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AAT Bioquest

Fluorescent Oligonucleotide Labeling Reagents

Introduction


As the use of synthetic oligonucleotides in biomedical research gets more sophisticated, the simple modification of oligonucleotides becomes an urgent need. Although the automated oligonucleotide synthesis rapidly advances, there are still challenges in meeting the needs for increasingly larger quantities of modified oligonucleotides for therapeutic applications; better high-throughput methods for the screening and PCR markets; and improved synthesis quality of dye modified oligonucleotides for the diagnostic industry.

In recent years, dye-labeled oligonucleotides have received great attentions due to their important biological applications. For certain applications, such as DNA sequencing and in situ hybridization (e.g. FISH), oligonucleotides are usually required to be singly labeled. Subsequent detection and analysis relies on the fluorescent properties of the dye, most of which emit light in the visible spectrum. On the other hand, there are some types of biological applications, e.g. probes for real-time PCR quantification of DNA and RNA and allele discrimination (Molecular Beacons™), which require that oligonucleotides be doubly labeled. In the molecules of doubly labeled oligonucleotides one dye acts as a fluorophore, the other as a quencher. When dual-labeled probes are inactive, the light emission from the fluorophore must remain undetected and is absorbed by the quencher dye via a process of so called Fluorescent Resonance Energy Transfer (FRET). Because FRET is a distance-dependent interaction between the excited state of the donor and acceptor dye molecules, their eventual separation in the detection event allows the fluorescence to be detected.

To maximize the FRET efficiency, the FRET pairs need to be carefully selected based on the consideration of quite a few factors such as fluorescence lifetime, the spectral overlap of donor emission with acceptor excitation. AAT Bioquest offers the most comprehensive product line of FRET building blocks for labeling oligonucleotides, including both the classic dyes and our outstanding Tide Fluor™ (donors) and Tide Quenchers™ (acceptors).

 

5'-Labeling of Oligonucleotides Using Dye Phosphoramidites


Because conventional automated synthesis proceeds from 3' to 5', the 5'-terminus is clearly a good choice for modifying oligonucleotides. As reported in a number of publications, the ability to attach a suitable molecule to the 5'-terminus for use as a label plays a critical role in the continuing development of non-radioactive probes and in DNA sequencing and amplification. A general approach to the modification of the 5'-terminus is to use reagents that would couple to the 5'-hydroxyl of an oligonucleotide.

Dye phosphoramidite reagents have been readily adapted for use in automated synthesizers with little or no modification to existing protocols. These reagents are well compatible with automated DNA synthesizers. In general, dye-labeled oligonucleotides can be deprotected at room temperature in concentrated ammonium hydroxide for a minimum of 24 hours, or shorter time that is appropriated for the protecting groups on the monomers being used. FAM, Dabcyl and Tide Quencher™ (TQ)-labeled oligos can be heated to 55°C in ammonium hydroxide for extended periods of time. However, TET, TF-3 and Cy-3 labeled oligos are less stable and survive only for a few hours at 55°C. HEX, TF-5 and Cy-5 labeled oligonucleotides must be deprotected at room temperature and the residual ammonia should be removed immediately after deprotection.

Fluorescein Labeling: AAT Bioquest offers fluorescein-based phosphoramidites that contains no 4, 4'- dimethoxytrityl (DMT) group and can be added only once at the 5'-terminus, thereby terminating synthesis. These fluorescein products include FAM, TET and HEX. FAM phosphoramidite is designed to produce the same fluorescein-type structure as previously prepared using fluorescein isothiocyanate (FITC). The TET and HEX phosphoramidites are designed to take advantage of the multicolor detection capability of modern DNA sequencers and genetic analyzers. For stronger fluorescence intensity, pH-insensitivity and high photostability, we highly recommend that you try our Tide Fluor™ 1 (TF-1) which has the spectral properties that are essentially identical to those of fluorescein.

Rhodamine Labeling: The light-absorbing properties of TAMRA, and spectral overlap with several commonly used fluorophores, including FAM, HEX, TET and JOE, make it useful as a quencher for the duallabeled oligo probes. However, its intrinsic fluorescence contributes to the background signal, potentially reducing the sensitivity of assays based on TAMRA. Despite these limitations, TAMRA has been used extensively in the design of probe-based assays, perhaps most notably for Real-Time PCR.

Oligonucleotides can be labeled with TAMRA using two distinct methodologies. Under standard deprotection conditions, TAMRA is not sufficiently stable. It degrades in the presence of ammonium hydroxide. If standard deprotection is required, the oligonucleotide is normally synthesized with an amino group at either the 3'-, or 5'-end and labeled with TAMRA post-synthetically using TAMRA, SE (see below). Oligonucleotides synthesized using UltraMILD monomers can also be labeled directly with TAMRA at the 3'-end using 3'-TAMRA CPG support. Subsequent deprotection of the oligo using potassium carbonate in methanol adequately removes the base protecting groups.

