115899-40-6

Basic information

• Product Name: TFA-ap-dU
• Synonyms: TFA-ap-dU;2'-Deoxy-5-[3-[(2,2,2-trifluoroacetyl)aMino]-1-propyn-1-yl]uridine;5-TFA-ap-2'-Deoxyuridine
• CAS NO: 115899-40-6
• Molecular Formula: C₁₄H₁₄F₃N₃O₆
• Molecular Weight: 377.2726696
• Mol File: 115899-40-6.mol

Chemical Properties

• Appearance: /
• Density: 1 +-.0.1 g/cm3(Predicted)
• Storage Temp.: 2-8°C
• Solubility: DMSO (Slightly), Methanol (Slightly)
• PKA: 8.17±0.10(Predicted)
• CAS DataBase Reference: TFA-ap-dU(CAS DataBase Reference)
• NIST Chemistry Reference: TFA-ap-dU(115899-40-6)
• EPA Substance Registry System: TFA-ap-dU(115899-40-6)

Safety Data

• Hazardous Substances Data: 115899-40-6(Hazardous Substances Data)

Usage

Uses

Used in Biotechnology and Molecular Biology:
TFA-ap-dU is used as an intermediate compound for the synthesis of fluorescent labeling agents in DNA research. Its application is primarily focused on enhancing the visualization and detection of specific DNA sequences, which is essential for various molecular biology and biotechnology applications.
Used in Diagnostics:
In the diagnostics industry, TFA-ap-dU is used as a component in the development of diagnostic tools that rely on DNA sequencing and analysis. The fluorescent labeling compounds synthesized using TFA-ap-dU can help improve the accuracy and efficiency of disease detection and monitoring.
Used in Research and Development:
TFA-ap-dU is employed as a key intermediate in the synthesis of novel fluorescent probes for research and development purposes. These probes can be used to study various biological processes, such as DNA replication, transcription, and repair, as well as to develop new therapeutic strategies targeting DNA-related diseases.
Used in Drug Discovery:
In the pharmaceutical industry, TFA-ap-dU can be utilized in the development of new drugs that target DNA or DNA-related processes. The fluorescent labeling compounds derived from TFA-ap-dU can aid in the identification and characterization of potential drug candidates, contributing to the advancement of drug discovery efforts.

Upstream product

• 14719-21-2 trifluoroacetyl-propargyl amine 
• 54-42-2 5-Iodo-2'-deoxyuridine 

Downstream Products

• 666847-54-7 5’-O-(tert-butydimethylsilyl)-5-[3-(2,2,2-trifluoroacetamido)-prop-1-ynyl]-2’-deoxyuridine 
• 118573-62-9 5-(3-aminopropyl)-2'-deoxyuridine 
• 96102-26-0 5-[3-N-(trifluoroacetyl)aminopropyl]-5'-O-(4,4'-dimethyltrityl)-2'deoxyuridine 
• 244285-86-7 3'-O-acetyl-5-(3''-trifluoroacetamidopropynyl)-5'-O-dimethoxytrityl-2'-deoxyuridine 
• 179101-49-6 5-(3-amino-1-propynyl)-2'-deoxyuridine 5'-triphosphate 
• 120016-97-9 5-(3-trifluoroacetamidopropargyl)-5'-O-(4,4'-dimethoxytrityl)-2'-deoxyuridine 

Relevant articles and documents

Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates

We describe the synthesis of 2′-deoxyuridine-5′-triphosphate derivatives bearing linkers of varying length, bulk and flexibility, at position 5 of the pyrimidine base. Nucleotide analogues with terminal functional groups are of interest due to their appli

Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA

The amino group of 5-aminopropargyl-2′-deoxyuridine-5′- triphosphate was labelled with dibenzocyclooctyne (DIBO) and two derivatives of bicyclo [6.1.0] non-4-yne (BCN) with short and long linkers to produce three different cycloalkyne-modified deoxyuridine triphosphates. BCN was successfully incorporated into DNA at multiple sites by enzyme-mediated primer extension and the polymerase chain reaction (PCR). Efficient fluorescent labelling of the BCN-DNA and DIBO-DNA with Cy3-azide was demonstrated.

