duplex
effects
The design of primers is frequently complicated by the degeneracy
of the genetic code. Three strategies are now available to confront this
problem. In the first, a mixed base addition (N) is used to form the degenerate
site. This approach is best if the number of degenerate sites is small.
A second option is the use of 2’-deoxyInosine or 2’-deoxyNebularine
which exhibit low, but unequal, hydrogen bonding to the other four bases.
The third option is the use of a universal nucleoside. In this strategy,
the base analog does not hybridize significantly to the other four bases
and makes up some of the duplex destabilization by acting as an intercalating
agent. 3-Nitropyrrole 2’-deoxynucleoside (M) is the first example
of a set of universal bases. Subsequently, 5-nitroindole was determined
to be an effective universal base and to be superior to 3-nitropyrrole,
based on duplex melting experiments.
The modified bases designated P and K show considerable promise as degenerate
bases. The pyrimidine derivative P, when introduced into oligonucleotides,
base pairs with either A or G, while the purine derivative K base pairs
with either C or T. A dP+dK mix also can serve as a mixed base with much
less degeneracy than dA+dC+dG+dT (N).
| 10-1002-02 |
0.25g |
40.00 |
| 10-1013-02 |
0.25g |
40.00 |
| 10-1023-02 |
0.25g |
40.00 |
| Other mixed base combinations
and custom doping of individual monomers are available on request. Also, mixed base columns are available in 0.2 and 1.0 µmole sizes
on request. |
| 10-1040-90 |
100 µmole |
50.00 |
| |
10-1040-02 |
0.25g |
120.00 |
| 20-2040-01 |
0.1g |
30.00 |
| 1 µmole columns |
20-2190-41 |
Pack of 4 |
120.00 |
| 0.2 µmole columns |
20-2190-42 |
Pack of 4 |
72.00 |
| 20-2041-01 |
0.1g |
30.00 |
| 1 µmole columns |
20-2191-41 |
Pack of 4 |
120.00 |
| 0.2 µmole columns |
20-2191-42 |
Pack of 4 |
72.00 |
| 10-1050-90 |
100 µmole |
35.00 |
| |
10-1050-02 |
0.25g |
100.00 |
| 20-2050-01 |
0.1g |
30.00 |
| 1 µmole columns |
20-2150-41 |
Pack of 4 |
120.00 |
| 0.2 µmole columns |
20-2150-42 |
Pack of 4 |
72.00 |
| 20-2051-01 |
0.1g |
50.00 |
| 1 µmole columns |
20-2151-41 |
Pack of 4 |
200.00 |
| 0.2 µmole columns |
20-2151-42 |
Pack of 4 |
120.00 |
| 10-1041-90 |
100 µmole |
105.00 |
| (Purine) |
10-1041-02 |
0.25g |
255.00 |
| 10-1043-90 |
100 µmole |
125.00 |
| |
10-1043-02 |
0.25g |
325.00 |
| 10-1044-90 |
100 µmole |
125.00 |
| |
10-1044-02 |
0.25g |
325.00 |
| 10-1047-90 |
100 µmole |
195.00 |
| |
10-1047-02 |
0.25g |
595.00 |
| 10-1048-90 |
100 µmole |
195.00 |
| |
10-1048-02 |
0.25g |
595.00 |
| 10-1049-90 |
100 µmole |
195.00 |
| |
10-1049-02 |
0.25g |
595.00 |
Unnatural base pairs display unique abilities in duplex DNA and in nucleic acid and protein biosyntheses. A standard Watson and Crick base pair is formed between iso-C and iso-G, but the hydrogen bonding pattern is quite different from the natural base pairs A-T and C-G. (The 5-methyl analogue was chosen as the synthetic target due to the reported instability of 2’-deoxyisocytidine caused by deamination during oligonucleotide synthesis or deprotection.)