Tide Fluor™ Labeling: TF dyes are optimized to maximize FRET performance through enhancing donor fluorescence intensity. Although EDANS, FAM, TAMRA, ROX, Cy 3 and Cy5 have been widely used to develop a variety of FRET probes, there are still a few limitations for using these dyes. For example, the weak absorption and environment-sensitive fluorescence of EDANS have severely limited its sensitivity for developing nucleic acid detection probes. Compared to EDANS, fluorescein-based probes (such as FAM, HEX, JOE and TET) have stronger absorption and fluorescence. However the fluorescence of fluorescein-based probes is strongly dependent on pH. They only exhibit the strongest fluorescence at higher pH. This pH dependence makes the fluorescein-based fluorescent probes inconvenient for the assays that require low pH. In addition, most of fluorescein-based probes have quite low photostability, which limits their applications in fluorescence imaging. Among cyanine dyes, nonsulfonated Cy3 and Cy5 are widely used for developing a variety of nucleic acid probes, but they have quite low fluorescence quantum yield in aqueous media. The sulfonated Cy3 and Cy5 have improved fluorescence quantum yield than those of non-sulfonate cyanines. However, the sulfonated Cy3 and Cy5 are more difficult to use in the synthesis of fluorescent oligonucleotides due to the lack of the corresponding sulfonated cyanine phosphoramidites, and are quite cost-prohibitive.

To address these limitations, we have developed Tide Fluor™ donor dyes that are optimized as building blocks for developing FRET oligonucleotides and peptides for a variety of biological applications. Our Tide Fluor™ dyes (such as TF1, TF2, TF3, TF4 and TF5) have stronger fluorescence and higher photostability than the typical fluorophores such as fluoresceins, rhodamines and cyanines as described above. Our TF2 has essentially the same excitation and emission wavelengths to those of carboxyfluoresceins (FAM), making them readily available for the biological applications done with fluoresceins, but has an enhanced performance with our TF2 probes. TF2 has much stronger fluorescence at physiological conditions, and it is much more photostable than FAM probes. Moreover, compared to other fluorescent dyes alternative to fluoresceins and Cy dyes (such as Alexa Fluor™ and Cy3, Cy5 and Cy7), Tide Fluor™ dyes are much more cost-effective with comparable or even better performance for some biological applications.

 

Key Features of Tide Fluor™ Donors


  • Optimized to pair with Tide Quencher™ dark acceptors to maximize the FRET potentials
  • Stronger fluorescence intensity to enhance assay sensitivity
  • pH-insensitive and environment-insensitive fluorescence to simplify assays
  • Higher photostability to improve the quality of fluorescence imaging
  • A variety of reactive forms available for conjugations

 

