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Nucleic Acid Modifications

概要

長年にわたる多くの実績を持つBio-Synthesis Inc ( Texas )によるサービスです。
オリゴ合成中、または合成後の広範な修飾をおこなうことができます。Digoxigeninといくつかの蛍光色素については合成中の修飾ができませんが、この場合、合成後にNHSエステル法を使いオリゴに付加させます。
NHSエステルは1級アミンと反応し安定な共有結合のアタッチメントとなります。1級アミンはそれゆえに、希望するNHSエステルとの反応のため、オリゴ合成中にオリゴに加えられます。
オリゴ合成中の直接修飾に比べ、オリゴ合成後の修飾はその効率が低くなります。
全てのNHSエステルの修飾ではHPLC精製が必要となります。PAGEによる精製は収率が悪く、ときに修飾自体を壊してしまうこともあります。
各料金についてはお気軽にお問い合わせください。

Terminus and Internal Modifications

アクリジン | アルデヒド | アミノ | 分岐 | カルボキシ | ターミネーター | コレステリル | デンドリマー | グリセリル | リン酸化 | ソラレン | スペーサー | チオール

◆Acridine

Acridine is an effective intercalating agent as well as being a lipophilic carrier molecule. Acridine labeled oligonucleotides are sometimes used in antisense research. Oligos containing acridine cannot be HPLC purified, nor can they be analyzed by HPLC, as they bind irreversibly to the column. Acridine is available as both a 3′ and a 5′ modifier. Labeling is performed during synthesis and is not a benchtop reaction.

  • Acridine
  • MeO-Cl-Acridine

◆Aldehyde

Aldehydes are attractive electrophiles for bioconjugation, since they react with nucleophiles such as amines to form a Schiff’s base, with hydrazino groups to form hydrazones, and with semicarbazides to form semi-carbazones. The Schiff’s base is unstable and must be reduced with sodium borohydride to form a stable linkage but hydrazones and semicarbazides are very stable linkages.

  • Aldehyde C2

◆Amino modifiers

A primary amino group can be used to attach a variety of modifiers (such as fluorescent dyes) to an oligonucleotide or used to attach an oligonucleotide to a solid surface, for example, a primary amine (NH2) at at the 5’-position is used to functionalize the corresponding terminus of the nucleotide for conjugation with e.g. an activated NHS ester or isothiocyanate fluorescent label. The 3′-NH2 modification allows the prevention of the 3′ to 5′ exonuclease degradation of oligonucleotides in biological fluids such as cell culture medium. Several spacers arm are available, C3, C6, C12 methylene (CH2) or longer and all of them are hydrophobic. Uni-Link TM Amino Modifier provides a free primary amine attached to the 5′-end of an oligo via a six carbon aliphatic spacer arm. It is functionally interchangeable with Amino Modifier C6.
Amino-Modifier dA, Amino-Modifier dC, Amino-Modifier dG and both Amino-Modifier dT products can be added in place of a dA, dC, dG and dT residue, respectively, during oligonucleotide synthesis.

  • Amino-Modifier C3
  • Amino-Modifier C6
  • 5′-Amino-Modifier C12
  • Amino-Modifier C7
  • Amino C6 dT / C2 dT
  • Amino C6 dC
  • Amino C6 dA
  • Amino C6 dG
  • Amio C6 dU
  • PC Amino Modifier

◆Branching

A branching monomer is required to construct comb-like oligonucleotide probes. The Symmetric Branching generates two identical branches at the 5′ terminus of an oligonucleotide during automated DNA synthesis. The number of branches added increases exponentially with each addition of the branching modifier. The Asymmetric Branching modifier generates two asymmetric branches at the 5′ terminus of oligonucleotide during automated DNA synthesis. Multiple additions of this phosphoramidite generate “comb” type oligonucleotide structures.

  • Symmetric Branching
  • Asymmetric Branching
  • 5-Me-dC Branching

◆Carboxy modifiers

Carboxy-dT can be used in place of a dT in an internal position of the oligo, or as the 5′ terminal base. The carboxy-dT modifier allows direct coupling of an oligo to a molecule or surface with a primary amino by a standard peptide coupling or via the intermediate N-hydroxy-succinimide (NHS) ester. This modifier is added to the oligo on the machine during synthesis.

  • Carboxy dT
  • Carboxy C10

Chain terminator

◆Cholesteryl

Cholesterol and cholesteryl modifiers are used to facilitate the permeation of cell membranes. These oligos can be used in conjunction with lipofectin, or liposome incorporation of the oligo.

