115899-38-2

Basic information

• Product Name: TFA-ap-dC
• Synonyms: TFA-ap-dC;2'-Deoxy-5-[3-[(trifluoroacetyl)amino]-1-propynyl]cytidine;5-TFA-ap-2-Deoxycytidine;5-TFA-ap-dC;2'-Deoxy-5-[3-[(trifluoroacetyl)amino]-1-propyn-1-yl]-cytidine
• CAS NO: 115899-38-2
• Molecular Formula: C₁₄H₁₅F₃N₄O₅
• Molecular Weight: 376.2879096
• EINECS: 2017-001-1
• Mol File: 115899-38-2.mol
• Article Data: 10

Chemical Properties

• Appearance: /
• Density: 1.65±0.1 g/cm3(Predicted)
• Storage Temp.: under inert gas (nitrogen or Argon) at 2–8 °C
• PKA: 9.24±0.46(Predicted)
• CAS DataBase Reference: TFA-ap-dC(CAS DataBase Reference)
• NIST Chemistry Reference: TFA-ap-dC(115899-38-2)
• EPA Substance Registry System: TFA-ap-dC(115899-38-2)

Safety Data

• Hazardous Substances Data: 115899-38-2(Hazardous Substances Data)

Usage

General Description

TFA-ap-dC is a chemical compound that contains the modified base dC, which stands for deoxycytidine, and is typically used in laboratory research and studies related to nucleic acids and DNA. The compound is often used as a building block in the synthesis of modified oligonucleotides for various applications, including gene editing, molecular biology research, and the development of therapeutic nucleic acid-based drugs. TFA-ap-dC is typically synthesized and purified to high levels of quality to ensure accurate and reliable results in experimental and diagnostic settings. The compound may undergo further modifications or be used in conjunction with other chemical agents to create specific nucleic acid sequences or structures for the desired research or therapeutic purposes.

Upstream product

• 14719-21-2 trifluoroacetyl-propargyl amine 
• 611-53-0 5-Iodo-2'-deoxycytidine 
• 611-53-0 1-((4S,5R)-4-Hydroxy-5-hydroxymethyl-tetrahydro-furan-2-yl)-4-imino-5-iodo-3,4-dihydro-1H-pyrimidin-2-one 

Downstream Products

• 115899-39-3 5-[3-aminoprop-1-ynyl]-2'-deoxycytidine-5'-O-triphosphate 

Relevant articles and documents

A versatile toolbox for variable DNA functionalization at high density

To broaden the applicability of chemically modified DNAs in nano- and biotechnology, material science, sensor development, and molecular recognition, strategies are required for introducing a large variety of different modifications into the same nucleic acid sequence at once. Here, we investigate the scope and limits for obtaining functionalized dsDNA by primer extension and PCR, using a broad variety of chemically modified deoxynucleotide triphosphates (dNTPs), DNA polymerases, and templates. All natural nucleobases in each strand were substituted with up to four different base-modified analogues. We studied the sequence dependence of enzymatic amplification to yield high-density functionalized DNA (fDNA) from modified dNTPs, and of fDNA templates, and found that GC-rich sequences are amplified with decreased efficiency as compared to AT-rich ones. There is also a strong dependence on the polymerase used. While family A polymerases generally performed poorly on "demanding" templates containing consecutive stretches of a particular base, family B polymerases were better suited for this purpose, in particular Pwo and Vent (exo-) DNA polymerase. A systematic analysis of fDNAs modified at increasing densities by CD spectroscopy revealed that single modified bases do not alter the overall B-type DNA structure, regardless of their chemical nature. A density of three modified bases induces conformational changes in the double helix, reflected by an inversion of the CD spectra. Our study provides a basis for establishing a generally applicable toolbox of enzymes, templates, and monomers for generating high-density functionalized DNAs for a broad range of applications.

Based on molecular glue of the fluorescence-labeled nucleotide and its use in DNA sequencing

The invention discloses a fluorescence labelled nucleotide based on a molecular glue and a use thereof in DNA sequencing. The structure formula of the fluorescence labelled nucleotide is shown in a formula (I) in the specification, wherein R1 is shown in the specification, R2 is fluorescein or shown in the specification, and dNTP is ribonucleoside triphosphote which contains four different base groups; the fluorescein is selected from one of the BODIPY, rhodamine, coumarin, xanthene, cyanin, pyrene, phthalocyanine, alexa, a squarene dye, a composition for generating energy transfer dye and the derivatives thereof. The fluorescence labelled nucleotide can be used for DNA sequencing; simultaneously the raw materials for synthesizing the fluorescence labelled nucleotide are simple and easy to obtain and the fluorescence labelled nucleotide can be used for large-scale popularization. The biological assessment result shows that all the requirements of the high-throughput sequencing biochemical reaction can be satisfied by the reversible terminal, and the reversible terminal has good practical prospect.

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.