Table 1. Tide Fluor™ Dyes for Developing FRET Probes

Tide Fluor™ Donor
Ex (nm)
Em (nm)
Features and Benefits
Ordering Information
Tide Fluor™ 1 (TF1)345442
  • Alternative to EDANS
  • Much stronger absorption
  • Much stronger fluorescence
  • Less environmental sensitivity
Cat# 2236 (TF1 azide, click chemistry)
Cat# 2237 (TF1 alkyne, click chemistry)
Cat# 2238 (TF1 acid)
Cat# 2239 (TF1 amine)
Cat# 2242 (TF1 maleimide, SH-reactive)
Cat# 2244 (TF1 SE, NH2-reactive)
Tide Fluor™ 2 (TF2)500527
  • Alternative to FAM, FITC and Alexa Fluor® 488
  • pH-insensitive fluorescence
  • Good photostability
Cat# 2245 (TF1 acid)
Cat# 2246 (TF2 amine)
Cat# 2247 (TF2 maleimide SH-reactive)
Cat# 2248 (TF2 SE, NH2-reactive)
Cat# 2252 (TF2 azide, click chemistry)
Cat# 2253 (TF2 alkyne, click chemistry)
Tide Fluor™ 3 (TF3)555584
  • Alternative to Cy3® and Alexa Fluor® 555
  • Strong fluorescence
  • Good photostability
Cat# 2254 (TF3 azide, click chemistry)
Cat# 2255 (TF3 alkyne, click chemistry)
Cat# 2268 (TF3 acid)
Cat# 2269 (TF3 amine)
Cat# 2270 (TF3 maleimide, SH-reactive)
Cat# 2271 (TF3 SE, NH2-reactive)
Tide Fluor™ 3WS (TF3WS)555565
  • Alternative to Cy3® and Alexa Fluor® 555
  • Strong fluorescence
  • Good photostability
Cat# 2345 (TF3WS acid)
Cat# 2346 (TF3WS SE, NH2-reactive)
Tide Fluor™ 4 (TF4)590618
  • Alternative to ROX, Texas Red® and Alexa Fluor® 594
  • Strong fluorescence
  • Good photostability
Cat# 2285 (TF4 acid)
Cat# 2286 (TF4 amine)
Cat# 2287 (TF4 maleimide, SH-reactive)
Cat# 2289 (TF4 SE, NH2-reactive)
Cat# 2300 (TF4 azide, click chemistry)
Cat# 2301 (TF4 alkyne, click chemistry)
Tide Fluor™ 5WS (TF5WS)649664
  • Alternative to Cy5® and Alexa Fluor® 647
  • Strong fluorescence
  • Good photostability
Cat# 2275 (TF5WS azide, click chemistry)
Cat# 2276 (TF5WS alkyne, click chemistry)
Cat# 2278 (TF5WS, acid)
Cat# 2279 (TF5WS amine)
Cat# 2280 (TF5WS maleimide, SH-reactive)
Cat# 2281 (TF5WS SE, NH2-reactive)
Tide Fluor™ 6WS (TF6WS)676695
  • Alternative to Cy5.5®, IRDye® 700 and Alexa Fluor® 680
  • Strong fluorescence
  • Good photostability
Cat# 2291 (TF6WS acid)
Cat# 2292 (TF6WS amine)
Cat# 2293 (TF6WS maleimide, SH-reactive)
Cat# 2294 (TF6WS SE, NH2-reactive)
Cat# 2302 (TF6WS azide, click chemistry)
Cat# 2303 (TF6WS alkyne, click chemistry)
Tide Fluor™ 7WS (TF7WS)749775
  • Alternative to Cy7® and Alexa Fluor® 750
  • Strong fluorescence
  • Good photostability
Cat# 2304 (TF7WS azide, click chemistry)
Cat# 2305 (TF7WS alkyne, click chemistry)
Cat# 2330 (TF7WS acid)
Cat# 2331 (TF7WS amine)
Cat# 2332 (TF7WS maleimide, SH-reactive)
Cat# 2333 (TF7WS SE, NH2-reactive)
Tide Fluor™ 8WS (TF8WS)775807
  • Alternative to IRDye® 800
  • Strong fluorescence
  • Good photostability
Cat# 2306 (TF8WS azide, click chemistry)
Cat# 2307 (TF8WS alkyne, click chemistry)
Cat# 2335 (TF8WS acid)
Cat# 2336 (TF8WS amine)
Cat# 2337 (TF8WS maleimide, SH-reactive)
Cat# 2338 (TF8WS SE, NH2-reactive)
  1. *Texas Red® is the trademark of Molecular Probes, Inc.

Tide Quencher™ Acceptor Dyes: TQ dyes are optimized to maximize FRET performance through enhancing quenching efficiency. Although DABCYL has been used to develop a variety of FRET applications, its low quenching efficiency of longer wavelength dyes (such as fluoresceins, rhodamines and cyanines) have limited its use in the development of sensitive fluorogenic FRET probes. Additionally, the absorption spectrum of DABCYL is environment-sensitive. AAT Bioquest has developed the robust Tide Quencher™ acceptor dyes for the development of longer wavelength FRET probes. These Tide Quencher™ dark FRET acceptors (such as TQ1, TQ2, TQ3 and TQ4) are optimized to pair with our Tide Fluor™ dyes and the classic fluorophores (such as AMCA, EDANS, FAM, TAMRA, HEX, JOE, TET, ROX, Cy3, Cy5 and Cy7). Like our Tide Fluor™ donors dyes, our Tide Quencher™ acceptor dyes are much more cost-effective with comparable or even better performance for your desired biological applications than other similar products on the market.

We offer a variety of reactive forms for both our Tide Fluor™ donors and Tide Quencher™ acceptors. For in-synthesis labeling of oligonucleotides, we offer both phosphoramidites of our Tide Fluor™ and Tide Quencher™ dyes and their CPG supports. For post labeling of oligonucleotides, we offer both amino-reactive and thiol-reactive Tide Fluor™ and Tide Quencher™ dyes that are water-soluble. Our Tide Quencher™ dyes have been used for developing a variety of Molecular Beacon oligonucleotide probes. Tide Quencher™ dyes are great choice for you to eliminate the limitations of classic quenchers. Tide Quencher ™ dyes are excellent dark quenchers that are individually optimized to pair with all of the popular fluorescent dyes such as fluoresceins and rhodamines. Our Tide Quencher™ series of nonfluorescent dyes cover the full visible spectrum with unusually high efficiency. TQ2 has absorption maximum perfectly matching the emission of FAM while TQ3 is proven to be the best quencher for Cy3. In summary, our Tide Quencher™ dyes have the following advantages:
  • Most Powerful: enable you to explore the FRET potentials that might be impossible with other quenchers.
  • Versatile Reactive Forms: convenient for self-constructing your desired FRET biomolecules.
  • Complete Set of Dyes: perfectly match your desired fluorescent donors.
  • Enhanced Value: competitive price with the best performance.

