Labelling (Catalog as PDF)

Serinol Reagents for Modification and Labelling

Most popular non-nucleosidic phosphoramidites for modification and labelling are based on two structural types: 1,2-diols and 1,3-diols. Products based on a 1,2-diol backbone were first described to allow amino-modification and biotin labelling. Technically, the 1,2-diol backbone has some drawbacks relative to the 1,3-diol backbone. The 1,2-diol backbone can participate in a dephosphorylation reaction since the 1,2-diol can form a favored 5-membered cyclic phosphate intermediate. This reaction is competitive with simple hydrolysis of the protecting groups and leads to some loss of label. However, the degree of loss at the 3' terminus can be limited by the removal of the cyanoethyl protecting group using DBU or diethylamine prior to the cleavage and deprotection steps. Similarly, loss at the 5' terminus can be eliminated by retaining the DMT group until the oligo is fully deprotected. Fortunately, the elimination reaction is virtually non-existent in the 1,3-diol backbone since the cyclic intermediate would be a 6-membered ring which is not favored for a cyclic phosphate intermediate.

IVD customers have requested a new backbone based on a 1,3-diol that would overcome any technical or IP issues surrounding our current products. We now offer a line of products based on the serinol backbone, which have been developed in close collaboration between Glen Research and Nelson Biotechnologies. Protected Biotin Serinol Phosphoramidite and CPG are protected with a t-butylbenzoyl group on the biotin ring. This group is designed to stop any phosphoramidite reactions at this active position in biotin. This protection avoids branching when using nucleophilic activators like DCI. The protecting group is easily removed during oligonucleotide cleavage and deprotection. The BiotinLC versions are similarly protected and should be useful for the synthesis of highly sensitive biotinylated probes. 6-Fluorescein Serinol Phosphoramidite and CPG are designed to prepare oligonucleotides containing one or several 6-Fluorescein (6-FAM) residues. Amino-Modifier Serinol Phosphoramidite and CPG are used to add amino groups into one or several positions in oligonucleotides. The amino group is protected with Fmoc, which may be removed on the synthesis column prior to solid-phase conjugation to the amino groups, or which may be removed during deprotection for subsequent solution phase conjugation to the amino groups.

Combining lipoic acid and our patented serinol backbone, we now offer Dithiol Serinol Phosphoramidite and the related 3'-Dithiol Serinol CPG. This unique architecture incorporates a linker that moves the bulky dithiol away from the phosphate backbone. The long spacer arm of Dithiol Serinol also allows multiple consecutive incorporations of the modifier without the need for intermediate spacer phosphoramidite additions to achieve optimal stepwise coupling efficiency.We offer two products for use in Click Chemistry based upon our 1,3-diol product portfolio with the serinol backbone - a phosphoramidite for adding an alkyne group at the 5' terminus or within the sequence, and a synthesis support for labelling the 3' terminus of oligonucleotides with an alkyne group.

We offer three products for use in Click Chemistry based upon our 1,3-diol product portfolio with the serinol backbone - a phosphoramidite for adding an alkyne group at the 5' terminus or within the sequence, a synthesis support for labeling the 3' terminus of oligonucleotides with an alkyne group, and DBCO-Serinol phosphoramidite as a copper-free click reagent .
Item Catalog No. Pack Price ($)
10-1993-95 50µm 165.00
10-1993-90 100µm 295.00
10-1993-02 0.25g 675.00
10-1994-95 50µm 165.00
10-1994-90 100µm 295.00
10-1994-02 0.25g 595.00
10-1995-95 50µm 205.00
10-1995-90 100µm 365.00
10-1995-02 0.25g 675.00
10-1997-95 50µm 125.00
10-1997-90 100µm 225.00
10-1997-02 0.25g 595.00
10-1991-95 50µm 120.00
10-1991-90 100µm 215.00
10-1991-02 0.25g 585.00
10-1992-95 50µm 100.00
10-1992-90 100µm 185.00
10-1992-02 0.25g 575.00
10-1998-95 50µm 180.00
10-1998-90 100µm 340.00
10-1998-02 0.25g 895.00
20-2993-01 0.1g 120.00
20-2993-10 1.0g 995.00
  0.2 µmole columns 20-2993-42 Pack of 4 120.00
10-1992-02 0.25g 575.00
  1 µmole columns 20-2993-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2993-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2993-14 Pack of 1 450.00
20-2994-01 0.1g 120.00
20-2994-10 1.0g 995.00
  0.2 µmole columns 20-2994-42 Pack of 4 120.00
  1 µmole columns 20-2994-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2994-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2994-14 Pack of 1 450.00
20-2995-01 0.1g 120.00
20-2995-10 1.0g 995.00
  0.2 µmole columns 20-2995-42 Pack of 4 120.00
  1 µmole columns 20-2995-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2995-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2995-14 Pack of 1 450.00
20-2997-01 0.1g 95.00
20-2997-10 1.0g 675.00
  0.2 µmole columns 20-2997-42 Pack of 4 85.00
  1 µmole columns 20-2997-41 Pack of 4 140.00
  10 µmole column (ABI) 20-2997-13 Pack of 1 250.00
  15 µmole column (Expedite) 20-2997-14 Pack of 1 375.00
20-2991-01 0.1g 120.00
20-2991-10 1.0g 995.00
  0.2 µmole columns 20-2991-42 Pack of 4 120.00
  1 µmole columns 20-2991-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2991-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2991-14 Pack of 1 450.00
20-2992-01 0.1g 105.00
20-2992-10 1.0g 800.00
  0.2 µmole columns 20-2992-42 Pack of 4 100.00
  1 µmole columns 20-2992-41 Pack of 4 175.00
  10 µmole column (ABI) 20-2992-13 Pack of 1 260.00
  15 µmole column (Expedite) 20-2992-14 Pack of 1 390.00
Protected Biotin Serinol
Protected Biotin Serinol
6-Fluorescein Serinol
6-Fluorescein Serinol
Protected BiotinLC Serinol
Protected BiotinLC Serinol
3'-Amino-Modifier Serinol CPG
3'-Amino-Modifier Serinol CPG
Dithiol Serinol
Dithiol Serinol
Amino-Modifier Serinol
Amino-Modifier Serinol
3'-Dithiol Serinol CPG
3'-Dithiol Serinol CPG
DBCO-Serinol
DBCO-Serinol
Alkyne-Modifier Serinol
Alkyne-Modifier Serinol
3'-Alkyne-Modifier Serinol CPG
3'-Alkyne-Modifier Serinol CPG
3'-Protected Biotin Serinol CPG
3'-Protected Biotin Serinol CPG
3'-6-Fluorescein Serinol CPG
3'-6-Fluorescein Serinol CPG
3'-Protected BiotinLC Serinol CPG
3'-Protected BiotinLC Serinol CPG

