PCR/Sequencing Utilities (Catalog as PDF)

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).
Item Catalog No. Pack Price ($)
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 100µm 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 100µm 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 100µm 105.00
  (Purine) 10-1041-02 0.25g 255.00
10-1044-90 100µm 125.00
10-1044-02 0.25g 325.00
10-1047-90 100µm 195.00
10-1047-02 0.25g 595.00
10-1048-90 100µm 195.00
10-1048-02 0.25g 595.00
10-1049-90 100µm 195.00
10-1049-02 0.25g 595.00

dI
dI
dI-CPG 500
dI-CPG 500
dI-CPG 1000
dI-CPG 1000
dU
dU
dU-CPG 500
dU-CPG 500
dU-CPG 1000
dU-CPG 1000
2'-DeoxyNebularine (Purine)
2'-DeoxyNebularine (Purine)
5-Nitroindole
5-Nitroindole
dP
dP

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septumcapped 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.

Monomers  

For Instrument type
Add
Expedite
E
Mermade
M

Columns  

For Instrument type
Add
Expedite
E
Applied Biosystems 3900
A
Mermade
M

Please inquire for availability of columns for other instrument types.

Duplex Effects (Cont)

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.)
Item Catalog No. Pack Price ($)
10-1065-90 100µm 100.00
10-1065-02 0.25g 255.00
10-1078-90 100µm 165.00
10-1078-02 0.25g 355.00
dmf-5-Me-isodC
dmf-5-Me-isodC
dmf-isodG
dmf-isodG

Intellectual Property

These products are 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.

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septumcapped 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.

Monomers  

For Instrument type
Add
Expedite
E
Mermade
M

Columns  

For Instrument type
Add
Expedite
E
Applied Biosystems 3900
A
Mermade
M

Please inquire for availability of columns for other instrument types.

CleanAmp Monomers

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.
Item Catalog No. Pack Price ($)
10-1440-90 100µm 100.00
10-1440-02 0.25g 240.00
10-1440-05 0.5g 480.00
10-1450-90 100µm 100.00
10-1450-02 0.25g 240.00
10-1450-05 0.5g 480.00
10-1460-90 100µm 100.00
10-1460-02 0.25g 240.00
10-1460-05 0.5g 480.00
10-1470-90 100µm 100.00
10-1470-02 0.25g 240.00
10-1470-05 0.5g 480.00
CleanAmp™-Pac-dA
CleanAmp™-Pac-dA
CleanAmp™-Ac-dC
CleanAmp™-Ac-dC
CleanAmp™-Pac-dG
CleanAmp™-Pac-dG
CleanAmp™-dT
CleanAmp™-dT

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.

See Also

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.)
Item Catalog No. Pack Price ($)
10-1031-90 100µm 135.00
10-1031-02 0.25g 355.00
10-1932-90 100µm 150.00
10-1932-02 0.25g 400.00
20-2004-01 0.1g 400.00
  1 µmole columns 20-2104-41 Pack of 4 675.00
  0.2 µmole columns 20-2104-42 Pack of 4 225.00
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 100µm 130.00
10-7001-02 0.25g 545.00
10-7101-90 100µm 130.00
10-7101-02 0.25g 545.00
10-7201-90 100µm 145.00
10-7201-02 0.25g 675.00
10-7301-90 100µm 130.00
10-7301-02 0.25g 545.00
5'-OMe-dT
5'-OMe-dT
5'-Amino-dT
5'-Amino-dT
3'-dA-CPG
3'-dA-CPG
3'-dC-CPG
3'-dC-CPG
3'-dG-CPG
3'-dG-CPG
3'-dT-CPG
3'-dT-CPG
2',3'-ddC-CPG
2',3'-ddC-CPG
2',3'-ddA
2',3'-ddA
2',3'-ddC
2',3'-ddC
2',3'-ddG
2',3'-ddG
2',3'-ddT
2',3'-ddT

Reference(s)

  1. P.Y. Chen, et al., RNA, 2008, 14, 263- 274

OTHER INSTRUMENT TYPES

All minor bases, RNA products and modifiers are packaged in septumcapped 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.

Monomers  

For Instrument type
Add
Expedite
E
Mermade
M

Columns  

For Instrument type
Add
Expedite
E
Applied Biosystems 3900
A
Mermade
M

Please inquire for availability of columns for other instrument types.

See Also


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