 

Table 2. Tide Quencher™ Dyes for Developing FRET Probes

Dark FRET Acceptor
λmax (nm)
Features and Benefits
Ordering Information
Tide Quencher™ 1 (TQ1)490
  • Alternative to Dabcyl, QSY® 35 and BHQ®-0
  • Best paired with Tide Fluor™ 1 (TF1)
  • Excellent FRET efficiency with coumarins
Cat# 2188 (TQ1 azide, click chemistry)
Cat# 2189 (TQ1 alkyne, click chemistry)
Cat# 2190 (TQ1 acid)
Cat# 2192 (TQ1 amine)
Cat# 2193 (TQ1 CPG, OH-reactive)
Cat# 2196 (TQ1 maleimide, SH-reactive)
Cat# 2198 (TQ1 phosphoramidite, OH-reactive)
Cat# 2199 (TQ1 SE, NH2-reactive)
Tide Quencher™ 2 (TQ2)515
  • Alternative to BHQ®-1
  • Best paired with Tide Fluor™ 2 (TF2)
  • Better matched with FAM, FITC and Alexa Fluor® 488 than other commercial quenchers
Cat# 2211 (TQ2 azide, click chemistry)
Cat# 2212 (TQ2 alkyne, click chemistry)
Cat# 2200 (TQ2 acid)
Cat# 2202 (TQ2 amine)
Cat# 2203 & 2204 (TQ2 CPG, OH-reactive)
Cat# 2206 (TQ2 maleimide, SH-reactive)
Cat# 2208 (TQ2 phosphoramidite, OH-reactive)
Cat# 2210 (TQ2 SE, NH2-reactive)
Tide Quencher™ 2WS (TQ2WS)515
  • Alternative to BHQ®-1
  • Best paired with Tide Fluor™ 2 (TF2)
  • Better matched with FAM, FITC and Alexa Fluor® 488 than other commercial quenchers
Cat# 2050 (TQ2WS acid)
Cat# 2058 (TQ2WS SE, NH2-reactive)
Tide Quencher™ 3 (TQ3)570
  • Alternative to QSY® 7, QSY® 9 and BHQ®-2
  • Best paired with Tide Fluor™ 3 (TF3)
  • Excellent FRET efficiency with Cy3®, Alexa Fluor® 555 and TAMRA than other commercial quenchers
Cat# 2200 (TQ3 acid)
Cat# 2222 (TQ3 amine)
Cat# 2223 & 2224 (TQ3 CPG, OH-reactive)
Cat# 2226 (TQ3 maleimide, SH-reactive)
Cat# 2228 (TQ3 phosphoramidite, OH-reactive)
Cat# 2230 (TQ3 SE, NH2-reactive)
Cat# 2231 (TQ3 azide, click chemistry)
Cat# 2232 (TQ3 alkyne, click chemistry)
Tide Quencher™ 3WS (TQ3WS)578
  • Alternative to QSY® 7, QSY® 9 and BHQ®-2
  • Best paired with Tide Fluor™ 3 (TF3)
  • Excellent FRET efficiency with Cy3®, Alexa Fluor® 555 and TAMRA than other commercial quenchers
Cat# 2227 (TQ3WS acid)
Cat# 2229 (TQ3WS SE, NH2-reactive)
Tide Quencher™ 4 (TQ4)603
  • Strong absorption
  • Best paired with Tide Fluor™ 4 (TF4)
  • Better FRET efficiency with ROX, Texas Red® and Alexa Fluor® 594 than other commercial quenchers
Cat# 2062 & 2063 (TQ4 CPG, OH-reactive)
Tide Quencher™ 4WS (TQ4WS)~590
  • Strong absorption
  • Best paired with Tide Fluor™ 4 (TF4)
  • Better FRET efficiency with ROX, Texas Red® and Alexa Fluor® 594 than other commercial quenchers
Cat# 2060 (TQ4WS acid)
Cat# 2061 (TQ4WS amine)
Cat# 2064 (TQ4WS maleimide, SH-reactive)
Cat# 2067 (TQ4WS SE, NH2-reactive)
Cat# 2068 (TQ4WS azide, click chemistry)
Cat# 2069 (TQ4WS alkyne, click chemistry)
Tide Quencher™ 5 (TQ5)~670
  • Alternative to QSY® 21 and BHQ®-3
  • Best paired with Tide Fluor™ 5 (TF5)
  • Excellent FRET efficiency with Cy5®, DyLight® 649 and Alexa Fluor®647
Cat# 2077 & 2078 (TQ5 CPG, OH-reactive)
Tide Quencher™ 5WS (TQ5WS)~670
  • Alternative to QSY® 21 and BHQ®-3
  • Best paired with Tide Fluor™ 5 (TF5)
  • Excellent FRET efficiency with Cy5®, DyLight® 649 and Alexa Fluor®647
Cat# 2075 (TQ5WS acid)
Cat# 2076 (TQ5WS amine)
Cat# 2079 (TQ5WS maleimide, SH-reactive)
Cat# 2081 (TQ5WS SE, NH2-reactive)
Cat# 2082 (TQ5WS azide, click chemistry)
Cat# 2083 (TQ5WS alkyne, click chemistry)
Tide Quencher™ 6WS (TQ6WS)~700
  • Stronger absorption
  • Best paired with Tide Fluor™ 6 (TF6)
  • Better FRET efficiency with Cy5.5®, IRDye® 700 and Alexa Fluor® 680 than other commercial quenchers
Cat# 2090 (TQ6WS acid)
Cat# 2091 (TQ6WS amine)
Cat# 2094 (TQ6WS maleimide, SH-reactive)
Cat# 2096 (TQ6WS SE, NH2-reactive)
Cat# 2097 (TQ6WS azide, click chemistry)
Cat# 2098 (TQ5WS alkyne, click chemistry)
Tide Quencher™ 7WS (TQ7WS)~760
  • Stronger absorption
  • Best paired with Tide Fluor™ 7 (TF7)
  • Better FRET efficiency with Cy7® and Alexa Fluor® 750 than other commercial quenchers
Cat# 2105 (TQ7WS acid)
Cat# 2106 (TQ7WS amine)
Cat# 2109 (TQ7WS maleimide, SH-reactive)
Cat# 2111 (TQ7WS SE, NH2-reactive)
Cat# 2112 (TQ7WS azide, click chemistry)
Cat# 2113 (TQ7WS alkyne, click chemistry)
  1. *Texas Red® is the trademark of Molecular Probes, Inc.