Intellectual Property

Serinol products are covered by US Patent No.: 8,394,948.

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  

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Columns  

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Applied Biosystems 3900
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See Also

COT Serinol Phosphoramidite

Bright, long-lasting and non-phototoxic organic fluorophores are essential for the continued optimization of a diverse range of imaging applications. However, all currently available technologies remain susceptible to undesirable transitions to dark states. Dark states arise from non-fluorescent triplet electronic configurations from which the rate of return to the ground state is slow. When in the triplet state, the fluorophore is susceptible to photobleaching and fluorescence applications are compromised by unpredictably reducing the signal-to-noise ratio (SNR), as well as limiting the total duration of time over which information can be gathered. The direct conjugation of small-molecule protective agents (PAs) has enabled significant improvements through intra-molecular triplet quenching. Through a partnership with Lumidyne Technologies, Glen Research has created a novel PA-linked phosphoramidite using cyclooctatetraene (COT). COT Serinol Phosphoramidite provides a means to improve the photostability of virtually any fluorophore in a modular fashion. Our spectrofluorometric studies show that the presence of COT limited the amount of photobleaching of an oligo containing the cyanine 5 dye.
Item Catalog No. Pack Price ($)
10-1996-95 50µm 310.00
10-1996-90 100µm 600.00
10-1996-02 0.25g 1800.00
COT Serinol
COT Serinol

Intellectual Property

10-1996 is covered by US Patent Nos.: 8,394,948 and 8,945,515 B2.

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  

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Applied Biosystems 3900
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Dabcyl Labelling

A molecular beacon probe1 has its natural fluorescence quenched in solution unless it is hybridized to the target sequence. Consequently, the design of a molecular beacon requires a fluorophore to be in one part of the sequence and the quencher molecule to be in another, with both molecules being separated from the oligonucleotide by a hydrocarbon spacer. The Dabcyl group has been found to be a universal quencher. 3'-Dabsyl CPG and 3'-Dabcyl CPG are used to prepare probes with the quencher blocking the 3'-terminus. 5'-Dabcyl Phosphoramidite locates the quencher at the 5'-terminus and Dabcyl-dT places it within the sequence, leaving the 3'-terminus available for polymerase extension.
Item Catalog No. Pack Price ($)
20-5911-01 0.1g 120.00
20-5911-10 1.0g 975.00
  1 µmole columns 20-5911-41 Pack of 4 200.00
  0.2 µmole columns 20-5911-42 Pack of 4 120.00
  10 µmole column (ABI) 20-5911-13 Pack of 1 350.00
  15 µmole column (Expedite) 20-5911-14 Pack of 1 500.00
20-5912-01 0.1g 120.00
20-5912-10 1.0g 975.00
  1 µmole columns 20-5912-41 Pack of 4 200.00
  0.2 µmole columns 20-5912-42 Pack of 4 120.00
  10 µmole column (ABI) 20-5912-13 Pack of 1 350.00
  15 µmole column (Expedite) 20-5912-14 Pack of 1 500.00
26-5912-01 0.1g 125.00
26-5912-10 1.0g 1025.00
  200 nmole columns 26-5912-52 Pack of 10 300.00
  40 nmole columns 26-5912-55 Pack of 10 300.00
10-1058-95 50µm 180.00
10-1058-90 100µm 325.00
10-1058-02 0.25g 675.00
10-5912-95 50µm 125.00
10-5912-90 100µm 225.00
10-5912-02 0.25g 650.00
3'-Dabsyl CPG
3'-Dabsyl CPG
3'-Dabcyl CPG
3'-Dabcyl CPG
Dabcyl-dT
Dabcyl-dT
5'-Dabcyl
5'-Dabcyl
3'-Dabcyl PS
3'-Dabcyl PS

Reference(s)

  1. S. Tyagi and F.R. Kramer, Nature Biotechnology, 1996, 4, 303-308.

Biotin Labelling

Glen Research biotin phosphoramidites for direct labelling of synthetic oligonucleotides exhibit the following features:

  1. All are soluble in acetonitrile at concentrations useful for DNA synthesis.

  2. All include a DMT group for cartridge purifications which is essential for the preparation of biotinylated PCR primers because of the potential for cross contamination in HPLC purifications.

