Labelling (Catalog as PDF)

Acridine Labelling

Acridine phosphoramidite is designed to produce an oligonucleotide containing acridine at any position in the molecule. Acridine CPG is used to label the 3'-terminus. Acridine is an effective intercalating agent.
Item Catalog No. Pack Price ($)
10-1973-95 50µm 165.00
10-1973-90 100µm 295.00
10-1973-02 0.25g 675.00
20-2973-01 0.1g 120.00
20-2973-10 1.0g 995.00
  1 µmole columns 20-2973-41 Pack of 4 200.00
  0.2 µmole columns 20-2973-42 Pack of 4 120.00
  10 µmole column (ABI) 20-2973-13 Pack of 1 300.00
  15 µmole column (Expedite) 20-2973-14 Pack of 1 450.00
Acridine
Acridine
3'-Acridine CPG
3'-Acridine CPG

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DNP Labelling

An analytical test based on detection of 2,4-dinitrophenyl (DNP) labelled oligonucleotides with anti-DNP antibodies has been proposed. We have chosen the branched triethylene glycol (TEG) spacer in our version of DNP phosphoramidite since it can be added once or several times to the 3' or 5' terminus.
Item Catalog No. Pack Price ($)
10-1985-95 50µm 165.00
10-1985-90 100µm 295.00
10-1985-02 0.25g 675.00
DNP-TEG
DNP-TEG

Cholesterol Labelling

Potential therapeutic oligonucleotides must permeate the cell membrane for optimal activity. The addition of lipophilic groups to an oligonucleotide would be expected to enhance cellular uptake/membrane permeation. The use of cholesteryl oligos and the consequent improvement in activity has been described. We have designed our Cholesteryl products with triethyleneglycol (TEG) spacers for maximum solubility.
Item Catalog No. Pack Price ($)
10-1975-95 50µm 140.00
10-1975-90 100µm 265.00
10-1975-02 0.25g 545.00
10-1976-95 50µm 95.00
10-1976-90 100µm 175.00
10-1976-02 0.25g 525.00
20-2975-01 0.1g 85.00
20-2975-10 1.0g 700.00
  1 µmole columns 20-2975-41 Pack of 4 140.00
  0.2 µmole columns 20-2975-42 Pack of 4 84.00
  10 µmole column (ABI) 20-2975-13 Pack of 1 210.00
  15 µmole column (Expedite) 20-2975-14 Pack of 1 315.00
Cholesteryl-TEG
Cholesteryl-TEG
5'-Cholesteryl-TEG
5'-Cholesteryl-TEG
3'-Cholesteryl-TEG CPG
3'-Cholesteryl-TEG CPG

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See Also

Tocopherol Labelling

Vitamin E is both lipophilic and non-toxic even at high doses so would be an excellent candidate as a lipophilic carrier for oligonucleotides. Therefore, as an addition to our cholesteryl product line, we offer simple α-tocopheryl (vitamin E) labelling. Totally synthetic α-tocopherol is racemic at its three chiral centers and is used to prepare this product.
Item Catalog No. Pack Price ($)
10-1977-95 50µm 160.00
10-1977-90 100µm 300.00
10-1977-02 0.25g 575.00
α-Tocopherol-TEG
α-Tocopherol-TEG

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Stearyl Labelling

We now offer a simple C18 lipid as an economical and effective carrier molecule. We envisage that the 5'-stearyl group will become a favored lipophilic carrier for experimentation with synthetic oligonucleotides.
Item Catalog No. Pack Price ($)
10-1979-90 100µm 45.00
10-1979-02 0.25g 180.00
Stearyl
Stearyl

N-Acetylgalactosamine (GalNAc) Oligonucleotide Conjugates

A directed approach to the delivery of therapeutic oligonucleotides specifically to the liver has been to target the asialoglycoprotein receptor (ASGPR) using a suitable glycoconjugate. Indeed, ASGPR is the ideal target for delivery of therapeutic oligonucleotides to the liver since it combines tissue specificity, high expression levels and rapid internalization and turnover. The use of oligonucleotide glycoconjugates has led to significant advances in therapeutic delivery as evidenced by the work of Alnylam Pharmaceuticals and Ionis Pharmaceuticals using multivalent N-acetylgalactosamine (GalNAc) oligonucleotide conjugates.

