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. 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 |
| 10-1523-90 |
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 investigational 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 application. 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.
|
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. |
|