 

3'-Labeling of Oligonucleotides Using Dye CPG Supports


Besides the dye CE phosphoramidites described above, AAT Bioquest also offers dye CPG supports. Dye CPG supports have traditionally been used to add the dye labels at the 3'-terminus. Dye CPGs are used to introduce a dye molecule to the 3'-terminus of oligonucleotides. Our dye CPGs are derived from dye carboxylic acids and are attached via an amide linkage, giving an oligo product that is much easier to be purified by HPLC. The use of dye CPGs in oligonucleotide synthesis proceeds in a manner analogous to the use of a normal nucleoside support with some necessary modifications. Different dye CPGs might require different cleavage methods. The cleavage of the oligonucleotides from the FAM and Tide Quenchers™ (TQs) supports is similar to the standard ammonium hydroxide cleavage. TAMRA CPG has to be deprotected under very mild conditions to safeguard the base-labile TAMRA fluorophore. We recommend the use of UltraMild monomers and the use of potassium carbonate in methanol for deprotection. An alternative procedure using t-butylamine/methanol/water (1:1:2) might allow the use of regular monomers.

 

Indirect Modification of Oligonucleotides


AAT Bioquest currently offers 5'-amino-modifiers (Cat. # 4300 and Cat. # 4304). These reagents are designed for use in automated synthesizers to functionalize the 5'-terminus of a target oligonucleotide with a primary amine moiety. The resulted amino-modified oligonucleotides can be conjugated to a variety of tag molecules such as fluorophores, biotins, alkaline phosphatase and HRP. Due to the increased possibility of side reactions during the deprotection of modified oligonucleotides, it is recommended that the ammonium hydroxide treatment be carried out at a lower temperature than that used for unmodified oligonucleotides. The MMT protecting group of the 5'-amino-modifier (Cat. # 4300) can be removed on the synthesizer by deblocking until the yellow color elutes totally. The solution of MMT cation produced by acid deprotection is yellow and is not well quantified by trityl monitors. The modified oligonucleotide may be purified using a Poly-Pak cartridge, HPLC or gel electrophoresis. Poly-Pak cartridge purification is accomplished using the trityl-on procedure. HPLC may be performed either before or after the attachment of the label. If purification is desired prior to the label attachment, the MMT group should not be removed from the oligonucleotide as the lipophilic character of the MMT group aids in HPLC purification.

AAT Bioquest also offers Chemical Phosphorylation Reagent (CPR, Cat. # 6001). CPR has proved to be fast and convenient for chemical phosphorylation of the 5'-terminus of oligonucleotides. In addition, this reagent has proved its utility for simple phosphorylation of the 3'-terminus. It is introduced as the first addition to any nucleoside support, followed by normal synthesis of the target oligonucleotide. After the standard ammonium hydroxide deprotection, the linkage decomposes and is ß-eliminated from the target molecule, leaving a phosphate group at the 3'-terminus. The final DMT group may be removed on the synthesizer or it may be retained to aid in purification. If the DMT group is retained, it may be removed on a purification cartridge or, by treating the oligonucleotide with acetic acid:water (80:20) at room temperature for 1 hour following purification.

