115899-38-2

Usage

Uses

Used in Gene Editing Applications:
TFA-ap-dC is used as a building block for the synthesis of modified oligonucleotides that are essential in gene editing techniques. These modified oligonucleotides can be designed to target specific DNA sequences, allowing for precise manipulation and modification of genes, which is crucial for studying gene function and developing gene therapies.
Used in Molecular Biology Research:
In molecular biology research, TFA-ap-dC is employed as a component in the synthesis of modified oligonucleotides that can be used to study various biological processes, such as gene expression, regulation, and interaction. These modified oligonucleotides can be used in techniques like polymerase chain reaction (PCR), DNA sequencing, and microarrays to gain insights into the molecular mechanisms underlying various biological phenomena.
Used in Pharmaceutical Industry:
TFA-ap-dC is used as a key component in the development of therapeutic nucleic acid-based drugs. These drugs, such as antisense oligonucleotides and small interfering RNAs (siRNAs), can be designed to modulate gene expression or interfere with specific RNA molecules, offering potential treatments for various diseases, including genetic disorders, viral infections, and cancer.
Used in Diagnostic Applications:
In diagnostic settings, TFA-ap-dC can be utilized in the synthesis of probes and primers for detecting and identifying specific nucleic acid sequences. These probes and primers can be employed in techniques like real-time PCR, in situ hybridization, and DNA microarrays, enabling the accurate diagnosis of diseases and the monitoring of treatment responses.
Overall, TFA-ap-dC plays a vital role in various applications across different industries, including gene editing, molecular biology research, pharmaceutical development, and diagnostics, due to its unique properties and versatility in the synthesis of modified oligonucleotides.

Upstream product

• 14719-21-2 trifluoroacetyl-propargyl amine 
• 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 
• 611-53-0 5-Iodo-2'-deoxycytidine 

Downstream Products

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

Relevant academic research and scientific papers

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.

NUCLEOTIDE CLEAVABLE LINKERS AND USES THEREOF

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

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.

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.

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.

A ligand-free solid-supported system for Sonogashira couplings: Applications in nucleoside chemistry

A mild heterogeneous, ligand-free protocol for Sonogashira and Heck couplings has been developed and used to access several biologically important deoxynucleoside derivatives in a facile manner. The Royal Society of Chemistry 2005.

Alkynylamino-nucleotides

Alkynylamino-nucleotides and labeled alkynylaminonucleotides useful, for example, as chain terminating substrates for DNA sequencing are provided along with several key intermediates and processes for their preparation. For some applications, longer, hydrophilic linkers are provided.

Alkynylamino-nucleotides

Alkynylamino-nucleotides and labeled alkynylamino-nucleotides useful, for example, as chain terminating substrates for DNA sequencing are provided along with several key intermediates and processes for their preparation.

Palladium-Catalyzed Synthesis of Alkynylamino Nucleosides. A Universal Linker for Nucleic Acid

A method for attaching alkynylamino "linkers" to nucleosides and nucleotides is described.Protected or unprotected alkynylamines are coupled to iodonucleosides in dimethylformamide using a 1:2 mol ratio of tetrakis(triphenylphosphine)palladium(0) and copper(I) iodide, a catalyst system superior to the standard system using palladium(II) species.The resulting alkynylamino nucleosides are useful for enzymatic or chemical labeling of all four bases of DNA.