The cholesterol type modifications are available to tag either the 5′ or 3′ end of the oligo. Cholesterol is available for labeling the 3′ end of oligo and cholesteryl is available for labeling the 5′ end. As with the 3′ modifier, labeling occurs during the course of synthesis. The 5′ cholesteryl modification results in a mixture of modified and unmodified oligos. As a consequence, two bands are generally visible on a gel photo after 5′ labeling. One band represents a full-length unmodified oligo, and the other band represents a full-length modified oligo. In general, cholesterol-modified oligos can be difficult to dissolve in aqueous solutions. In most cases a freeze/thaw cycle may help to get the oligo into solution. We recommend keeping cholesterol-modified oligos in solution and best purified using rpHPLC.

  • Cholesteryl TEG

◆Dendrimer

Dendrimers are discrete, highly branched, monodispersed polymers that possess patterns reminiscent of the branching of trees. Plain and mixed oligonucleotide dendrimers can be synthesized using novel doubling and trebling phosphoramidite synthons.1,2 Dendrimers offer the following advantages. Incorporation of label using g-32P-ATP and polynucleotide kinase increases in proportion to the number of 5′-ends. Fluorescent signal also increases in proportion to the number of 5′-ends, if spacers are incorporated between the labels and the ends of the branches. When using a dendrimeric oligonucleotide as a PCR primer, the strand bearing the dendrimer is resistant to degradation by T7 Gene 6 exonuclease making it easy to convert the double-stranded product of the PCR to a multiply labelled, single-stranded probe. For DNA dendrimers of different generations reassociated as complementary pairs in solution or with an array of complementary oligonucleotides on a solid support, duplex stability is greater than that of unbranched molecules of equal length. Enhanced stability of DNA dendrimers makes them useful as building blocks for the ‘bottom up’ approach to nano-assembly. These features also suggest applications in DNA chip technology when higher temperatures are required, for example, to melt secondary structure in the target.

  • Symmetric Doubler
  • Assymmetric Doubler
  • Trebler
  • Long Trebler

◆Glyceryl

Oligonucleotide with 3′ glyceryl modification can be oxidized by sodium periodate to form 3′ phosphoglycaldehyde. This aldehyde can be further oxidized to the corresponding carboxylic acid. Either the aldehyde or the carboxylate may then be used for subsequent conjugation to Amine-containing products.

◆Phosphorylation

5′ Phosphorylation is needed for the direct ligation to a vector without prior use of T4 polynucleotide kinase. While 3′-PO4 will inhibit degradation by some 3′-exonucleses and used to block extension by DNA polymerase. Both 3′ and 5′ -PO4 oligonucleotides are been used for either further chemical modification or as a substrate in DNA repair studies. This phosphorylation permits the labeling of large quantities and is more reproducible than enzymatic procedures.

◆Psoralen

Psoralen is an intercalating agent that forms photoadducts with thymine residues when exposed to longwave UV. Psoralen is available for 5′ oligo labeling. HPLC purification cannot be performed on oligos that contain this modifier.

  • Psorlaen C2, C6

◆Spacer

Bio-Synthesis offers a number of different Spacer Modified Oligonucleotide Synthesis for both DNA and RNA oligonucleotide. These spacers differ in number of atoms and are typically used to create distance between a functional moiety and the hybridizing region of an oligonucleotide. Spacers are also often used when there is a concern about steric hindrance between the oligonucleotide and the desired functional group interaction or as a blocking group when oligonucleotide extension is not desired . Spacer modifiers can be incorporated into oligonucleotide during chemical synthesis using C3, C12, hydrophilic PEG spacer 18. They can be inserted in the multiple additions when a longer spacer is required especially when coupling an enzyme or antibody to an oligonucleotide, where there is a need to add a hydrophilic spacer such as spacer 18 to optimize the coupling reaction. Addition of a spacer at 3′ end may also act as a blocker of exonuclease and polymerase activity at the 3′-terminus. dSpacer is used to introduce a stable abasic site within an oligonucleotide. Photocleavable PC Spacer modifier is available to be modified during oligonucleotide synthesis.

  • C3 Spacer
  • C6 Spacer
  • C12 Spacer
  • Spacer 9
  • Spacer 18 (hexaethyleneglycol)
  • dSpacer (Abasic furan)
  • ribospacer rSpacer
  • Photocleavable PC Spacer

◆Thiol

Thiol (SH) group can be linked to the 5′ or 3′ terminus of an oligonucleotide. This modification is used for oligo activation prior to linking to various types of molecules or support. The thiol groups can be used to attach a variety of products to the oligonucleotide. Common thiol-reactive groups include maleimides, halogens, iodoacetamides and pyridyldisulfides. This DNA modification is commonly used for the attachment of enzymes such as horseradish peroxidase or alkaline phosphatase.