  3. For the development of diagnostic probes, biotin phosphoramidite is capable of branching to allow multiple biotins to be introduced at the 3'- or 5'-terminus. BiotinTEG Phosphoramidite contains a 15 atom mixed polarity spacer arm based on a triethylene glycol.

  4. Protected Biotin Serinol Phosphoramidite and CPG are protected with a t-butylbenzoyl group on the biotin ring. This group is designed to stop any phosphoramidite reactions at this active position in biotin. This protection avoids branching when using nucleophilic activators like DCI. The protecting group is easily removed during oligonucleotide cleavage and deprotection. The BiotinLC versions are similarly protected and should be useful for the synthesis of highly sensitive biotinylated probes.

  5. Item Catalog No. Pack Price ($)
    10-1953-95 50µm 165.00
    10-1953-90 100µm 295.00
    10-1953-02 0.25g 675.00
    10-1955-95 50µm 165.00
    10-1955-90 100µm 295.00
    10-1955-02 0.25g 675.00
    10-1993-95 50µm 165.00
    10-1993-90 100µm 295.00
    10-1993-02 0.25g 675.00
    10-1995-95 50µm 205.00
    10-1995-90 100µm 365.00
    10-1995-02 0.25g 675.00
    Biotin
    Biotin
    Protected Biotin Serinol
    Protected Biotin Serinol
    BiotinTEG
    BiotinTEG
    Protected BiotinLC Serinol
    Protected BiotinLC Serinol

Intellectual Property

Serinol products are covered by US Patent No.: 8,394,948.

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
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Expedite
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Columns  

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Applied Biosystems 3900
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See Also

Biotin Labelling (Part 2)

Biotin-dT can replace dT residues within the oligonucleotide sequence. 5'-Biotin phosphoramidite can be added ONLY ONCE to the 5'-terminus of an oligonucleotide. However, the DMT group on the biotin can be used in RP cartridge and HPLC purification techniques. PC Biotin is a photocleavable 5'-biotin phosphoramidite. BiotinTEG CPG and Protected BiotinLC Serinol CPG are designed for the direct synthesis of oligonucleotides containing biotin at the 3' terminus.

Desthiobiotin is a biotin analogue that exhibits lower binding to biotin-binding proteins such as streptavidin. This biotin analogue is lacking the sulfur group from the molecule and has a dissociation constant (Kd) several orders of magnitude less than biotin/streptavidin. As a result, biomolecules containing desthiobiotin are dissociated from streptavidin simply in the presence of buffered solutions of biotin. We offer desthiobiotinTEG phosphoramidite and the corresponding CPG.

ABI-style vials and columns are supplied unless otherwise requested (see note box).
Item Catalog No. Pack Price ($)
10-5950-95 50µm 125.00
10-5950-90 100µm 225.00
10-5950-02 0.25g 650.00
10-1038-95 50µm 167.50
10-1038-90 100µm 325.00
10-1038-02 0.25g 625.00
10-4950-95 50µm 145.00
10-4950-90 100µm 280.00
10-4950-02 0.25g 675.00
10-1952-95 50µm 185.00
10-1952-90 100µm 335.00
10-1952-02 0.25g 775.00
20-2955-01 0.1g 120.00
20-2955-10 1.0g 995.00
  0.2 µmole columns 20-2955-42 Pack of 4 120.00
  1 µmole columns 20-2955-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2955-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2955-14 Pack of 1 450.00
26-2955-01 0.1g 125.00
26-2955-10 1.0g 1025.00
  200 nmole columns 26-2955-52 Pack of 10 300.00
  40 nmole columns 26-2955-55 Pack of 10 300.00
20-2993-01 0.1g 120.00
20-2993-10 1.0g 995.00
  0.2 µmole columns 20-2993-42 Pack of 4 120.00
  1 µmole columns 20-2993-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2993-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2993-14 Pack of 1 450.00
20-2995-01 0.1g 120.00
20-2995-10 1.0g 995.00
  0.2 µmole columns 20-2995-42 Pack of 4 120.00
  1 µmole columns 20-2995-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2995-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2995-14 Pack of 1 450.00
20-2952-01 0.1g 140.00
20-2952-10 1.0g 1150.00
  0.2 µmole columns 20-2952-42 Pack of 4 140.00
  1 µmole columns 20-2952-41 Pack of 4 230.00
  10 µmole column (ABI) 20-2952-13 Pack of 1 345.00
  15 µmole column (Expedite) 20-2952-14 Pack of 1 520.00
PC Biotin
PC Biotin
5'-Biotin
5'-Biotin
Biotin-dT
Biotin-dT
DesthiobiotinTEG
DesthiobiotinTEG
3'-BiotinTEG CPG
3'-BiotinTEG CPG
3'-BiotinTEG PS
3'-BiotinTEG PS
3'-Protected Biotin Serinol CPG
3'-Protected Biotin Serinol CPG
DesthiobiotinTEG-CPG
DesthiobiotinTEG-CPG
3'-Protected BiotinLC Serinol CPG
3'-Protected BiotinLC Serinol CPG

Intellectual Property

Glen Research offers PC Biotin, PC Amino-Modifier and PC Spacer products in association with AmberGen, Inc. and Link Technologies, Ltd. For a commercial application license, please contact AmberGen, Inc., +617-975-0680, http://www.ambergen.com/..