Glen Research is delighted to introduce a GalNAc modification strategy using a monomeric GalNAc support and the equivalent GalNAc phosphoramidite. Our experimental work has shown that these products are fully compatible with regular oligonucleotide synthesis and deprotection. Oligonucleotides containing GalNAc can be deprotected using standard procedures during which the acetyl protecting groups on the GalNAc group are removed. We have demonstrated that 5'-GalNAc C3 phosphoramidite can be used to prepare oligonucleotides with multiple consecutive GalNAc additions at the 5' terminus.
Glen Research offers these GalNAc C3 products under an agreement with AM Chemicals LLC.
Item Catalog No. Pack Price ($)
10-1974-95 50µm 137.50
10-1974-90 100µm 255.00
10-1974-02 0.25g 500.00
20-2974-01 0.1g 40.00
20-2974-10 1.0g 320.00
  1 µmole columns 20-2974-41 Pack of 4 100.00
  0.2 µmole columns 20-2974-42 Pack of 4 60.00
  10 µmole column (ABI) 20-2974-13 Pack of 1 180.00
  15 µmole column (Expedite) 20-2974-14 Pack of 1 280.00
5'-GalNAc C3
5'-GalNAc C3
GalNAc C3 CPG
GalNAc C3 CPG

Intellectual Property

GalNAc C3 products are sold under agreement with AM Chemicals LLC.

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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.

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CDPI3 MGBTM-Oligonucleotide conjugates and their applications

The tripeptide of dihydropyrroloindole-carboxylate (CDPI3) is a minor groove binding (MGB) moiety derived from the natural product CC-1065 with strong DNA binding properties. Synthetic oligonucleotides with covalently-attached CDPI3 have enhanced DNA affinity and have improved the hybridization properties of sequence-specific DNA probes. Short CDPI3-oligonucleotides hybridize with single-stranded DNA to give more stable DNA duplexes than unmodified ODNs of similar length. CDPI3 MGβ-oligonucleotide conjugates have been found to be useful in the following applications:


  • Arrest of primer extension and PCR blockers

  • Short and fluorogenic PCR primers

  • Real-time PCR probes

  • miRNA Inhibitors



The simplest approach to MGB probe design is to use an MGB support, add a quencher molecule as the first addition and complete the synthesis with a 5'-fluorophore. Alternatively, a fluorophore support could be used with the 5' terminus containing a quencher molecule followed by a final MGB addition at the 5' terminus. Glen Research offers 5'-CDPI3 MGB™ Phosphoramidite and 3'-CDPI3 MGB™ CPG.

5'-CDPI3 MGB phosphoramidite was found to be hydrophobic enough that it required 10% THF in ACN to go completely into solution at a 0.1 M concentration and required a 3 minute coupling time. Deprotection can be carried out in EtOH/NH4OH 1:3 (v/v) 17 hr at 55°C and CDPI3 MGBis compatible with GlenPak™ purification.

With the CDPI3 MGB CPG, the optimal results are obtained if UltraMild monomers and Cap A are used during synthesis along with 0.5 M CSO oxidizer. However, the use of standard monomers with iodine oxidation followed by deprotection with EtOH/NH4OH 1:3 (v/v) for 17 hr at 55 °C will give acceptable results.

Item Catalog No. Pack Price ($)
10-5924-95 50µm 705.00
10-5924-90 100µm 1390.00
10-5924-02 0.25g 2600.00
20-5924-01 0.1g 215.00
20-5924-10 1.0g 1800.00
  1 µmole columns 20-5924-41 Pack of 4 325.00
  0.2 µmole columns 20-5924-42 Pack of 4 165.00
  10 µmole column (ABI) 20-5924-13 Pack of 1 925.00
  15 µmole column (Expedite) 20-5924-14 Pack of 1 1395.00
5'-CDPI3 MGB™
5'-CDPI3 MGB™
CDPI3 MGB™ CPG
CDPI3 MGB™ CPG

Intellectual Property

This product is sold under licensing arrangements between ELITechGroup Inc. and Glen Research. The purchase price of this product includes limited, nontransferable rights to use the product solely for activities of the purchaser which are directly related to human diagnostics. Other uses, including incorporation of the product into another commercial product, are prohibited without additional license rights. For information on purchasing a license to this product for purposes other than those stated above, contact:

ELITech Group Molecular Diagnostics, 21720 23rd Drive SE,
Suite 150,
Bothell, WA 98021.
Phone (425) 482-5555.
Fax (425) 482-5550.
Email: mdx@elitechgroup.com.

This limited license permits the person or legal entity to which this product has been provided to use the product, and the data generated by use of the product, only for human diagnostics. Neither ELITechGroup Inc. nor its licensors grants any other licenses, expressed or implied for any other purposes.