  • Thiol C3 S-S
  • Dithiol (DTPA)
  • Thiol C6
  • Thiol C6 S-S

Non-radioactive Labelings

ビオチン | ジゴキシゲニン | DNP

◆Biotin

A variety of molecular biology assays and purification methods employ biotin to be used in non radioactive detection method. These biotin-modified oligos bind tightly to straptavidin, the streptavidin can then be labeled with fluorescent dyes and enzymes or mediate attachment to a solid surface. Biotin can be added to the 5’- or 3’-ends of an oligo using either a C6 (standard) or TEG (tetra-ethyleneglycol, 15 atom) spacer arm. 5′ Biotin-TEG requires purification. Internal biotin modification can be introduced using a biotin dT base, which also requires additional purification.

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.

  • 5′ Biotin
  • Biotin
  • Desthiobiotin TEG
  • Biotin dT
  • Biotin TEG
  • 5′ Dual Biotin
  • PC Biotin

◆Digoxigenin

Like biotin, digoxigenin (DIG) is mainly used as a non-isotopic label for DNA and oligonucleotides in a wide range of applications. This small hapten can be conjugated to amino-modified oligos with digoxigenin-NHS-ester. The positions of amino-modification can be specified within an oligo. The 5′ terminus can be labeled with a C6 or C12 linker. C12 may be preferable. Linker arm length determines accessibility of the digoxigenin label to the detecting antibody. Amino-dT can be substituted for dT at internal positions of the oligo. The spacing between labels should be maintained at 10 or more bases to prevent steric limitations on antibody recognition of the digoxigenin label. Multiple labels are necessary for northern and southern hybridization probes.

  • Digoxigenin
  • Digoxigenin dT

◆2,4-dinitrophenyl (DNP)

Oligonucleotides labelled with DNP (2,4-dinitrophenyl) can be used in analytical tests based on anti-DNP antibodies. This DNP with triethylene glycol (TEG) spacer can be introduced anywhere in the sequence and on either terminus.

  • TEG-Dinitrophenol
  • Dinitrophenol

Bases with Altered Pairing

DNA損傷・修復 | デオキシウリジン | ハロゲン化 | イソシトシン・イソグアノシン | スパイク | ユニバーサル | 縮重

◆DNA damage/repair studies

Cellular DNA is constantly being damaged by oxidation and alkylation, by free radicals, and by ultraviolet and ionizing radiation. The body has therefore evolved a number of repair enzyme systems to excise and repair these lesions. The 8-oxo purine monomers allow investigation of the structure and activity of oligonucleotides containing an 8-oxo mutation which is formed naturally when DNA is subjected to oxidative conditions or ionizing radiation. 5,6-Dihydro pyrimidines are naturally occurring compounds that are structural components of alanine transfer RNA. Dihydrouracil and the hydroxy pyrimidines are major base damage products formed by exposure of DNA to ionizing radiation.

  • 8-Oxo-dA
  • 8-Oxo-dG
  • 5-OH-dC
  • 5-OH-dU
  • 5-Hydroxymethyl-dU
  • 1-Me-dA
  • N3-Cyanoethyl-dT
  • 5,6-Dihydro-dU
  • Pyrene-dU
  • Perylene-dU

◆DeoxyUridine (dUracil)

Deoxy-uridine is incorporated in place of deoxyT under circumstances, the enzyme Uracil-N-glycosylase can specifically remove uracil to create baseless sites at the deoxyUridine positions. This property can be used to generate specific strand breaks in a DNA structure.

◆Halogenated Bases

Brominated and iodinated nucleosides are used in crystallography studies of oligonucleotide structure. They are also photolabile and are used for cross-linking studies to probe the structure of protein-DNA complexes. Antibodies exist to Br-dU and oligonucleotides containing Br-dU can be used as probes.

  • br-dU
  • 5-Br-dC
  • 8-Br-dA
  • 8-Br-dG
  • 5-I-dC
  • 5-I-dU
  • 5-F-dU

◆isoCytosine (iso-dC) and isoGuanosine (iso-dG)

The technology developed by EraGen consists of two additional bases (isoCytosine (iso-dC) and isoGuanosine (iso-dG) that form the third base pair.

  • IsoCytosine (iso-dC)
  • IsoGuanosine (iso-dG)

◆Spiked Oligos

Spiked bases refer to non-equimolar mixtures of bases. Spiked oligonucleotides are useful when a determined ratio of degenerated bases is required at precise positions within the sequence. This is generally required when one wants to use the preferential genetic codons rather than to degenerate the wobble position with a statistical mix of dNTP.