Serinol products are covered by US Patent No.: 8,394,948.

Fluorescein Labelling

5'-Fluorescein phosphoramidite contains no 4,4'-dimethoxytrityl (DMT) group and can be added only once at the 5'-terminus, thereby terminating synthesis. This product is prepared using the 6-carboxyfluorescein derivative. The tetrachloro (TET)-, hexachloro (HEX) - and dichloro-dimethoxy (JOE)- fluorescein phosphoramidites are designed to take advantage of the multicolor detection capability of modern DNA sequencers and genetic analyzers. Fluorescein phosphoramidite is designed to produce the same fluorescein-type structure as had been previously prepared using fluorescein isothiocyanate (FITC). Our fluorescein phosphoramidite also contains a DMT group to allow quantification of coupling. The analogous structure, 6-Fluorescein Phosphoramidite, prepared using 6-FAM, is also available, along with 6-Fluorescein Serinol Phosphoramidite. Fluorescein-dT can be inserted into the desired sequence as a replacement for a dT residue.

We offer five fluorescein supports. Fluorescein CPG has traditionally been used to add the fluorescein label at the 3'-terminus. The analogous structure, 3'-(6-Fluorescein) CPG, prepared using 6-FAM, is now also available, along with 6-Fluorescein Serinol CPG. We also offer 3'-(6-FAM) CPG and Fluorescein-dT CPG, both derivatives of 6-carboxyfluorescein (6-FAM). Both are single isomers and use an amide linkage which is stable during cleavage and deprotection and does not allow isomer formation. 3'-(6-FAM) CPG allows effective blockage of the 3'-terminus from polymerase extension as well as exonuclease digestion. Fluorescein-dT CPG allows both of these enzymatic activities to proceed. Normal cleavage and deprotection with ammonium hydroxide readily generates the fluorescein labelled oligos.

The spectral characteristics of these dyes are detailed on the following page.
Item Catalog No. Pack Price ($)
10-5901-95 50µm 110.00
  (6-FAM) 10-5901-90 100µm 215.00
10-5901-02 0.25g 575.00
10-5902-95 50µm 190.00
  (HEX) 10-5902-90 100µm 375.00
10-5902-02 0.25g 875.00
10-5903-95 50µm 180.00
  (TET) 10-5903-90 100µm 350.00
10-5903-02 0.25g 875.00
10-5906-95 50µm 105.00
  (JOE) 10-5906-90 100µm 198.00
10-5906-02 0.25g 495.00
10-1963-95 50µm 165.00
10-1963-90 100µm 295.00
10-1963-02 0.25g 595.00
10-1964-95 50µm 165.00
10-1964-90 100µm 295.00
10-1964-02 0.25g 595.00
10-1994-95 50µm 165.00
10-1994-90 100µm 295.00
10-1994-02 0.25g 595.00
10-1056-95 50µm 180.00
10-1056-90 100µm 325.00
10-1056-02 0.25g 675.00
20-2963-01 0.1g 120.00
20-2963-10 1.0g 995.00
  1 µmole columns 20-2963-41 Pack of 4 200.00
  0.2 µmole columns 20-2963-42 Pack of 4 120.00
  10 µmole column (ABI) 20-2963-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2963-14 Pack of 1 450.00
20-2964-01 0.1g 120.00
20-2964-10 1.0g 995.00
  1 µmole columns 20-2964-41 Pack of 4 200.00
  0.2 µmole columns 20-2964-42 Pack of 4 120.00
  10 µmole column (ABI) 20-2964-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2964-14 Pack of 1 450.00
20-2961-01 0.1g 120.00
20-2961-10 1.0g 995.00
  1 µmole columns 20-2961-41 Pack of 4 200.00
  0.2 µmole columns 20-2961-42 Pack of 4 120.00
  10 µmole column (ABI) 20-2961-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2961-14 Pack of 1 450.00
26-2961-01 0.1g 130.00
26-2961-10 1.0g 1045.00
  200 nmole columns 26-2961-52 Pack of 10 300.00
  40 nmole columns 26-2961-55 Pack of 10 300.00
20-2994-01 0.1g 120.00
20-2994-10 1.0g 995.00
  0.2 µmole columns 20-2994-42 Pack of 4 120.00
  1 µmole columns 20-2994-41 Pack of 4 200.00
  10 µmole column (ABI) 20-2994-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2994-14 Pack of 1 450.00
20-2056-01 0.1g 120.00
20-2056-10 1.0g 995.00
  1 µmole columns 20-2056-41 Pack of 4 200.00
  0.2 µmole columns 20-2056-42 Pack of 4 120.00
  10 µmole column (ABI) 20-2056-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2056-14 Pack of 1 450.00
5'-Fluorescein
5'-Fluorescein
5'-Hexachloro-Fluorescein
5'-Hexachloro-Fluorescein
6-Fluorescein Serinol
6-Fluorescein Serinol
5'-Tetrachloro-Fluorescein
5'-Tetrachloro-Fluorescein
3'-(6-FAM) PS
3'-(6-FAM) PS
5'-Dichloro-dimethoxy-Fluorescein II
5'-Dichloro-dimethoxy-Fluorescein II
Fluorescein
Fluorescein
6-Fluorescein
6-Fluorescein
Fluorescein-dT
Fluorescein-dT
3'-6-Fluorescein Serinol CPG
3'-6-Fluorescein Serinol CPG
3'-Fluorescein CPG
3'-Fluorescein CPG
3'-(6-Fluorescein) CPG
3'-(6-Fluorescein) CPG
3'-(6-FAM) CPG
3'-(6-FAM) CPG
3'-Fluorescein-dT CPG
3'-Fluorescein-dT CPG