Some components of nucleic acid analysis, such as specific methods and compositions for manipulating or visualizing nucleic acids for analysis, may be covered by one or more patents owned by other parties. Similarly, nucleic acids containing specific nucleotide sequences may be patented. Making, using, offering for sale, or selling such components or nucleic acids may require one or more licenses. Nothing in this document should be construed as an authorization or implicit license to make, use or sell any so covered component or nucleic acid under any such patents.

Psoralen Labelling

Psoralen C2 at the 5'-terminus of an oligonucleotide serves effectively as a cross-linking reagent in double-stranded oligonucleotides. The 6 atom spacer arm of Psoralen C6 allows cross-linking with a triplex oligonucleotide strand. Click Chemistry with psoralen azide and one of our many nucleosidic and non-nucleosidic alkyne derivatives has the potential to generate a variety of practical cross-linkers. The well known reversible cross-linking behavior of psoralen with an adjacent thymidine residue could be very useful.
Item Catalog No. Pack Price ($)
10-1982-90 100µm 195.00
10-1982-02 0.25g 495.00
10-1983-90 100µm 195.00
10-1983-02 0.25g 495.00
50-2009-92 25 µmole 115.00
50-2009-90 100 µmole 350.00
Psoralen Azide
Psoralen Azide
Psoralen C2
Psoralen C2
Psoralen C6
Psoralen C6

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EDTA Labelling

EDTA-C2-dT phosphoramidite contains the triethyl ester of EDTA which allows sequence-specific cleavage of single- and double-stranded DNA and RNA. The cleavage reaction is only initiated once Fe(II) and dithiothreitol are added and so is readily controlled. Coupling of EDTA-dT is normal but cleavage and deprotection should be carried out with sodium hydroxide in aqueous methanol (0.4M NaOH in methanol/water 4:1) overnight at room temperature.
Item Catalog No. Pack Price ($)
10-1059-95 50µm 250.00
10-1059-90 100µm 495.00
10-1059-02 0.25g 975.00
EDTA-C2-dT
EDTA-C2-dT

Ferrocene Labelling

With an excellent stability profile, ferrocene has always attracted considerable interest for DNA labelling to generate probes for electrochemical detection. Based on our Amino-Modifier C6-dT structure, Ferrocene-dT is easily added to oligonucleotides with no disruption of regular hybridization behavior. Multiple incorporations into an oligonucleotide probe are also simply achieved. Oligonucleotides are deprotected using standard techniques. Ferrocene oligonucleotides should be stored under Argon and aqueous solutions should be degassed immediately.
Item Catalog No. Pack Price ($)
10-1576-95 50µm 170.00
10-1576-90 100µm 330.00
10-1576-02 0.25g 670.00
Ferrocene-dT
Ferrocene-dT

Methylene Blue Labelling

Methylene Blue, which belongs to the phenothiazine family of dyes, is a unique dye with a variety of useful properties. Despite its high extinction coefficient in the visible region (81,000 L/mol.cm), it is weakly fluorescent due to its high rate of intersystem crossing from the S1 excited state to the T1 triplet state. This property makes it an excellent photosensitizer, and it has been used extensively to produce highly reactive singlet oxygen. Methylene blue has the ability to both intercalate in duplex DNA, preferring G:C over T:A base pairs, and can act as an electrochemical redox probe. Methylene blue has also been shown to be unmatched in performance as a redox-active reporter for electrochemical biosensors.

Earlier, we introduced Methylene Blue C3 Phosphoramidite but this product proved to have quite limited stability and has been discontinued. As an alternative option, we introduced Methylene Blue NHS Ester to allow researchers to label amino-modified oligonucleotides with this interesting dye. With the encouragement and technical expertise of Carole Chaix and her colleagues at the University of Lyon, we decided to prepare an alternative structure that seemed to have a much superior stability profile - Methylene Blue II Phosphoramidite. Fortunately, this structure did indeed prove more stable and we are now able to offer again a Methylene Blue Phosphoramidite.
Item Catalog No. Pack Price ($)
50-1960-23 5.4mg 540.00
  (Dissolve 5.4mg in 60µL of DMSO)
10-5961-95 50µm 310.00
10-5961-90 100µm 595.00
10-5961-02 0.25g 1500.00
Methylene Blue NHS Ester
Methylene Blue NHS Ester
Methylene Blue II
Methylene Blue II

Labelling with Metal Chelates

2,2'-Dipicolylamine Phosphoramidite has been discontinued This product was manufactured and developed by Syntrix Biosystems Inc. For further information, please contact:

Dean Y. Maeda, Ph.D., M.B.A.
Director, Chemistry and Preclinical Development
Syntrix Biosystems
215 Clay St NW Ste B5
Auburn, WA 98001
tel: 253-833-8009 ext. 23
fax: 253-833-8127

Intellectual Property

Manufactured and developed by Syntrix Biosystems Inc. Patents Pending. For Research Use Only.