The unnatural base pair between 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) is formed by specific hydrophobic shape complementation. The shape of the Ds-Pa pair is different from those of the natural A-T and G-C pairs, but the Ds-Pa pair works together with the natural pairs in in vitro replication and transcription. Pa also functions as a template base for incorporating another unnatural base, 2-amino-6-(2-thienyl)purine (s), into RNA. The s base also acts as a unique fluorescent base analog in DNA and RNA fragments. dDss is strongly fluorescent and is useful as a fluorescent tag for DNA detection. dDss also forms a base pair with dPa. Biotin PaTP can be site-specifically incorporated into RNA, opposite dDs at a desired position in DNA templates, by T7 transcription. Similarly, the fluorescent s base can be site-specifically incorporated into RNA opposite dPa in DNA templates.
| 10-1065-90 |
100 µmole |
100.00 |
| |
10-1065-02 |
0.25g |
255.00 |
| 10-1078-90 |
100 µmole |
165.00 |
| |
10-1078-02 |
0.25g |
355.00 |
| 10-1521-90 |
100 µmole |
145.00 |
| |
10-1521-02 |
0.25g |
420.00 |
| 10-1522-90 |
100 µmole |
170.00 |
| |
10-1522-02 |
0.25g |
420.00 |
| 10-1524-95 |
50 µmole |
130.00 |
| |
10-1524-90 |
100 µmole |
250.00 |
| |
10-1524-02 |
0.25g |
675.00 |
| 10-1523-90 |
100 µmole |
130.00 |
| |
10-1523-02 |
0.25g |
420.00 |
| 81-3522-02 |
25 µL |
350.00 |
| 81-3525-02 |
25 µL |
450.00 |
|
|
OTHER INSTRUMENT TYPES
All minor bases, RNA products and modifiers are packaged in septum-capped vials suitable for ABI and other instruments. If you would like another type of vial/column add the following to the end of the catalog number.
Expedite |
E |
Beckman Oligo 1000 |
B |
Pharmacia Gene Assembler |
P |
Mermade |
M |
Applied Biosystems 3900 |
A |
Expedite |
E |
Mermade |
M |
|
Please inquire for availability
of columns for other
instrument types.
|
INTELLECTUAL PROPERTY
Iso-bases are supplied under license from EraGen Biosciences,
Inc. US Patents 5,432,272, 6,001,983, 6,037,120, and 6,140,496.
Products containing Ds, s or Pa bases
This product is covered by patents or patents pending owned by TagCyx Biotechnologies. Purchase of this product includes a limited license to use this product solely for research. This license specifically excludes: (a) therapeutic or diagnostic applications (including products or services that incorporate this product), (b) any in vivo toxicity/safety study in support of an invest-igational new drug application (or foreign counterpart), (c) resale, or (d) gene functionalization activities (including products or services that incorporate data derived from gene functionalization activities) if such activities have commercial appli-cation. All of the above require a separate license from TagCyx Biotechnologies. Neither this product nor any product created through its use may be used in human clinical trials.
|
CleanAmp™ Primers
CleanAmp™ Primers offer an alternative to other Hot Start technologies and allow greater control of primer hybridization and extension during PCR. It has been demonstrated that CleanAmp™ Primers outperform other technologies in multiple applications. Indeed, over a broad range of applications, CleanAmp™ Primers reduce or eliminate off-target amplification. Greater amplicon yield is also achieved, due to improvement in specificity and sensitivity. By using either the slow-releasing Precision primers with two CleanAmp™ phosphotriester linkages or the faster-releasing Turbo Primers with a single CleanAmp™ phosphotriester linkage, the rate of formation of unmodified primer can be controlled to suit reaction needs. A table to aid in the selection of Turbo and Precision Primers for specific applications is shown below.
| Turbo Primers |
Precision Primers |
| Fast cycling |
Standard cycling |
| Multiplex PCR |
One-step reverse-transcription PCR |
| Improves amplicon yield |
Improved specificity and limit of detection |
| Reduces mis-priming/ primer dimer formation |
Greatest reduction in mis-priming/primer dimer formation |
Synthesis of CleanAmp™ Primers requires the use of UltraMild Chemistry.
| 10-1440-90 |
100 µmole |
100.00 |
| |
10-1440-02 |
0.25g |
240.00 |
| |
10-1440-05 |
0.5g |
480.00 |
| 10-1450-90 |
100 µmole |
100.00 |
| |
10-1450-02 |
0.25g |
240.00 |
| |
10-1450-05 |
0.5g |
480.00 |
| 10-1460-90 |
100 µmole |
100.00 |
| |
10-1460-02 |
0.25g |
240.00 |
| |
10-1460-05 |
0.5g |
480.00 |
| 10-1470-90 |
100 µmole |
100.00 |
| |
10-1470-02 |
0.25g |
240.00 |
| |
10-1470-05 |
0.5g |
480.00 |
CleanAmp is a Trademark of TriLink BioTechnologies |
SEE ALSO
UltraMild DNA Synthesis p24
INTELLECTUAL PROPERTY
CleanAmp™ is a trademark of TriLink BioTechnologies, Inc. CleanAmp™ products or portions thereof are covered by TriLink pending Patent Applications, US 2007281308 and WO2007139723, US Provisional Patent Application Serial # 61/056,324 and US Patent 6762298 licensed from the Department of Health and Human Services. CleanAmp™ products are sold exclusively for R&D use by the purchaser. They may not be resold, distributed or re-packaged. No license is granted or implied with the purchase of this product. Amplification methods used in connection with Polymerase Chain Reaction (“PCR”) Process are covered by many patents. It may be necessary to obtain a separate license for certain patented applications in which the product is used. CleanAmp™ Licenses are available directly from TriLink BioTechnologies.