 

Post-Labeling of Oligonucleotides Using Dye Succinimidyl Esters


Labeling
Labeling
Succinimidyl esters are proven to be the best reagents for labeling amine-modified oligos because the amide bonds formed are essentially identical to, and as stable as the natural peptide bonds. These reagents are generally stable and show good reactivity and selectivity with aliphatic amines. AAT Bioquest offers highly purified classic fluorescent dye succinimidyl esters and our outstanding Tide Fluor™ (TF) and Tide Quencher™ (TQ) succinimidyl esters. Our dye succinimidyl esters are packed under nitrogen to enhance their shelf life, and also packed in different sizes to provide you the maximum convenience in handling these moisture-sensitive reagents.

There are a few factors that need to be considered when SE compounds are used for conjugation reactions:

Solvents: For the most part, reactive dyes are hydrophobic molecules and should be dissolved in anhydrous dimethylformamide (DMF) or dimethylsulfoxide (DMSO).

Reaction pH: The labeling reactions of aliphatic amine-containing oligonucleotides with succinimidyl esters are strongly pH dependent. Amine-reactive reagents react with non-protonated aliphatic amine groups, including the amine groups of oligos. Thus amine acylation reactions are usually carried out above pH 7.5. Oligo modifications by succinimidyl esters can typically be done at pH ranging from 7.5 to 8.5, whereas isothiocyanates may require a pH 9.0-10.0 for optimal conjugations.

Reaction Buffers: Buffers that contain free amines such as Tris and glycine and thiol compounds must be avoided when using an amine-reactive reagent. Ammonium salts (such as ammonium sulfate and ammonium acetate) must also be removed (such as via dialysis) before performing dye conjugations.

Reaction Temperature: Most conjugations are done at room temperature. However, either elevated or reduced temperature may be required for a particular labeling reaction.

 

Why should you use our Tide Quencher™ dyes (TQ1, TQ2, TQ3, TQ4 and TQ5)?


  • Most Powerful: TQs enable you to explore the maximum FRET potentials with oligonucleotides;
  • Versatile Reactive Forms: TQs are convenient for self-constructing your desired FRET biomolecules;
  • A Complete Set of Dyes: TQs perfectly match any fluorescent donors that you select;
  • Enhanced Value: We offer you the most competitive price with the best performance.

 

Why should you use our Tide Fluor™ dyes (TF1, TF2, TF3, TF4 and TF5)?


  • Optimized to pair with Tide Quencher™ dark acceptors to maximize the FRET potentials
  • Stronger fluorescence intensity to enhance assay sensitivity
  • pH-insensitive and environment-insensitive fluorescence to simplify assays
  • Higher photostability to improve the quality of fluorescence imaging
  • A variety of reactive forms available for conjugations

 

Table 3. Tide Fluor™ dyes for labeling peptides, oligonucleotides and other biomolecules.

