178420-75-2

Basic information

• Product Name: 7-TFA-ap-7-Deaza-dA
• Synonyms: 7-TFA-ap-7-Deaza-dA;N-[3-[4-Amino-7-(2-deoxy-β-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]-2-propyn-1-yl]-2,2,2-trifluoroacetamide;7-TFA-ap-7-Deaza-2'-dA
• CAS NO: 178420-75-2
• Molecular Formula: C₁₆H₁₆F₃N₅O₄
• Molecular Weight: 399.3245496
• EINECS: -0
• Mol File: 178420-75-2.mol

Chemical Properties

• Boiling Point: 717.4±60.0 °C(Predicted)
• Appearance: /
• Density: 1.67±0.1 g/cm3(Predicted)
• PKA: 9.63±0.46(Predicted)
• CAS DataBase Reference: 7-TFA-ap-7-Deaza-dA(CAS DataBase Reference)
• NIST Chemistry Reference: 7-TFA-ap-7-Deaza-dA(178420-75-2)
• EPA Substance Registry System: 7-TFA-ap-7-Deaza-dA(178420-75-2)

Safety Data

• Hazardous Substances Data: 178420-75-2(Hazardous Substances Data)

Upstream product

• 14719-21-2 trifluoroacetyl-propargyl amine 
• 166247-63-8 7-deaza-2'-deoxy-7-iodoadenosine 

Downstream Products

• 1448510-88-0 7-[N-4-(methoxytrityl)-1H-imidazol-5-yl-ethylamino-3-(carbamido)propynyl]-5′-O-(4,4′-dimethoxytrityl)-3′-O-acetyl-7-deaza-2′-deoxyadenosine 
• 1448510-87-9 7-[N-4-(methoxytrityl)-1H-imidazol-5-yl-ethylamino-3-(carbamido)propynyl]-5′-O-(4,4′-dimethoxytrityl)-7-deaza-2′-deoxyadenosine 
• 637330-18-8 4-amino-5-(prop-2-ynylamino)-7-(5'-(4,4'-dimethoxytrityl)-2'-deoxy-1'-β-D-ribofuranosyl)pyrrolo{2,3-d}pyrimidine 
• 637330-17-7 4-amino-5-(trifluoroacetamidoprop-2-ynyl)-7-(5'-O-(4,4'-dimethoxytrityl)-2'-deoxy-1'-β-D-ribofuranosyl)pyrrolo{2,3-d}pyrimidine 
• 200066-19-9 7-[2-deoxy-5-O-(4,4'-dimethoxytriphenylmethyl)-β-D-erythro-pentofuranosyl]-N⁴-[(dimethylamino)methylidene]-5-[3-(trifluoroacetamido)prop-1-ynyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine 3'-(2-cyanoethyl diisopropylphosphoramidite) 
• 200066-17-7 7-[2-deoxy-5-O-(4,4'-dimethoxytriphenylmethyl)-β-D-erythro-pentofuranosyl]-N⁴-[(dimethylamino)methylidene]-5-[(3-trifluoroacetamido)prop-1-ynyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine 

Relevant articles and documents

NUCLEOSIDE ANALOGUE, PREPARATION METHOD AND APPLICATION

Nucleoside or nucleotide analog compounds having the structure shown below, a method for preparing them, and applications in nucleic acid sequencing are disclosed. The compounds have formula (I): wherein L1, L2, and L3 are each independently a covalent bond or a covalently linked group; B is a base or a base derivative selected from purines, pyrimidines, or analogs thereof; R1 is —OH, a phosphate group, or a nucleotide; R2 as H or a cleavable group; R3 is a detectable group or a targeting group; R5 is an inhibitory group; R4 is H, —NH2, or —OR6, wherein R6 is H or a cleavable group; and C is a cleavable group or a cleavable bond.

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.

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 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.

Oligonucleotides containing 7-deazaadenines: The influence of the 7- substituent chain length and charge on the duplex stability

Oligonucleotides carrying alkynyl and aminoalkynyl chains at the position 7 of 7-deazaadenine are synthesized, and the chain lengths as well as the bulkiness of the substituents are varied. The corresponding nucleosides 1a-f are prepared from 7-deaza-2'-d

Duplex stability of oligonucleotides containing 7-substituted 7-deaza- and 8-aza-7-deazapurine nucleosides

The synthesis of 7-substituted 7-deaza- and 8-aza-7-deazapurine 2'deoxyribonucleosides, their incorporation into oligonucleotides, and the stability of corresponding duplexes is described.