www.trilinkbiotech.com |
chain terminators
In situations where ligation must be blocked at the 5’ terminus, 5’-OMe-dT may be used. 5’-OMe modification of a strand of siRNA using 5’-OMe-T can control guide strand selection and targeting specificity.1 5’-Amino-dT terminates an oligonucleotide with a 5’-amino group which may be used for attaching a peptide or a PNA sequence. To avoid polymerase extension at the 3’ terminus, 2’,3’-dideoxynucleoside and 3’-deoxynucleoside CPGs have proved to be effective. 2’,3’- Phosphoramidites are designed to be used with the 5’-phosphoramidites and supports. Since these phosphoramidites have no DMT group, they are not compatible with purification by the DMT-on technique. Ion exchange HPLC or PAGE should be used to purify these dideoxy terminated oligos to ensure that shorter sequences (containing 3’-OH) groups are removed. (3’-Termination can also be effected using a 3’-3’ linkage formed using 5’-supports, or 3’-spacer C3 CPG.)
| 10-1031-90 |
100 µmole |
135.00 |
| |
10-1031-02 |
0.25g |
355.00 |
| 10-1932-90 |
100 µmole |
150.00 |
| |
10-1932-02 |
0.25g |
400.00 |
| 20-2004-01 |
0.1g |
300.00 |
| 1 µmole columns |
20-2104-41 |
Pack of 4 |
600.00 |
| 0.2 µmole columns |
20-2104-42 |
Pack of 4 |
200.00 |
| 20-2064-01 |
0.1g |
300.00 |
| 1 µmole columns |
20-2164-41 |
Pack of 4 |
600.00 |
| 0.2 µmole columns |
20-2164-42 |
Pack of 4 |
200.00 |
| 20-2074-01 |
0.1g |
300.00 |
| 1 µmole columns |
20-2174-41 |
Pack of 4 |
600.00 |
| 0.2 µmole columns |
20-2174-42 |
Pack of 4 |
200.00 |
| 20-2084-01 |
0.1g |
300.00 |
| 1 µmole columns |
20-2184-41 |
Pack of 4 |
600.00 |
| 0.2 µmole columns |
20-2184-42 |
Pack of 4 |
200.00 |
| 20-2017-01 |
0.1g |
300.00 |
| 1 µmole columns |
20-2117-41 |
Pack of 4 |
600.00 |
| 0.2 µmole columns |
20-2117-42 |
Pack of 4 |
200.00 |
| 10-7001-90 |
100 µmole |
130.00 |
| |
10-7001-02 |
0.25g |
545.00 |
| 10-7101-90 |
100 µmole |
130.00 |
| |
10-7101-02 |
0.25g |
545.00 |
| 10-7201-90 |
100 µmole |
230.00 |
| |
10-7201-02 |
0.25g |
975.00 |
| 10-7301-90 |
100 µmole |
130.00 |
| |
10-7301-02 |
0.25g |
545.00 |
|
SEE ALSO
5’-Phosphoramidites
p33
5’-Supports
p34
3’-Spacer
C3 CPG p72
Reference
(1) P.Y. Chen, et al., RNA, 2008, 14, 263-274..
OTHER INSTRUMENT TYPES
All minor bases, RNA products and modifiers are packaged in septum-capped vials suitable for ABI and other instruments. If you would like another type of vial/column add the following to the end of the catalog number.
Expedite |
E |
Beckman Oligo 1000 |
B |
Pharmacia Gene Assembler |
P |
Mermade |
M |
Applied Biosystems 3900 |
A |
Expedite |
E |
Mermade |
M |
|
Please inquire for availability
of columns for other
instrument types. |
|