◆Universal Bases

Universal bases can be used to replace degenerate bases. This type of modifier can base pair with all four of the standard bases. Designing primers from protein sequences by backtranslation usually results in degenerate oligonucleotides. Universal bases are used to reduce oligonucleotide degeneracy. The best known of these types of modified bases are 2′-DeoxyInosine and 2′-DeoxyNebularine. Neither of these two bases binds to all four bases evenly, but they are a frequently used method of reducing degeneracy. As an alternative, bases such as 3-Nitropyrrole 2′-deoxynucleoside and 5-Nitroindole 2′-deoxynucleoside can be used to take advantage of duplex stabilization by base stacking effects. The degenerate bases dP and dK can form base pairs with purines and pyrimidines, respectively, and can also be used to reduce the overall degeneracy of an oligonucleotide.

  • Deoxy Inosine (dI)
  • Nitroindole
  • 2′-DeoxyNebularine
  • 3-Nitropyrrole
  • dP
  • dK
  • dP + dK

◆Degenerate Base – Wobble

Standard “wobbles” are equimolar mixtures of two or more different bases at a given position within an oligonucleotide. Oligos with wobbles can be used as probes to hybridize to an unknown gene that encodes a known protein sequence, for random mutagenesis, and combinatorial chemistry.

Inosine occurs naturally in the wobble position of the anticodon of some transfer RNAs and is known to form base pairs with A, C and U during the translation process.

Please always refer to the International Union of Biochemistry (IUB) base codes to introduce wobbles in your oligo sequences.

  • Inosine dI
  • dA+dG (R)
  • dC+dT (Y)
  • dA + dC (M)
  • dG + dT (K)
  • dC + dG (S)
  • dA + dT (W)
  • dA + dC + dT (H)
  • dC + dG + dT (B)
  • dA + dC + dG (V)
  • dA +dG + dT (D)
  • dA+dC+dG+dT (N)

PCR/Sequencing Utilities

二本鎖効果 | ターミネーター

◆Duplex Effects

The design of primers is frequently complicated by the degeneracy of the genetic code. Three strategies are now available to confront this problem. In the first, a mixed base addition (N) is used to form the degenerate site. This approach is best if the number of degenerate sites is small. A second option is the use of 2′-deoxyInosine or 2′-deoxyNebularine which exhibit low, but unequal, hydrogen bonding to the other four bases. The third option is the use of a universal nucleoside. In this strategy, the base analog does not hybridize significantly to the other four bases and makes up some of the duplex destabilization by acting as an intercalating agent. 3-Nitropyrrole 2′-deoxynucleoside (M) is the first example of a set of universal bases. Subsequently, 5-nitroindole was determined to be an effective universal base and to be superior to 3-nitropyrrole, based on duplex melting experiments. The modified bases designated P and K show considerable promise as degenerate bases. The pyrimidine derivative P, when introduced into oligonucleotides, base pairs with either A or G, while the purine derivative K base pairs with either C or T. A dP+dK mix also can serve as a mixed base with much less degeneracy than dA+dC+dG+dT (N). A standard Watson and Crick base pair is formed between iso-C and iso-G, but the hydrogen bonding pattern is quite different from the natural base pairs A-T and C-G. (The 5-methyl analogue was chosen as the synthetic target due to the reported instability of 2′-deoxyisocytidine caused by deamination during oligonucleotide synthesis or deprotection.)

  • Deoxy Inosine (dI)
  • deoxyUridine (dUracil)
  • Nitroindole
  • 2′-DeoxyNebularine
  • 3-Nitropyrrole
  • dP
  • dK
  • dP + dK
  • dmf-5-Me-isodC
  • dmf-isodG
  • dA+dG (R)
  • dC + dT (Y)
  • dA + dC (M)
  • dG + dT (K)
  • dG + dT (K)
  • dC + dG (S)
  • dA + dT (W)
  • dA + dC + dT (H)
  • dC + dG + dT (B)
  • dA + dC + dG (V)
  • dA +dG + dT (D)
  • dA+dC+dG+dT (N)

◆Chain Terminators

Bio-Synthesis provides 3′ chain terminator or end blocker oligo modifications to block ligation at 5′ terminus or preventing polymerase extension from the 3′ terminus. These bases can also be used internally to create a 5′-2′ phosphate linkage in the oligo. All four bases are available with the deoxyribose sugar blocked at the 3′ position, to give 3′-deoxy terminator G, T, C, and A. Cordecypin is an alternative name for the 3′-deoxy A terminator. These modifiers are preferred in place of dideoxy modifications. 2′,3′- dideoxy chain terminator are designed to be used with reverse 5′ to 3′ synthesis and support.

In situations where ligation must be blocked at the 5′ terminus, 5′-OMe-dT may be used. 5′-OMe modification of a strand of siRNA using 5′-OMe-T can control guide strand selection and targeting specificity.1 5′-Amino-dT terminates an oligonucleotide with a 5′-amino group which may be used for attaching a peptide or a PNA sequence.