MODIFIED NUCLEOTIDES AND USES THEREOF

Disclosed herein, inter alia, are compounds, modified nucleotides, compositions, and methods of using the same.

DISULFIDE-LINKED REVERSIBLE TERMINATORS

The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3'-OH group and a base that is attached to a detectable label through a cleavable linker comprising a disulfide bond. In addition, the disulfide bond(s) can be cleavable by a reducing reagent. In addition, after the disulfide bond(s) is/are cleaved by the reducing reagent, there is no free thiol group linked to the nucleotides. Examples of chemical compounds according to the present disclosure are shown as Formulae (IV) and (V).

NUCLEOTIDE CLEAVABLE LINKERS AND USES THEREOF

Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof for sequencing a nucleic acid.

Fluorescently-labeled nucleotide as well as preparation method and application thereof

The invention discloses fluorescently-labeled nucleotide. The fluorescently-labeled nucleotide has a structure represented as the formula I in the description. Stable covalent bonding is formed between dNTP (deoxyribonucleoside triphosphate) and fluorescent dye molecules represented as the formula Q, and the fluorescently-labeled nucleotide has high stability in detection environments such as serum and the like, and is high in biocompatibility and suitable for detecting nucleic acid molecules in and out of cells. Due to large Stokes shift of the fluorescent dye molecules, the fluorescently-labeled nucleotide further has the advantages of good fluorescent stability, high fluorescent quantum yield and high signal-to-noise ratio of an imaging result. The invention further discloses a preparation method of the fluorescently-labeled nucleotide. The compound with the structure shown as the formula I is prepared by a click chemical reaction, reaction conditions are mild, operation is simple,reaction selectivity is high, and the fluorescently-labeled nucleotide with high yield can be prepared.

DISULFIDE-LINKED REVERSIBLE TERMINATORS

The present disclosure provides methods of sequencing polynucleotides and compounds, compositions useful for sequencing of polynucleotides. The chemical compounds include nucleotides and their analogs which possess a sugar moiety comprising a cleavable chemical group capping the 3'-OH group and a base that is attached to a detectable label through a cleavable linker comprising a disulfide bond. In addition, both the disulfide bond and the cleavable chemical group are cleavable by a chemical reagent. Furthermore, after the disulfide bond is cleaved by the chemical reagent, there is no free thiol group linked to the base of the nucleotides.

Three nitrogen alkene company unit thereof in the synthesis of the use of DNA sequencing

The invention discloses synthesis of a triazene connection unit and an application of the triazene connection unit in DNA sequencing. The triazene connection unit has a structural formula as shown in the description, wherein -CH2OH and -CH2N3 are respecti

Synthesis of acid-sensitive connection unit and its use in DNA sequencing

The invention discloses a synthesis method of an acid sensitive connection unit, and a use of the acid sensitive connection unit in DNA sequencing. The structural formula of the acid sensitive connection unit is shown in the specification. In the structural formula, R is NH2 or N3, m is an integer from 0 to 44, and n is an integer from 0 to 44; R1 and R2 respectively represent an aliphatic alkyl group, or R1 and R2 respectively represent an aromatic derivative, or R1 is a phenyl group, a naphthyl group, a phenyl derivative or a naphthyl derivative, and R2 is an aliphatic alkyl group or hydrogen; or R2 is a phenyl group, naphthyl group, a phenyl derivative or a naphthyl derivative, R1 is an aliphatic alkyl group or hydrogen, or R1 and R2 form a cyclohexyl group, a cyclopentyl group or a cyclobutyl group. A reversible terminal obtained through connecting the acid sensitive connection unit with nucleotide and fluorescein can be used in DNA sequencing-by-synthesis. The reversible terminal can be used in the DNA sequencing; and raw materials required by the synthesis method are simple and can be easily obtained, and the synthesis process is a routine chemical reaction, so the method can realize large scale popularization use.

Modified nucleotides for polynucleotide sequencing

The invention provides a kit comprising four modified nucleotide triphosphate molecules, each comprising a purine or pyrimidine base and a deoxyribose sugar moiety wherein the 3' carbon atom of the sugar moiety has attached a group of the structure???????? -O-Zwherein Z is of the formula -CH2N3.