FLUORESCENT DYES

Absorbance
Max
Emission
Max
Color
Fluorescein 494nm 525nm Green
Tetrachloro-
Fluorescein
521nm 536nm Orange
Hexachloro-
Fluorescein
535nm 556nm Pink
SIMA (HEX) 538nm 551nm Pink
Dichloro-
dimethoxy-
Fluorescein
525nm 548nm Orange/
Pink
TAMRA 565nm 580nm Rose
Cyanine 3 546nm 563nm Red
Cyanine 3.5 588nm 604nm Purple
Cyanine 5 646nm 662nm Violet
Cyanine 5.5 683nm 707nm Dark
Blue
Yakima
Yellow
530nm 549nm Yellow
Redmond
Red
579nm 595nm Red

Intellectual Property

Serinol products are covered by US Patent No.: 8,394,948.

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.

Fluorescein Labelling (SIMA)

Dichloro-diphenyl-fluorescein, SIMA (HEX) exhibits virtually identical absorbance and emission spectra to HEX. SIMA (HEX) is much more stable to basic deprotection conditions than HEX and oligonucleotides can be deprotected using ammonium hydroxide at elevated temperatures and even ammonium hydroxide/methylamine (AMA) at room temperature or 65°C for 10 minutes. SIMA absorption maximum was 3 nm blue-shifted compared to HEX at pH 7. The absorbance is broader, so the extinction coefficient is smaller than that of HEX, but when exciting at 500 nm where the absorbance was normalized, the emission was still 90% of HEX and the emission was red-shifted by 5 nm. A second SIMA (HEX) product, SIMA (HEX)-dT, can be used to introduce SIMA (HEX) in the synthetic oligonucleotide sequence, usually as a replacement for the native dT linkage. Again, this product is fully compatible with deprotection schemes using ammonium hydroxide at elevated temperatures or AMA at room temperature and 65°C.
Item Catalog No. Pack Price ($)
10-5905-95 50µm 90.00
10-5905-90 100µm 175.00
10-5905-02 0.25g 400.00
10-5945-95 50µm 345.00
10-5945-90 100µm 675.00
10-5945-02 0.25g 995.00
SIMA (HEX)
SIMA (HEX)
SIMA (HEX)-dT
SIMA (HEX)-dT

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.

Cyanine Labelling

Two cyanine derivatives, Cyanine 3 and Cyanine 5, which differ in structure simply by the number of carbons in the conjugated poly- ene linkage, are joined by the closely related analogues, Cyanine 3.5 and Cyanine 5.5, and are available as phosphoramidites. Cyanine dyes are normally added once at the 5'-terminus and the MMT group should be removed on the synthesizer. The absorbance of the MMT cation (yellow) is noticeably different from the DMT cation (orange), and so, absorbance-based trityl monitors will detect it incorrectly as a low coupling. On the other hand, conductivity detectors will interpret the release more correctly. Cyanine dye phosphoramidites have also been used successfully adjacent to the 3'-terminus. Cyanine 3 and Cyanine 5 supports are also offered to allow simpler production of 3' cyanine dye-labelled oligonucleotides.

Deprotection of oligos containing Cyanine dyes may be carried out with ammonium hydroxide at room temperature, regardless of the base protecting groups on the monomers used. If there is a need to use ammonium hydroxide at elevated temperature, Cyanine 3 and Cyanine 3.5 are more stable than Cyanine 5 and Cyanine 5.5. However, it is always prudent to use monomers with base labile protecting groups to limit the exposure time to 2 hours or less at 65°C during deprotection.