3′-Termination can also be effected using a 3′-3′ linkage formed using 5′-supports, other non-nucleoside blocker of 3′-terminus such as 3′-Spacer C3, 3′-Phosphate can also be use as 3′ terminator. Ion exchange HPLC or PAGE should be used to purify these dideoxy terminated oligos to ensure that shorter sequences (containing 3′-OH) groups are removed.

End Blocker Oligo Modification

Bio-Synthesis end blocker modification can be incorporate at 5′ or 3′ end of an oligonucleotide using 5′-5” or 3′-5′ synthesis strategy.

Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

  • 1,2-Dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate tripeptide
  • 2′, 3′ Dideoxyadenosine (2,3ddA)
  • 2′, 3′ Dideoxycytosine (2,3ddC)
  • 2′, 3′ Dideoxythymidine (2,3ddT)
  • 2′,3′ Dideoxyguanosine (2,3ddG)
  • 3′ Phosphate
  • 3′-Deoxycytidine(3′-dA)
  • 3′-Deoxycytidine(3′-dC)
  • 3′-Deoxycytidine(3′-dG)
  • 3′-Deoxycytidine(3’dT)
  • 3′-Spacer C3

Bases Increasing Duplex Stability

2′-5’Linked | 2′-O-メチル | C-プロピン | C5-メチル | キメラ | モルフォリノ | フォスフォロチオエート

 

◆2′-5′ Linked Oligonucleotides

◆2′-O-methyl Modified Oligonucleotides

◆C-Propyne Analogues

◆C5-Methyl Analog

◆Chimeric Oligos

 

◆Methylphosphonate

◆Morpholino Oligonucleotides

◆Phosphorothioate

Photo Cleavable

アミノ | スペーサー | ビオチン | リンカー

◆PC-Amino

Amino-modified oligonucleotides have proven to be very useful for the attachment of a variety of haptens and fluorophores, as well as for the tethering of the oligonucleotides to a diversity of beads and surfaces. PCAmino-modified oligonucleotides are used for the subsequent photocleavage.

  • 5’PC-Amino

◆PC-Spacer

PC Biotin can be used to prepare 5′-biotinylated oligonucleotides suitable for capture by streptavidin in a mode similar to our popular 5′ Biotin modifications. Amino- and thiol-modified oligonucleotides have proven to be very useful for the attachment of a variety of haptens and fluorophores, as well as for the tethering of the oligonucleotides to a diversity of beads and surfaces. PC Amino-Modifier is used to prepare 5′-amino-modified oligonucleotides suitable for subsequent photocleavage. PC Spacer Phosphoramidite can be used as an intermediary to attach any modification reagent, available as a phosphoramidite, to the terminus of oligonucleotides. After photocleavage, a 5′-phosphate is generated on the DNA, rendering it suitable for further biological transformations, such as gene construction and cloning after ligation.

◆PC-Biotin

PC Biotin can be use for capture by streptavidin in a mode similar to our popular 5′ Biotin oligonucleotide. DNA researchers have long sought effective ways to capture oligonucleotides or PCR products from a crude mixture and then to release them in a pure, biologically active form. Now such a technique developed by AmberGen, Inc. is available using PC Biotin and related photocleavable (PC) modifiers. After capturing biotin labeled DNA with streptavidin beads or attaching modified DNA to a surface, the DNA can be released into solution by simply illuminating with a hand-held UV light source.1 Moreover, once freed from its tether the DNA is biologically active.

  • PC-LC Biotin

◆PC-Linker

A versatile photocleavable DNA building block has been described by researchers in Washington University, Missouri and used in phototriggered hybridization.1 This reagent has also been used in the design of multifunctional DNA and RNA conjugates2 for the in vitro selection of new molecules catalyzing biomolecular reactions. Researchers at Bruker Daltonik in Germany have also developed genoSNIP, a method for single-nucleotide polymorphism (SNP) genotyping by MALDI-TOF mass spectrometry.3 This method uses size reduction of primer extension products by incorporation of the photocleavable linker for phototriggering strand breaks near to the 3′ end of the extension primer. PC Linker can be incorporated into oligonucleotides at any position by standard automated DNA synthesis methodology. PC Linker has the added advantage in that photocleavage results in monophosphate fragments at both the 3′- and 5′-termini of the oligonucleotide fragments.

