Download MGB_LNA_Substitutes

Design and Synthesis of Nucleic Acids
with Enhanced Hybridization Properties
Interested in replacing your MGBTM
or LNATM probes?
The
(minor groove binding) and
(locked nucleic acid) technologies are used to
enhance the affinity of a standard oligonucleotide
sequence to its complementary nucleotide strand.
Since both technologies are patent protected, its
use, distribution as well as pricing are selectively
controlled.
To overcome this disadvantage, Microsynth has
established a cost-effective alternative to enhance
the affinity properties of normal DNA/RNA oligonucleotide sequences. Microsynth offers four
different modifiers that can be used as substitutes
for the normal bases C, U, and A during synthesis
(see table below and figure to the right). Thus, it is
possible to design and synthesize oligonucleotide
sequences with the desired hybridization
properties.
Name of DNA/ RNA
65.5
LNATM
St andard Bas e t o
ΔTm/ bas e
Subs t it ut e
be Replac ed
[ + °C]
Propynyl-dC*
Cytosine
up to 2.8
Propynyl-dU*
Uracil/Thymidine
up to 1.7
5-Methyl-dC
Cytosine
up to 1.3
2-Amino-dA
Adenine
up to 3.0
* Propynyl-dC and -dU are only available, if used for research purposes
(you will have to confirm this by signing a notification sheet)
0.8
0x
1x
2x
3x
0.7
0.6
relative Fluorescence
MGBTM
Melting curves of a molecular beacon containing
0, 1, 2, or 3 propynyl-dC bases
67.5
68.5
70.0
pdC
pdC
pdC
pdC
0.5
0.4
0.3
0.2
0.1
0
55
60
65
70
75
-0.1
Temperature [°C]
The above melting curves of a molecular beacon (FAM-BHQ)
show that the incorporation of 3 propynyl-dC bases into its
hairpin region increase its melting temperature by 4.5°C. It is
important to note that the effective increase of melting
temperature per single nucleotide exchange is subject to
variation. The main parameters are the position of the respective base to be substituted as well as the whole sequence.
When to use?
 Generally, in any application with short DNA/RNA
targets where normal oligonucleotides do not
show sufficient affinity or specificity
 SNP genotyping
 Allele-specific real-time PCR
Why use our design and synthesis
service?
 To optimize detection of short DNA/RNA targets
by generating shorter probes with higher Tms
 To achieve high affinity by increasing the thermal
stability of duplexes
Need more information?
 Call us at +41-71-722 83 33
 E-mail us at [email protected]
 To enhance the discrimination properties of your
probes
 To benefit from a cost-effective alternative as
compared to the MGBTM and LNATM probes
 To obtain full transparency over your experiment
and to be compliant with MIQE guidelines
 To benefit from our free design service as well as
from 22 years experience in the design and
synthesis of high-quality oligonucleotides
An ISO 9001:2008-certified company
Microsynth AG, Schützenstr. 15, CH-9436 Balgach T: +41-71-722 83 33 www.microsynth.ch