To better address applications in near-infrared (NIR) imaging, Glen Research is offering a water soluble Disulfo-Cyanine 7 azide that can be easily conjugated to DNA and RNA through standard click chemistry. This long wavelength dye offers the benefits of improved solubility, reduced aggregation, and improved stability in the near-infrared spectrum along with the convenience of click chemistry.
Item Catalog No. Pack Price ($)
10-5913-95 50µm 205.00
10-5913-90 100µm 375.00
10-5913-02 0.25g 925.00
10-5914-95 50µm 220.00
10-5914-90 100µm 400.00
10-5914-02 0.25g 925.00
10-5915-95 50µm 205.00
10-5915-90 100µm 375.00
10-5915-02 0.25g 925.00
10-5916-95 50µm 245.00
10-5916-90 100µm 450.00
10-5916-02 0.25g 925.00
20-5913-01 0.1g 160.00
20-5913-10 1.0g 1250.00
  1 µmole columns (TWIST format only for 1µm cols.) 20-5913-41 Pack of 4 250.00
  0.2 µmole columns 20-5913-42 Pack of 4 70.00
20-5915-01 0.1g 160.00
20-5915-10 1.0g 1250.00
  1 µmole columns (TWIST format only for 1µm cols.) 20-5915-41 Pack of 4 250.00
  0.2 µmole columns 20-5915-42 Pack of 4 70.00
50-2010-92 25 µmole 325.00
50-2010-90 100 µmole 975.00
Cyanine 3
Cyanine 3
Cyanine 3.5
Cyanine 3.5
Cyanine 5
Cyanine 5
Cyanine 5.5
Cyanine 5.5
Disulfo-Cyanine 7 Azide
Disulfo-Cyanine 7 Azide
Cyanine 3 CPG
Cyanine 3 CPG
Cyanine 5 CPG
Cyanine 5 CPG

SPECTRAL DATA FOR CYANINE DYES

Absorbance
Max
Emission
Max
Color
Cyanine 3 546nm 563nm Red
Cyanine 3.5 588nm 604nm Purple
Cyanine 5 646nm 662nm Violet
Cyanine 5.5 683nm 707nm Dark Blue
Cyanine 7 750nm 773nm Dark Green

(Measured in an oligo in 0.1M TEAA buffer, pH7.)

ELITECHGROUP DYES AND QUENCHER

Glen Research's agreement with ELITechGroup, formerly Epoch Biosciences, allows us to offer several of their proprietary products designed for the synthesis of novel DNA probes. We are pleased to offer products based on ELITechGroup's Redmond Red®, Yakima Yellow® and AquaPhluor® 593 fluorophores and Eclipse® non-fluorescent quencher. Under our agreement we also supply PPG, a modified nucleoside, and 5'-Aldehyde-Modifier C2 Phosphoramidite. The fluorescent dyes, Yakima Yellow, Redmond Red and AquaPhluor 593, are available as phosphoramidites and supports. Yakima Yellow has an absorbance maximum at 530 nm and emission maximum at 549 nm, Redmond Red's absorbance and emission maxima are at 579 nm and 595 nm, respectively, and AquaPhluor 593 has an absorbance maximum at 593 nm and emission maximum at 613 nm. The fluorescein alternative, Gig Harbor Green, has been discontinued.

The Eclipse quencher from ELITechGroup solves most of the problems inherent in the synthesis of molecular beacon and FRET probes. The Eclipse molecule is highly stable and can be used safely in all common oligo deprotection schemes. The absorbance maximum for Eclipse Quencher is at 522 nm, compared to 479 nm for dabcyl. In addition, the structure of the Eclipse Quencher is substantially more electron deficient than that of dabcyl and this leads to better quenching over a wider range of dyes, especially those with emission maxima at longer wavelengths (red shifted) such as Redmond Red and Cyanine 5. In addition, with an absorption range from 390 nm to 625 nm, the Eclipse Quencher is capable of effective performance in a wide range of colored FRET probes.
Item Catalog No. Pack Price ($)
10-5920-95 50µm 220.00
10-5920-90 100µm 420.00
10-5920-02 0.25g 1045.00
10-5921-95 50µm 230.00
10-5921-90 100µm 440.00
10-5921-02 0.25g 1045.00
10-5923-95 50µm 405.00
10-5923-90 100µm 795.00
10-5923-02 0.25g 1575.00
10-5925-95 50µm 250.00
10-5925-90 100µm 480.00
10-5925-02 0.25g 1185.00
20-5920-01 0.1g 180.00
20-5920-10 1.0g 1500.00
  1 µmole columns 20-5920-41 Pack of 4 300.00
  0.2 µmole columns 20-5920-42 Pack of 4 150.00
  10 µmole column (ABI) 20-5920-13 Pack of 1 750.00
  15 µmole column (Expedite) 20-5920-14 Pack of 1 1125.00
20-5921-01 0.1g 180.00
20-5921-10 1.0g 1500.00
  1 µmole columns 20-5921-41 Pack of 4 300.00
  0.2 µmole columns 20-5921-42 Pack of 4 150.00
  10 µmole column (ABI) 20-5921-13 Pack of 1 750.00
  15 µmole column (Expedite) 20-5921-14 Pack of 1 1125.00
20-5923-01 0.1g 215.00
20-5923-10 1.0g 1800.00
  1 µmole columns 20-5923-41 Pack of 4 325.00
  0.2 µmole columns 20-5923-42 Pack of 4 165.00
  10 µmole column (ABI) 20-5923-13 Pack of 1 925.00
  15 µmole column (Expedite) 20-5923-14 Pack of 1 1395.00
20-5925-01 0.1g 230.00
20-5925-10 1.0g 1925.00
  1 µmole columns 20-5925-41 Pack of 4 350.00
  0.2 µmole columns 20-5925-42 Pack of 4 175.00
  10 µmole column (ABI) 20-5925-13 Pack of 1 995.00
  15 µmole column (Expedite) 20-5925-14 Pack of 1 1495.00
Redmond Red®
Redmond Red®
Yakima Yellow®
Yakima Yellow®
5'-AquaPhluor® 593 CE
5'-AquaPhluor® 593 CE
Eclipse® Quencher
Eclipse® Quencher
Redmond Red® CPG
Redmond Red® CPG
Yakima Yellow® CPG
Yakima Yellow® CPG
AquaPhluor® 593 CPG
AquaPhluor® 593 CPG
Eclipse® Quencher CPG
Eclipse® Quencher CPG