Bioconjugations

小分子標識 | 小分子同士 | 固定

We offer a personalized solutions to assist client cross link various molecules and compound and solid support attachment. More…

◆Biomolecule-small molecule labelings

◆Biomolecule-biomolecule conjugations

◆Immobilization on solid supports

Antisense Oligonucleotides

フォスフォロチオエート (Sオリゴ) | ENA・ZNA | 2′-OMe | その他

Use antisense oligonucleotides for your gene silencing experiments. We hybrid designs using various types of nucleotide analogs to increase high affinity for a successful knockdown experiments. More….

◆Phosphorothioate oligos

◆Constrained ribose (ENA, ZNA)

◆2′ OMethyl Base

◆2′ Fluoro RNA

◆Morpholino

◆5-Me-dC

◆PropynedC or dU

Quencher

BHQ™ | Eclipse® | DABCYL | TAMRA

A quencher is a molecule that is able to absorb the energy emitted by a fluorophore. Through FRET (Fluorescence Resonance Energy Transfer), it emits the energy at different wavelength, reducing the fluorescence of the fluorophore. This quencher any also act through collisional quenching where the fluorophore and quencher are in close contact. Bio-Synthesis can incorporate oligonucleotide with several quenchers. See details and price listing on Quencher Modified Oligonucleotides.

◆Black Hole QuencherTM

◆Eclipse® Dark Quencher

◆DABCYL

◆TAMRA

Fluorophore Labelings

AlexaFluor® | Epoch | ATTO-TEC | FITC | Bodipy® | Oregon Green | Cyanine | その他分子プローブ | Dyomic | Oyster | Rhodamine

◆Alexa Fluor® Dyes

These dyes are available as NHS Esters and are conjugated post synthesis to an amino-modified oligo and two step HPLC purifications are required. The spectral diversity of the Alexa Fluor dyes make them ideal tools for multicolor applications such as fluorescence in situ hybridization (FISH) and microarray experiments. Our wide selection of dyes spans the visible spectrum and beyond, providing enormous flexibility in choosing a label that is compatible with microarray scanners and fluorescence microscopes. The Alexa Fluor dyes have several properties that make them superior to other fluorescent dyes and oligonucleotides labeled with Alexa Fluor have many advantages:

  • High water solubility.The Alexa Fluor dyes are highly water soluble, making them ideal for hybridization experiments. Nucleic acids labeled with the Alexa Fluor dyes do not aggregate or precipitate, even in high-salt conditions.
  • pH independence. Fluorescence of the Alexa Fluor conjugates is not pH sensitive in the ranges used for hybridization solutions and microscopy mounting media.
  • Resistance to photobleaching. The enhanced photostability of Alexa Fluor dyes makes them ideal for applications requiring imaging, such as FISH and microarrays.
  • High signal correlation.

The Alexa Fluor 555/Alexa Fluor 647 dye pair provides better signal correlation and therefore higher resolution of diff erentially expressed genes than the commonly used Cy3/Cy5 dye pair.
Similar alternatives include the DyLight Fluors and the Atto.

  • Alexa FluorTM 350
  • Alexa FluorTM 405
  • Alexa FluorTM 430
  • Alexa FluorTM 488
  • Alexa FluorTM 514
  • Alexa FluorTM 532
  • Alexa FluorTM 546
  • Alexa FluorTM 555
  • Alexa FluorTM 555
  • Alexa FluorTM 568
  • Alexa FluorTM 594
  • Alexa FluorTM 610
  • Alexa FluorTM 633
  • Alexa FluorTM 647
  • Alexa FluorTM 660
  • Alexa FluorTM 680
  • Alexa FluorTM 700
  • Alexa FluorTM 750

◆Epoch Dye and Quencher

We are pleased to offer products based on Epoch’s Redmond Red™, Yakima Yellow™ and Gig Harbor Green™ fluorophores and Eclipse™ non-fluorescent quencher. The two fluorescent dyes, Yakima Yellow and Redmond Red, are available to be labeled at 5′ or 3′ end of an oligo. Yakima Yellow has an absorbance maximum at 530 nm and emission maximum at 549 nm, while Redmond Red’s absorbance and emission maxima are at 579 nm and 595 nm, respectively. Gig Harbor Green and 6-FAM are based on the same fluorescein core structure but Gig Harbor Green is 15-20% brighter than FAM. The Eclipse quencher from Epoch 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 Cy5. 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.

  • Epoch Redmond Red™
  • Epoch Gig Harbor Green™
  • Yakima Yellow
  • Epoch Eclipse™ Quencher

◆ATTO-TEC Dyes

New set of excellent fluorescent dyes from ATTO-Tec has added to our broad portfolio of labels for oligonucleotides. These activated fluorescent dyes have become the standard procedure for stable labelling of proteins, nucleic acids, ligands and other biomolecules, which are widely used for applications as fluorescence microscopy, flow cytometry, fluorescence in situ hybridisation (FISH), receptor binding assays, or enzyme assays.