Product Name
Unit Size
Cat#
FMOC-Asp(TF3)-OH100 mg5007
FMOC-Glu(TF3)-OH100 mg5016
FMOC-Lys(TF3)-OH100 mg5051
Tide Fluor™ 1 acid [TF1 acid] *Superior replacement for EDANS*100 mg2238
Tide Fluor™ 1 alkyne [TF1 alkyne]5 mg2237
Tide Fluor™ 1 amine [TF1 amine] *Superior replacement for EDANS*5 mg2239
Tide Fluor™ 1 azide [TF1 azide]5 mg2236
Tide Fluor™ 1 CPG [TF1 CPG] *1000 Å* *Superior replacement for EDANS*100 mg2241
Tide Fluor™ 1 CPG [TF1 CPG] *500 Å* *Superior replacement for EDANS*100 mg2240
Tide Fluor™ 1 maleimide [TF1 maleimide]5 mg2242
Tide Fluor™ 1 succinimidyl ester [TF1 SE]*Superior replacement for EDANS*5 mg2244
Tide Fluor™ 2 acid [TF2 acid] *Superior replacement for fluorescein*25 mg2245
Tide Fluor™ 2 alkyne [TF2 alkyne]1 mg2253
Tide Fluor™ 2 amine [TF2 amine] *Superior replacement for fluorescein*1 mg2246
Tide Fluor™ 2 azide [TF2 azide]1 mg2252
Tide Fluor™ 2 maleimide [TF2 maleimide] *Superior replacement for fluorescein*1 mg2247
Tide Fluor™ 2, succinimidyl ester [TF2 SE]*Superior replacement for fluorescein*5 mg2248
Tide Fluor™ 2WS acid [TF2WS acid] *Superior replacement for FITC*10 mg2348
Tide Fluor™ 2WS amine [TF2WS amine] *Superior replacement for FITC*1 mg2351
Tide Fluor™ 2WS maleimide [TF2WS Maleimide] *Superior replacement for FITC*1 mg2350
Tide Fluor™ 2WS succinimidyl ester [TF2WS SE] *Superior replacement for FITC*5 mg2349
Tide Fluor™ 3 acid [TF3 acid] *Superior replacement for Cy3*25 mg2268
Tide Fluor™ 3 alkyne [TF3 alkyne]1 mg2255
Tide Fluor™ 3 amine [TF3 amine] *Superior replacement for Cy3*1 mg2269
Tide Fluor™ 3 azide [TF3 azide]1 mg2254
Tide Fluor™ 3 maleimide [TF3 maleimide] *Superior replacement for Cy3*1 mg2270
Tide Fluor™ 3 phosphoramidite [TF3 CEP] *Superior replacement to Cy3  phosphoramidite*100 µmoles2274
Tide Fluor™ 3 succinimidyl ester [TF3 SE]*Superior replacement for Cy3*5 mg2271
Tide Fluor™ 3WS acid [TF3WS acid] *Superior replacement for Cy3*10 mg2345
Tide Fluor™ 3WS amine [TF3WS amine] *Superior replacement for Cy3*1 mg2347
Tide Fluor™ 3WS maleimide [TF3WS maleimide] *Superior replacement for Cy3*1 mg2344
Tide Fluor™ 3WS succinimidyl ester [TF3WS SE] *Superior replacement for Cy3*5 mg2346
Tide Fluor™ 4 acid [TF4 acid] *Superior replacement for ROX and Texas Red*10 mg2285
Tide Fluor™ 4 alkyne [TF4 alkyne]1 mg2301
Tide Fluor™ 4 amine [TF4 amine] *Superior replacement for ROX and Texas Red*1 mg2286
Tide Fluor™ 4 azide [TF4 azide]1 mg2300
Tide Fluor™ 4 maleimide [TF4 maleimide] *Superior replacement for ROX and Texas Red*1 mg2287
Tide Fluor™ 4, succinimidyl ester [TF4 SE]*Superior replacement for ROX and Texas Red*5 mg2289
Tide Fluor™ 5WS acid [TF5WS acid] *Superior replacement for Cy5*10 mg2278
Tide Fluor™ 5WS alkyne [TF5WS alkyne]1 mg2276
Tide Fluor™ 5WS amine [TF5WS amine] *Superior replacement for Cy5*1 mg2279
Tide Fluor™ 5WS azide [TF5WS azide]1 mg2275
Tide Fluor™ 5WS maleimide [TF5WS maleimide] *Superior replacement for Cy5*1 mg2280
Tide Fluor™ 5WS succinimidyl ester [TF5WS SE]*Superior replacement for Cy5*5 mg2281
Tide Fluor™ 6WS acid [TF6WS acid] *Superior replacement for Cy5.5*10 mg2291
Tide Fluor™ 6WS alkyne [TF6WS alkyne]1 mg2303
Tide Fluor™ 6WS amine [TF6WS amine] *Superior replacement for Cy5.5*1 mg2292
Tide Fluor™ 6WS azide [TF6WS azide]1 mg2302
Tide Fluor™ 6WS maleimide [TF6WS maleimide] *Superior replacement for Cy5.5*1 mg2293
Tide Fluor™ 6WS succinimidyl ester [TF6WS SE]*Superior replacement for Cy5.5*1 mg2294
Tide Fluor™ 7WS acid [TF7WS acid] *Superior replacement for Cy7*10 mg2330
Tide Fluor™ 7WS alkyne [TF7WS alkyne]1 mg2305
Tide Fluor™ 7WS amine [TF7WS amine] *Superior replacement for Cy5.5*1 mg2331
Tide Fluor™ 7WS azide [TF7WS azide]1 mg2304
Tide Fluor™ 7WS maleimide [TF7WS maleimide] *Superior replacement for Cy5.5*1 mg2332
Tide Fluor™ 7WS, succinimidyl ester [TF7WS SE]*Superior replacement for Cy7*1 mg2333
Tide Fluor™ 8WS acid [TF8WS acid] *Near Infrared Emission*10 mg2335
Tide Fluor™ 8WS alkyne [TF8WS alkyne]1 mg2307
Tide Fluor™ 8WS amine [TF8WS amine] *Superior replacement for Cy5.5*1 mg2336
Tide Fluor™ 8WS azide [TF8WS azide]1 mg2306
Tide Fluor™ 8WS maleimide [TF8WS maleimide] *Superior replacement for Cy5.5*1 mg2337
Tide Fluor™ 8WS, succinimidyl ester [TF8WS SE]*Near Infrared Emission*1 mg2338