FLUORESCENT DYES

Absorbance
Max
Emission
Max
Color
Yakima
Yellow
530nm 549nm Yellow
Redmond
Red
579nm 595nm Red
AquaPhluor® 494nm 613nm Red

Intellectual Property

These products are for research purposes only, and may not be used for commercial, clinical, diagnostic or any other use. The Product is subject to proprietary rights of ELITechGroup and is made and sold under license from ELITechGroup. There is no implied license for commercial use with respect to this Product and a license must be obtained directly from ELITechGroup. with respect to any proposed commercial use of this Product. "Commercial use" includes but is not limited to the sale, lease, license or other transfer of the Product or any material derived or produced from it, the sale, lease, license or other grant of rights to use the Product or any material derived or produced from it, or the use of the Product to perform services for a fee for third parties (including contract research). AquaPhluor®, Yakima Yellow®, Redmond Red® and Eclipse® are registered trademarks of ELITechGroup.

A simple agreement must be signed before end-users and custom oligo services may purchase these products for use as defined above. http://www.glenresearch.com/ Reference/EpochProducts.pdf.

Eclipse, Gig Harbor Green, Redmond Red and Yakima Yellow are trademarks of Epoch Biosciences, Inc.

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

Black Hole Quencher Dyes

With the growing popularity of red and near-infrared dyes, we are offering the Black Hole Quencher™ dyes (BHQs), whose physical properties are detailed in Table 1. BHQ dyes are robust dark quenchers that very nicely complement our existing product line. They are compatible with ammonium hydroxide deprotection, exhibit excellent coupling efficiencies, have large extinction coefficients and are completely non-fluorescent. Their absorbances are well-tuned to quench a variety of popular fluorophores - even those far into the red, such as Cy3 and Cy5. The dark quencher most typically used in a Molecular Beacon is Dabcyl. Because the quenching does not involve FRET, there is little, if any, dependence upon donor-acceptor spectral overlap. In a comprehensive paper by Marras, Kramer and Tyagi,1 the ability of BHQ-1 and BHQ-2 to quench 22 different fluorophores was evaluated. For shorter wavelength fluorophores such as fluorescein, the quenching efficiency was roughly the same as Dabcyl (91% - 93%). However, for dyes emitting in the far red, such as Cy5, the BHQ dyes were far superior - quenching the Cy5 with 96% efficiency, compared to 84% with Dabcyl. This may reflect the BHQ's ability to form stable, non-fluorescent complexes which can be a plus even in FRET probes. Indeed, recent work suggests that these non-fluorescent complexes will form even in the absence of a hairpin stem structure used by Molecular Beacons.2
Item Catalog No. Pack Price ($)
10-5931-95 50µm 100.00
10-5931-90 100µm 200.00
10-5931-02 0.25g 700.00
10-5932-95 50µm 100.00
10-5932-90 100µm 200.00
10-5932-02 0.25g 700.00
10-5941-95 50µm 265.00
10-5941-90 100µm 525.00
10-5941-02 0.25g 925.00
10-5942-95 50µm 265.00
10-5942-90 100µm 525.00
10-5942-02 0.25g 925.00
20-5931-01 0.1g 190.00
20-5931-10 1.0g 1500.00
  1 µmole columns 20-5931-41 Pack of 4 300.00
  0.2 µmole columns 20-5931-42 Pack of 4 80.00
  10 µmole column (ABI) 20-5931-13 Pack of 1 575.00
  15 µmole column (Expedite) 20-5931-14 Pack of 1 825.00
20-5932-01 0.1g 190.00
20-5932-10 1.0g 1500.00
  1 µmole columns 20-5932-41 Pack of 4 300.00
  0.2 µmole columns 20-5932-42 Pack of 4 80.00
  10 µmole column (ABI) 20-5932-13 Pack of 1 575.00
  15 µmole column (Expedite) 20-5932-14 Pack of 1 825.00
20-5933-01 0.1g 190.00
20-5933-10 1.0g 1500.00
  1 µmole columns 20-5933-41 Pack of 4 300.00
  0.2 µmole columns 20-5933-42 Pack of 4 80.00
  10 µmole column (ABI) 20-5933-13 Pack of 1 575.00
  15 µmole column (Expedite) 20-5933-14 Pack of 1 825.00
5'-BHQ-1
5'-BHQ-1
5'-BHQ-2
5'-BHQ-2
BHQ-1-dT
BHQ-1-dT
BHQ-2-dT
BHQ-2-dT
3'-BHQ-1 CPG
3'-BHQ-1 CPG
3'-BHQ-2 CPG
3'-BHQ-2 CPG
3'-BHQ-3 CPG
3'-BHQ-3 CPG