ATTO dyes are a series of fluorescent dyes which provide all the crucial properties required for modern fluorescent technologies.

  • Strong absorption (high extinction coefficient)
  • High fluorescence quantum yield
  • High photostability
  • Good water solubility
  • Low triplet formation
  • Ideally suited for bioanalytical applications

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any Amino Modifier C6 dA, dT, dG, dC for internal labeling, a double HPLC purification is required.

Contact your Account Representative for pricing on ATTO labeled oligonucleotides.

  • ATTO390
  • ATTO465
  • ATTO465
  • ATTO488
  • ATTO495
  • ATTO520
  • ATTO532
  • ATTO540 Quencher
  • ATTO550
  • ATTO565
  • ATTO580 Quencher
  • ATTO590
  • ATTO594
  • ATTO610
  • ATTO612 Quencher
  • ATTO620
  • ATTO633
  • ATTO637
  • ATTO647N
  • ATTO655
  • ATTO680
  • ATTO700
  • ATTO720
  • ATTO740

◆Fluorescein Dye

There are different possibilities for labeling fluorescein dye to an oligonucleotide:

All of our dyes can be attached post synthetically to the 5′- terminus of an oligonucleotide via an amino- or thiol- linker with a 6-Carbon spacer arm. This method is available for JOE .

Another possibility for labeling an oligonucleotide at the 5′ or internal terminus is to couple the dye directly during synthesis via its phosphoramidite. This method is available for 6-FAM, Fluorescein, Fluorescein dT, 6-Fluorescein, HEX, TET .

Post synthetic labeling of oligonucleotides at internal sites of the sequence is possible by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine. All dyes available for 5′- labeling can also be attached internally.

It is also possible to label the 3′- end of oligonucleotides post synthetically via an amino link. This method is available for all dyes. For the 3′- labeling with fluoresce in , BSI has special solid supports [CPGs] with the dyes already attached. This is very useful for high quality production of labeled probes.

  • Fluorescein (6-FAM)
  • Fluorescein
  • 6-Fluorescein
  • Fluorescein dT
  • 3′-(6-FAM) PS
  • JOE
  • Hexachloro-Fluorescein (HEX)
  • Tetrachloro-Fluorescein (TET)

* Product Note – This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

◆Bodipy® Fluorophores

Bodipy® Dyes have a narrow spectral characteristics and are highly fluorescent that are often superior to those of fluorescein, tetramethylrhodamine, Texas Red and longer-wavelength dyes. These dyes are unusual in that they are:

Higher quantum yields
Narrower emission bandwidths
Greater photostability
Insensitive to pH changes
Useful for DNA sequencing because the dye exhibits minimal effect on the mobility of the fragment during electrophoresis

Bodipy labels are attached at the 5′- , Internal, or 3′- end of an oligonucleotide. In a post-synthetic step, the dye is coupled to an amino-modified oligo.

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any Amino Modifier C6 dA, dT, dG, dC for internal labeling, a double HPLC purification is required.

  • BODIPY 493/503™
  • BODIPY 558/568TM
  • BODIPY 564/570TM
  • BODIPY 576/589TM
  • BODIPY 581/591TM
  • BODIPY TMR-X™
  • BODIPY TR-XTM
  • BODIPY 530/550TM
  • BODIPY-FL BR2TM
  • BODIPY-FL-X™

◆Oregon Green

There are different possibilities for labeling fluorescein dye to an oligonucleotide:

Oregon Green, an alternative to fluorescein with greater photostability and higher fluorescence.

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

  • Oregon Green® 488, 5- Isomer
  • Oregon Green® 488, 6- Isomer
  • Oregon Green® 514

◆Cyanine Dye

Cy® dyes exhibit excellent spectroscopic performance with high quantum yields, high extinction coefficient, and good stability of fluorescence signal against changes in pH in various buffer conditions. In addition to labeling oligonucleotides chemical during synthesis, we can also attached Cy3, Cy3.5, Cy5, Cy5.5 and Cy7 fluorescent DNA probes by chemically by preparing 5′-amino-end-labeled oligonucleotide probes on a DNA synthesizer. The amino-group containing probes are then labeled with a fluorescent tag containing an isothiocyanate group or a succinimidyl active ester.

