1022-79-3

Basic information

• Product Name: 5-Bromo-2'-deoxycytidine
• Synonyms: 5-bromo-2’-deoxy-cytidin;2'-DEOXY-5-BROMOCYTIDINE;5-BR-DC;5-BROMO-2'-DEOXYCYTIDINE;5-BROMO-2'-DEOXYCYTIDINE MONOHYDRATE;5-BROMODEOXYCYTIDINE;5-Bromo-2'-deoxy-D-cytidine;5-BROMO-2''-DEOXYCYTIDINE(5-BRDC)
• CAS NO: 1022-79-3
• Molecular Formula: C₉H₁₂BrN₃O₄
• Molecular Weight: 306.11
• EINECS: 213-824-2
• Product Categories: Nucleotides and Nucleic Acids
• Mol File: 1022-79-3.mol
• Article Data: 7

Chemical Properties

• Boiling Point: 510.81 °C at 760 mmHg
• Flash Point: 262.728 °C
• Appearance: White to Pale Yellow/Powder
• Density: 2.13 g/cm³
• Storage Temp.: Store at 0°C
• PKA: 14.03±0.60(Predicted)
• CAS DataBase Reference: 5-Bromo-2'-deoxycytidine(CAS DataBase Reference)
• NIST Chemistry Reference: 5-Bromo-2'-deoxycytidine(1022-79-3)
• EPA Substance Registry System: 5-Bromo-2'-deoxycytidine(1022-79-3)

Safety Data

• Hazard Codes: Xn
• Statements: 40
• Safety Statements: 22-36
• RTECS: HA3705000
• Hazardous Substances Data: 1022-79-3(Hazardous Substances Data)

Usage

General Description

5-Bromo-2'-deoxycytidine is a chemical compound that is widely used in molecular biology. It is a derivative of the nucleoside deoxycytidine and known to be a potent inhibitor of DNA methyltransferases, the enzymes that methylate DNA. The additional bromine atom allows the molecule to be easily incorporated into DNA during replication, which can be used as a tool to study DNA repair and replication mechanisms. It has also been used in cancer research due to its potential to regulate gene expression. However, like many other brominated compounds, it can be potentially toxic and mutagenic and its use requires careful handling and disposal.

Upstream product

• 951-77-9 2'-Deoxycytidine 
• 3992-42-5 2'-deoxycytidine monohydrochloride 

Downstream Products

• 951-77-9 2'-Deoxycytidine 
• 148716-10-3 4-N-benzoyl-5-bromodeoxycytidine 
• 178925-43-4 4-N-benzoyl-5-bromo-5'-O-(4,4'-dimethoxytrityl)-deoxycytidine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite) 
• 100360-44-9 4-N-benzoyl-5-bromo-5'-O-(4,4'-dimethoxytrityl)-deoxycytidine 
• 119411-85-7 5-bromo-2'-deoxy-5'-O-p-toluenesulfonylcytidine 
• 218145-18-7 3-{(2R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-4-hydroxy-tetrahydro-furan-2-yl}-5,6,7,8-tetrafluoro-3H,9H-10-oxa-1,3,9-triaza-anthracen-2-one 

Relevant articles and documents

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Synthesis of a 5′-6-locked, 1,10-phenanthroline-containing nucleoside and its incorporation into DNA

A rigid nucleoside containing a phenanthroline ligand for metal-ion chelation was synthesized through condensation of 1,10-phenanthroline-5,6-dione with 5-amino-2′-deoxycytidine. During the condensation, a 5-6 ether linkage was formed between the sugar and the base. The hosphoramidite of the nucleoside was used to synthesize oligodeoxynucleotides by means of automated oligonucleotide synthesis, placing the phenanthroline nucleoside on the 5′-end of the oligomers. The free nucleoside is fluorescent; however, the fluorescence of the nucleoside was effectively quenched in both single- and double-stranded DNA. Thermal denaturation experiments on DNA duplexes ontaining the modified nucleoside showed similar base-pairing properties as T and Stronger stacking interactions with a flanking A·T base pair than with a G·C pair. CD spectra of helixes containing the modified nucleoside were characteristic of B-DNA. A model structure of a B-DNA helix, where the nucleoside was paired with A, showed only minor deviations from B-DNA parameters, except for a noticeable buckle of the modified base pair due to the constraints of the 5′-6 linkage. Due to the relative ease of the synthesis and minimal distortions of the helix structure, the phenanthroline nucleoside reported here shows promise for facile 5′-labeling of nucleic acids with metal complexes. This strategy can likely be extended to fusing other aromatic or aliphatic rings to a nucleotide base for incorporating the 5′-end of nucleic acid duplexes.

DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·CR1 where ψ and CR1 are base moieties 2′-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (C Br) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPIMe, having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson-Crick base pairs, such as T-A, C-G, A-ψ, and G-PPIMe, and TFOs containing T, C, CBr, and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.