Table 4. Ordering Info For Tide Quencher Products

Cat#
Product Name
Unit Size
2170Tide Quencher™ 2WS acid [TQ2WS acid]25 mg
2178Tide Quencher™ 2WS succinimidyl ester [TQ2WS, SE]5 mg
2179Tide Quencher™ 2WS maleimide [TQ2WS maleimide]1 mg
2060Tide Quencher™ 4WS acid [TQ4WS acid]5 mg
2061Tide Quencher™ 4WS amine [TQ4WS amine]1 mg
2062Tide Quencher™ 4 CPG [TQ4 CPG] *500 Å*100 mg
2063Tide Quencher™ 4 CPG [TQ4 CPG] *1000 Å*100 mg
2064Tide Quencher™ 4WS maleimide [TQ4WS maleimide]1 mg
2067Tide Quencher™ 4WS succinimidyl ester [TQ4WS SE]1 mg
2068Tide Quencher™ 4WS azide [TQ4WS azide]1 mg
2069Tide Quencher™ 4WS alkyne [TQ4WS alkyne]1 mg
2075Tide Quencher™ 5WS acid [TQ5WS acid]5 mg
2076Tide Quencher™ 5WS amine [TQ5WS amine]1 mg
2077Tide Quencher™ 5 CPG [TQ5 CPG] *500 Å*100 mg
2078Tide Quencher™ 5 CPG [TQ5 CPG] *1000 Å*100 mg
2079Tide Quencher™ 5WS maleimide [TQ5WS maleimide]1 mg
2081Tide Quencher™ 5WS succinimidyl ester [TQ5WS SE]1 mg
2082Tide Quencher™ 5WS azide [TQ5WS azide]1 mg
2083Tide Quencher™ 5WS alkyne [TQ5WS alkyne]1 mg
2090Tide Quencher™ 6WS acid [TQ6WS acid]5 mg
2091Tide Quencher™ 6WS amine [TQ6WS amine]1 mg
2094Tide Quencher™ 6WS maleimide [TQ6WS maleimide]1 mg
2096Tide Quencher™ 6WS succinimidyl ester [TQ6WS SE]1 mg
2097Tide Quencher™ 6WS azide [TQ6WS azide]1 mg
2098Tide Quencher™ 6WS alkyne [TQ6WS alkyne]1 mg
2105Tide Quencher™ 7WS acid [TQ7WS acid]5 mg
2106Tide Quencher™ 7WS amine [TQ7WS amine]1 mg
2109Tide Quencher™ 7WS maleimide [TQ7WS maleimide]1 mg
2111Tide Quencher™ 7WS succinimidyl ester [TQ7WS SE]1 mg
2112Tide Quencher™ 7WS azide [TQ7WS azide]1 mg
2113Tide Quencher™ 7WS alkyne [TQ7WS alkyne]1 mg
2188Tide Quencher™ 1 azide [TQ1 azide]5 mg
2189Tide Quencher™ 1 alkyne [TQ1 alkyne]5 mg
2190Tide Quencher™ 1 acid [TQ1 acid]100 mg
2192Tide Quencher™ 1 amine [TQ1 amine]5 mg
2193Tide Quencher™ 1 CPG [TQ1 CPG] *500 Å*100 mg
2194Tide Quencher™ 1 CPG [TQ1 CPG] *1000 Å*100 mg
2196Tide Quencher™ 1 maleimide [TQ1 maleimide]5 mg
2198Tide Quencher™ 1 phosphoramidite [TQ1 phosphoramidite]100 umoles
2199Tide Quencher™ 1 succinimidyl ester [TQ1 SE]25 mg
2200Tide Quencher™ 2 acid [TQ2 acid]100 mg
2202Tide Quencher™ 2 amine [TQ2 amine]5 mg
2203Tide Quencher™ 2 CPG [TQ2 CPG] *500 Å*100 mg
2204Tide Quencher™ 2 CPG [TQ2 CPG] *1000 Å*100 mg
2208Tide Quencher™ 2 phosphoramidite [TQ2 phosphoramidite]100 umoles
2210Tide Quencher™ 2 succinimidyl ester [TQ2 SE]25 mg
2211Tide Quencher™ 2 azide [TQ2 azide]5 mg
2212Tide Quencher™ 2 alkyne [TQ2 alkyne]5 mg
2213Tide Quencher™ 2WS alkyne [TQ2WS alkyne]1 mg
2214Tide Quencher™ 2WS alkyne [TQ2WS alkyne]5 mg
2220Tide Quencher™ 3 acid [TQ3 acid]100 mg
2222Tide Quencher™ 3 amine [TQ3 amine]5 mg
2223Tide Quencher™ 3 CPG [TQ3 CPG] *500 Å*100 mg
2224Tide Quencher™ 3 CPG [TQ3 CPG] *1000 Å*100 mg
2226Tide Quencher™ 3 maleimide [TQ3 maleimide]5 mg
2227Tide Quencher™ 3WS acid [TQ3WS acid]5 mg
2228Tide Quencher™ 3 phosphoramidite [TQ3 phosphoramidite]100 umoles
2229Tide Quencher™ 3WS succinimidyl ester [TQ3WS SE]1 mg
2230Tide Quencher™ 3 succinimidyl ester [TQ3 SE]25 mg
2231Tide Quencher™ 3 azide [TQ3 azide]5 mg
2232Tide Quencher™ 3 alkyne [TQ3 alkyne]5 mg


Original created on December 20, 2013, last updated on December 20, 2013
Tagged under: Oligonucleotide Labeling