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Labelling with Polyaromatic Hydrocarbons

Pyrene and perylene are fluorescent polycyclic aromatic hydrocarbons that have the ability to form 'excited state dimers' known as excimers. This unstructured, long-wavelength emission arises from the formation of a charge-transfer complex between the excited state and the ground state of two fluorescent molecules. In Pyrene-dU and perylene-dU, the hydrocarbon is attached at the 5 position of deoxyuridine through a triple bond and is electronically coupled to the deoxyuridine base. This electronic coupling of the base and the hydrocarbon makes the fluorescence sensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.
Item Catalog No. Pack Price ($)
10-1590-95 50µm 105.00
10-1590-90 100µm 210.00
10-1590-02 0.25g 550.00
10-1591-95 50µm 150.00
10-1591-90 100µm 300.00
10-1591-02 0.25g 720.00
Pyrene-dU
Pyrene-dU
Perylene-dU
Perylene-dU

FLUORESCENT DYES

Absorbance
Max
Emission
Max
Color
Pyrene-
dU
402nm 472nm 486nm
Perylene-
dU
473nm 490nm Not
Determined

Puromycin CPG

One of the most challenging requirements associated with combinatorial chemistry is the recovery of sequence information of the oligonucleotide or peptide selected by the screening assay. A method1 has been developed to generate a fusion product between mRNA and the polypeptide it encodes using in vitro translation of synthetic RNAs 3'-labeled with puromycin, an antibiotic that mimics transfer RNA. Puromycin binds in the ribosome's A site, forms a peptide bond with the growing peptide chain, and blocks further peptide elongation. By linking puromycin to mRNA, a peptide-RNA fusion product results from the translation of the message linking the encoding mRNA with its peptide product.
Item Catalog No. Pack Price ($)
20-4040-01 0.1g 120.00
20-4040-10 1.0g 995.00
  1 µmole columns 20-4140-41 Pack of 4 200.00
  0.2 µmole columns 20-4140-42 Pack of 4 120.00
  10 µmole column (ABI) 20-4140-13 Pack of 1 360.00
  15 µmole column (Expedite) 20-4140-14 Pack of 1 540.00
Puromycin-CPG
Puromycin-CPG

Reference(s)

  1. R.W. Roberts and J.W. Szostak, Proc. Natl. Acad. Sci. USA, 1997, 94, 12297-302.

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.

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Quenched Autoligation (QUAL) Probes

QUAL probes1 consist of two oligonucleotides, the first containing a nucleophilic group at the 3'-terminus, while the second has an electrophilic group at the 5'-terminus. When the probe pair finds the target, the oligos line up with the 3'-terminus of the first directly adjacent to the 5'-terminus of the second. An autoligation reaction then takes place to combine the two oligos into a single probe. As usual, the 3' nucleophilic group is the 3-thiophosphate, easily prepared using 3'-phosphate CPG with a sulfurizing step in the first cycle. In this case, the electrophilic group is a 5'-dabsyl group, which is an excellent leaving group as well as a fine quencher of fluorescence. The second oligo, therefore, contains a fluorophore which is quenched by the dabsyl group. A popular choice for fluorophore is fluorescein-dT but it is easy to imagine that a variety of fluorophores could be attached to any of the commercially available amino-modified nucleoside phosphoramidites.
Item Catalog No. Pack Price ($)
10-1532-90 100µm 250.00
10-1532-02 0.25g 775.00
5'-Dabsyl-dT
5'-Dabsyl-dT

Reference(s)

  1. S. Sando and E.T. Kool, J Amer Chem Soc, 2002, 124, 2096-2097.

See Also

Labelling for Photo-Regulation of Oligonucleotides

Photo-control, the use of ultraviolet or visible light to control a reaction, has a number of advantages over other external stimuli:



  • Light does not introduce contaminants into the reaction system,
  • Excitation wavelength can be controlled through the design of the photo-responsive molecule, and
  • It is now straightforward to control irradiation time and/or local excitation.

