
14 Buffer and Enhancer Building Blocks of Life

Buffer and Enhancer

Our Buffer and Enhancer section con-

tains components optimized for appli-
cations ranging from routine PCR over
DNA labeling to amplification of difficult
templates.
It includes kits to facilitate amplification
of GC-rich structures and to enhance PCR
yields.

Product Cat.-No. Amount

PCR-grade Water PCR-258S 10 × 1,2 ml

PCR-258L 50 ml
PCR-258XL 500 ml
Ruby Buffer PCR-272 5 × 1,2 ml
Crystal Buffer PCR-271 5 × 1,2 ml
KCl Buffer PCR-262 5 × 1,2 ml
Labeling Buffer PCR-263 5 × 1,2 ml
MgCl2 Stock PCR-266-25 4 × 1,5 ml (25 mM)
PCR Additives PCR-252 500 reactions
dNTP Mix GCamplifier PCR-257 100 μl
 www.jenabioscience.com Gel, Loading and Staining 15

Gel, Loading and Staining

Our Gel, Loading and Staining section includes agarose, loading buffer and DNA staining solutions
for gel electrophoresis. SYBR Green containing gel loading buffer provides an excellent DNA detection
sensitivity and is the ideal alternative to classical EtBr-based gel staining procedures.

Product Cat.-No. Amount

LE Agarose PCR-269S 100 g

PCR-269L 500 g
Gel Loading Buffer – Blue PCR-254-bl 5 × 1,8 ml
Gel Loading Buffer – Green PCR-254-gr 5 × 1,8 ml
Gel Loading Buffer – Orange PCR-254-or 5 × 1,8 ml
Gel Loading Buffer with DNA Stain – Blue PCR-255-bl 5 × 1,8 ml
Gel Loading Buffer with DNA Stain – Green PCR-255-gr 5 × 1,8 ml
Gel Loading Buffer with DNA Stain – Orange PCR-255-or 5 × 1,8 ml
SYBR DNA Stain PCR-273 5 × 1,8 ml
 Jena Bioscience GmbH
Loebstedter Str. 71 Test the exceptional performance
07749 Jena of our Endpoint PCR Mixes for yourself.
Germany

Phone +49 (0)3641- 62 85 000

Fax  +49 (0)3641- 62 85 100
Request a sample!
[email protected]
Our entire product range is available as samples.

www.jenabioscience.com

ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO
TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCAC-
GAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO TTCAGGGAAGAA CTAUAACTGCCAC ACCCACGAAAGGGAA ATAAGC AACO

Molecular Biology