  • Cy3™
  • Cy3.5Tm
  • Cy5Tm
  • Cy5.5Tm

* Product Note – This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

◆Other Molecular Probe Dyes

Molecular Probes has developed and patented a series of additional fluorescent dyes. Their unique characteristics make them particularly useful in applications such as DNA typing.
This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

  • Cascade Blue™
  • 2′-OMeMarina Blue®
  • Pacific Blue®
  • Texas Red® Mix-Isomer
  • Texas Red® Single-Isomer

◆Dyomic Dyes

We offer DY-labels oligonucleotide from Dyomics with more than 50 fluorophores covering the whole fluorescence spectrum. These coupled oligonucleotides are used in cDNA detection on microarray, fluorescence assays like FISH, Real time PCR or FRET assays and they may be an attractive alternative for traditional fluorescence dyes. Dy 647 is a bright orange dye with similar properties to CY®5 and Alex Fluore® 647, DY547 is also bright organic dye with similar properties to CY®3.

Other dyes (called Mega Stokes-Dyes) exhibit a large shift of fluorescence relative to the absorption (Stokes shift).

DY 480XL, 461XL and DY520XL, these dyes are compatible with the use of Taqman probes on Light cycler® Real-Time qPCR machine.

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

  • Dy415
  • Dy485XL
  • Dy495
  • Dy480XL
  • Dy505
  • Dy505-X
  • Dy510XL
  • Dy481XL
  • Dy520XL
  • Dy521XL
  • Dy555
  • Dy556
  • Dy554
  • Dy547
  • Dy548
  • Dy560
  • Dy590
  • Dy610
  • Dy615
  • Dy634
  • Dy631
  • Dy632
  • Dy633
  • Dy636
  • Dy635
  • Dy647
  • Dy648
  • Dy650
  • Dy652
  • Dy651
  • Dy660 Quencher
  • Dy661 Quencher
  • Dy677
  • Dy676
  • Dy680
  • Dy682
  • Dy681
  • Dy701
  • Dy700
  • Dy730
  • Dy734
  • Dy731
  • Dy732
  • Dy750
  • Dy752
  • Dy751
  • Dy776
  • Dy780
  • Dy782 (infrared!)
  • Dy781
  • Dy831

◆Oyster Dye

Oyster fluorophores is new class of cyanine dyes which can be use to substitute for Cy2, Cy3, Alexa or Fluorescein for FISH application. These dyes are unique in that they are:

  • High photostability
  • Bright fluorescence
  • Oyster-500 can substitute Cy2, Alexa Fluor® 488, Fluorescein
  • Oyster-556 can substitute Cy3, Alexa Fluor® 555
  • Oyster-645 can substitute Cy5, Alexa Fluor® 647
  • Oyster-656 matches the emission band of a 650 nm laser diode

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

  • Oyster® 550
  • Oyster® 556
  • Oyster® 645
  • Oyster® 650

◆Rhodamine Dyes

Rhodamine derivatives are not sufficiently stable to survive conventional deprotection and these must be attached to amino-modified oligonucleotides using post-synthesis labeling techniques for 5′ labeling.

This compound requires amino- or thiol- linker with a 6-Carbon spacer arm or by substituting any thymidine with 5-C6-Amino-2′-deoxythymidine for internal labeling, a double HPLC purification is required.

  • Rhodamine GreenTM-X NHS Ester
  • Rhodamine RedTM-X NHS Ester
  • TAMRA™
  • TAMRA™ NHS Ester
  • ROX™ NHS Ester

Redox Labels

ジカルボキシメチレンブルー | モノカルボキシメチレンブルー | フェロセン | アントラキノン

Redox active compounds for electrochemical studies.

◆Dicarboxymethylene Blue

◆Monocarboxymethylene Blue

◆Ferrocene, Ferrocene-C6

◆Anthraquinone, Anthraquinone-C6

Fluorogenic Probes and Primers for Real-time qPCR

標識プローブ | Amplifluor® | 分子ビーコン | Plexor™ | Black Hole Scorpions™

◆Labeled probes

◆Amplifluor® Direct Primer

◆Molecular Beacon for Gene Detection and Analysis

◆Plexor™ Primers

◆Black Hole Scorpions™ Primers

Probes for Multiplexing qPCR

標識プローブ | Amplifluor® | 分子ビーコン | Black Hole Scorpions™

◆Labeled probes

◆Amplifluor® Direct Primer

◆Molecular Beacon

◆Black Hole Scorpions™ Probe, Uni-molecular

Disclaimer: FAMTM, HEXTM, ROXTM, TAMRATM and TETTM are trademarks of Applied Biosystems, Inc. CyTM is a trademark of GE Healthcare; Texas RedTM is a trademark of Molecular Probes Eclipse® and Yakima Yellow® are registered trademarks of Epoch Biosiences, Inc. BHQ 1TM and BHQ 2TM are trademarks of Biosearch Technologies, Inc. BlackBerry (BBQ)TM is a trademark of Berry & Associates, Inc. LightCycler® probes are sold under the license from Roche Diagnostics Gmbh.


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