When a photo-responsive molecule is directly attached to DNA as a receptor, photo-regulation of the bioprocess regulated by that DNA molecule could, in principle, be achieved. Such photo-responsive DNA could also be used as a switch in a DNA-based nano-machine. Professor Hiroyuki Asanuma and his group at the department of Molecular Design and Engineering of the Graduate School of Engineering of the Nagoya University (Japan) have developed an efficient method to achieve this goal. They have attached azobenzene to DNA and made it photo-responsive1,2. Azobenzene is a typical photo-responsive molecule that isomerizes from its planar trans-form to the non-planar cis-form after UV-light irradiation with a wavelength between 300 nm and 400 nm (λmax is around 330 nm). Interestingly, the system reverts from the cis-form to the trans-form after further irradiation with visible light (wavelength over 400 nm). This process is completely reversible, and the azobenzene group does not decompose or induce undesirable side reactions even on repeated trans-cis isomerization. By introducing azobenzenes into DNA through D-threoninol as a linker, Asanuma and co-workers succeeded in achieving photo-regulation of:


  • Formation and dissociation of a DNA duplex3,4 and
  • Transcription by T7-RNA polymerase reaction5,6,7.
Item Catalog No. Pack Price ($)
10-5800-95 50µm 105.00
10-5800-90 100µm 200.00
10-5800-02 0.25g 550.00
Azobenzene
Azobenzene

Reference(s)

  1. H. Asanuma, et al., Angew Chem Int Ed, 2001, 40, 2671-2673.
  2. T. Takarada, et al., Chem Lett., 2001, 30, 732.
  3. H. Asanuma, X.G. Liang, T. Yoshida, and M. Komiyama, Chembiochem, 2001, 2, 39-44.
  4. H. Asanuma, D. Matsunaga, and M. Komiyama, NUCLEIC ACIDS SYMP SER (OXF), 2005, 49, 35.
  5. H. Asanuma, et al., Chembiochem, 2002, 3, 786.
  6. M. Liu, H. Asanuma, and M. Komiyama, J. Amer. Chem. Soc., 2006 , 128, 1009.
  7. H. Asanuma, et al., Nature Protocols, 2007, 2, 203-212..

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.

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Labelling with Ultrafast Photo Cross-Linker

When 3-cyanovinylcarbazole nucleoside (CNVK) is incorporated into an oligonucleotide, very rapid photo cross-linking to the complementary strand can be induced at one wavelength and rapid reversal of the cross-link is possible at a second wavelength. Neither wavelength has the potential to cause significant DNA damage. Irradiation of a duplex containing a single incorporation of CNVK at 366nm led to 100% cross-linking to thymine base in 1 second, although complete cross-linking to cytosine takes 25 seconds.1 A 30 second irradiation time should cover all situations. In addition, it was demonstrated that the purine bases were unreactive to cross-linking, allowing differentiation between pyrimidines and purines at the target site. The authors also determined the effect of sequence contexts around the CNVK site and demonstrated that the identity of bases on either side of the cross-linking site has little effect on the reaction. Once cross-linked, the UV melting temperature of the duplex was raised by around 30°C relative to the duplex before irradiation. Complete reversal of the cross-link takes place at 312nm in 3 minutes. This facile reversal reaction is, therefore, accomplished with no damage to normal DNA. In a later publication, a further application of this cross-linking technique was investigated.2 When CNVK was cross-linked with a dC residue in duplex DNA, heating at 90°C for 3.5 hours led to deamination of the cytosine base to form uracil in the complementary strand. Reversal of the cross-link at 312nm led to a DNA strand in which dC had been converted to dU. The authors showed that this transformation is specific for the dC residue opposite the CNVK and any further adjacent dC residues are unaffected. Similarly, the authors have shown that CNVK can be cross-linked to an adjacent RNA strand.3
Item Catalog No. Pack Price ($)
10-4960-95 50µm 200.00
10-4960-90 100µm 390.00
10-4960-02 0.25g 1125.00
3-Cyanovinylcarbazole (CNVK)
3-Cyanovinylcarbazole (CNVK)

Reference(s)

  1. H. Asanuma, et al., Angew Chem Int Ed, 2001, 40, 2671-2673.
  2. T. Takarada, et al., Chem Lett., 2001, 30, 732.
  3. H. Asanuma, X.G. Liang, T. Yoshida, and M. Komiyama, Chembiochem, 2001, 2, 39-44.
  4. H. Asanuma, D. Matsunaga, and M. Komiyama, NUCLEIC ACIDS SYMP SER (OXF), 2005, 49, 35.
  5. H. Asanuma, et al., Chembiochem, 2002, 3, 786.
  6. M. Liu, H. Asanuma, and M. Komiyama, J. Amer. Chem. Soc., 2006 , 128, 1009.
  7. H. Asanuma, et al., Nature Protocols, 2007, 2, 203-212..

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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