TABLE 1: BLACK HOLE
QUENCHERS

Quencher lmax E260 E max
(nm) (L/mol.cm) (L/mol.cm)
BHQ-1 534 8,000 34,000
BHQ-2 579 8,000 38,000
BHQ-3 672 13,000 42,700

Intellectual Property

'Black Hole Quencher', 'BHQ-0', 'BHQ-1', 'BHQ-2' and 'BHQ-3' are trademarks of Biosearch Technologies, Inc., Novato, CA. The BHQ dye technology is the subject of pending patents and is licensed and sold under agreement with Biosearch Technologies, Inc.. Products incorporating the BHQ dye moiety are sold exclusively for R&D use by the end-user. They may not be used for clinical or diagnostic purposes and they may not be re-sold, distributed or re-packaged.

Reference(s)

  1. S.A.E. Marras, F.R. Kramer, and S. Tyagi, Nucleic Acids Res., 2002, 30, E122.
  2. M.K. Johansson, H. Fidder, D. Dick, and R.M. Cook, J Am Chem Soc, 2002, 124, 6950-6956.

See Also

BlackBerry® Quencher (BBQ-650®)

We are happy to offer several products containing the BlackBerry® Quencher (BBQ-650® ), which exhibits a broad absorption profile from 550nm to 750nm, centered at 650nm. This range offers more effective quenching of some of our popular long wavelength dyes like TAMRA, Redmond Red, Cy dyes and DyLight dyes. We offer BBQ-650 products for the 3' and 5' termini, as well as BBQ-650-dT for inclusion within the oligonucleotide sequence, with the following properties:
  • Quenches the fluorescence of long wavelength dyes
  • Quenches in FRET and contact mode
  • Absorbance maximum at ~650nm
  • Quenching range - 550-750nm
  • Compatible with standard oligo synthesis chemistry
  • Compatible with regular deprotection but requires mild deprotection with AMA at room temperature
  • Available for 3', 5', and internal substitution
  • More stable than BHQ-3
Item Catalog No. Pack Price ($)
10-5934-95 50µm 160.00
10-5934-90 100µm 305.00
10-5934-02 0.25g 925.00
10-5944-95 50µm 280.00
10-5944-90 100µm 545.00
10-5944-02 0.25g 925.00
20-5934-01 0.1g 190.00
20-5934-10 1.0g 1500.00
  1 µmole columns 20-5934-41 Pack of 4 300.00
  0.2 µmole columns 20-5934-42 Pack of 4 80.00
  10 µmole column (ABI) 20-5934-13 Pack of 1 575.00
  15 µmole column (Expedite) 20-5934-14 Pack of 1 825.00
5'-BBQ-650®
5'-BBQ-650®
BBQ-650®-dT
BBQ-650®-dT
BBQ-650® CPG
BBQ-650® CPG

Intellectual Property

BlackBerry® Quencher technology: US Patent 7,879,986. The purchase of BlackBerry® Quencher reagents includes a limited license to use these reagents exclusively for research and development purposes. They may not be used for clinical or diagnostic purposes and they may not be re-sold, distributed, or re-packaged without prior agreement and consent of Berry & Associates, Inc. Subsequent sale of products that are derived from BlackBerry® Quencher reagents is permitted so long as the following written disclaimer is included in written and electronic catalogs, in commercial advertisement, and in packages with containers of such derivative products: "BlackBerry is a trademark of Berry & Associates, Inc. Products derived from BlackBerry® Quencher reagents are sold exclusively for research and development use by the purchaser. They may not be used for clinical or diagnostic purposes without prior agreement and consent of Berry & Associates, Inc."

Rhodamine (TAMRA) Labelling

Rhodamine derivatives are not sufficiently stable to survive conventional deprotection and these must be attached to amino-modified oligonucleotides using post-synthesis labelling techniques. Because Tetramethyl Rhodamine (TAMRA) is not base stable, the procedure to cleave and deprotect the labelled oligonucleotide must be carefully considered. Using the UltraMILD monomers and deprotection with potassium carbonate in methanol, TAMRA oligonucleotides can be fairly conveniently isolated. To streamline the preparation of TAMRA oligos, we offer 3'-TAMRA CPG for 3' labelling and TAMRA-dT for labelling within the sequence. We also offer TAMRA NHS ester for labelling amino-modified oligonucleotides.
Item Catalog No. Pack Price ($)
20-5910-01 0.1g 120.00
20-5910-10 1.0g 995.00
  1 µmole columns 20-5910-41 Pack of 4 200.00
  0.2 µmole columns 20-5910-42 Pack of 4 120.00
26-5910-01 0.1g 130.00
26-5910-10 1.0g 1045.00
  200 nmole columns 26-5910-52 Pack of 10 300.00
  40 nmole columns 26-5910-55 Pack of 10 300.00
10-1057-95 50µm 250.00
10-1057-90 100µm 495.00
10-1057-02 0.25g 975.00
50-5910-66 60µL 240.00
  (Solution in anhydrous DMSO)
3'-TAMRA CPG
3'-TAMRA CPG
TAMRA-dT
TAMRA-dT
TAMRA NHS Ester
TAMRA NHS Ester
3'-TAMRA PS
3'-TAMRA PS

See Also


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