1022-79-3

Usage

Uses

Used in Molecular Biology Research:
5-Bromo-2'-deoxycytidine is used as a research tool for studying DNA repair and replication mechanisms. Its incorporation into DNA during replication provides insights into the processes and can help identify potential therapeutic targets.
Used in Cancer Research:
5-Bromo-2'-deoxycytidine is used as a potential regulator of gene expression in cancer research. Its ability to inhibit DNA methyltransferases may offer new avenues for understanding and treating cancer, although its potential toxicity and mutagenicity must be carefully considered.
Used in Drug Development:
5-Bromo-2'-deoxycytidine is used as a starting point for the development of new drugs targeting DNA methylation and gene regulation. Its properties as an inhibitor of DNA methyltransferases make it a valuable compound for exploring the potential of epigenetic therapies in various diseases, including cancer.
Used in Diagnostic Applications:
5-Bromo-2'-deoxycytidine can be used as a diagnostic marker in molecular biology, helping to identify and track DNA methylation patterns that may be associated with specific diseases or conditions. This can aid in the development of personalized medicine approaches and improve disease management.
Used in Educational Settings:
5-Bromo-2'-deoxycytidine is used as an educational tool in molecular biology and genetics courses, providing students with hands-on experience in working with compounds that can affect DNA methylation and gene expression. This can help deepen their understanding of the molecular mechanisms underlying various biological processes.

Upstream product

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

Downstream Products

• 119411-85-7 5-bromo-2'-deoxy-5'-O-p-toluenesulfonylcytidine 
• 100360-44-9 4-N-benzoyl-5-bromo-5'-O-(4,4'-dimethoxytrityl)-deoxycytidine 
• 178925-43-4 4-N-benzoyl-5-bromo-5'-O-(4,4'-dimethoxytrityl)-deoxycytidine 3'-(2-cyanoethyl N,N-diisopropylphosphoramidite) 
• 148716-10-3 4-N-benzoyl-5-bromodeoxycytidine 
• 951-77-9 2'-Deoxycytidine 
• 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 academic research and scientific papers

Reaction of 2′-deoxycytidine with peroxynitrite in the presence of ammonium bromide

Peroxynitrite, a reactive nitrogen species generated from nitric oxide and superoxide anion radical, is an endogenous potential risk factor for human cancer. When 2′-deoxycytidine was incubated with peroxynitrite at neutral pH and 37 °C, the reaction was greatly enhanced by the addition of ammonium bromide. Both ammonium ion and bromide ion were required to exert the enhancing effect. In addition to ammonium ion, methylamine and dimethylamine exerted the enhancing effect in the presence of bromide ion. Two major products were identified as 5-hydroxy-2′-deoxycytidine and 5-bromo-2′-deoxycytidine. Hypochlorite solution and bromine water reacted with 2′-deoxycytidine generating 5-hydroxy-2′-deoxycytidine and 5-bromo-2′-deoxycytidine in the presence of ammonium bromide with the yields similar to those of the reaction of peroxynitrite with ammonium bromide. Fenton reaction of 2′-deoxycytidine was suppressed by the addition of ammonium bromide. Nitrogen dioxide gas did not react with 2′-deoxycytidine in the presence or the absence of ammonium bromide. These results suggest that in the presence of ammonium ion or amines, bromide ion interacts with peroxynitrous acid, which is a protonated form of peroxynitrite, but not with hydroxyl radical or nitrogen dioxide generated by homolysis of peroxynitrous acid, to form hypobromous acid. In the presence of ammonium ion or amines, bromide ion may play a role in enhancing the genotoxic effects of peroxynitrite in humans.

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.

An efficient and facile methodology for bromination of pyrimidine and purine nucleosides with sodium monobromoisocyanurate (SMBI)

An efficient and facile strategy has been developed for bromination of nucleosides using sodium monobromoisocyanurate (SMBI). Our methodology demonstrates bromination at the C-5 position of pyrimidine nucleosides and the C-8 position of purine nucleosides. Unprotected and also several protected nucleosides were brominated in moderate to high yields following this procedure.

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.

Highly efficient method for C-5 halogenation of pyrimidine-based nucleosides in ionic liquids

A novel, highly efficient, convenient, and benign methodology for C-5 halogenation of pyrimidine-based nucleosides has been developed using N-halosuccinimides as halogenating reagents without using any catalyst in ionic liquid medium. The ionic liquids were successfully recovered and reused for all the reactions. Georg Thieme Verlag Stuttgart.

Synthesis and binding property of an oligonucleotide containing tetrafluorophenoxazine

A tricyclic pyrimidine nucleoside analog, termed tetrafluorophenoxazine, has been synthesized and incorporated into an oligonucleotide. Tm analyses demonstrate that this analog is capable of enhanced recognition of both a complementary adenine and guanine within a DNA helix.

Measurement of oxidative damage at pyrimidine bases in γ-irradiated DNA

Oxidized nucleobases represent one of the main classes of damage induced in DNA by ionizing radiation. Emphasis was placed in this work on the measurement of four oxidized pyrimidine bases, including 5- (hydroxymethyl)uracil (5-HMUra), 5-formyluracil (5-ForUra), 5-hydroxy- cytosine (5-OHCyt), and 5-hydroxyuracil (5-OHUra), in isolated DNA upon exposure to γ radiation in aerated aqueous solution. For this purpose, both high performance liquid chromatography associated with electrochemical detection (HPLC-EC) and gas chromatography coupled to mass spectrometry (GC- MS) were used. Conditions of hydrolysis of the N-glycosidic bond were carefully checked in order to achieve a quantitative release of the lesions. We showed that 60% formic acid treatment leads to the decomposition of the four lesions studied. On the other hand, hydrolysis based on the use of either 88% formic acid or 70% hydrogen fluoride in pyridine (HF/Pyr) allowed the quantitative release of the modified bases, with the exception of 5- HMUra when the latter reagent was utilized. A dose course study of the radiation-induced formation of 5-HMUra and 5-ForUra in DNA by using the GC- MS assay showed that the latter lesion was produced in a 2.1-fold higher yield than the former one. HF/Pyr and 88% formic acid hydrolysis provided similar results for 5-ForUra, indicating the reliability of both techniques for the measurement of this lesion. For 5-OHUra and 5-OHCyt, the level of modification determined by GC-MS analysis was higher after 88% formic acid treatment than upon HF/Pyr hydrolysis. When DNA was enzymatically digested and analyzed by HPLC-EC for 5-OHdCyd and 5-OHdUrd, the results were very close to those obtained by GC-MS following HF/Pyr treatment. It was concluded that additional amounts of both 5-OHUra and 5-OHCyt are produced during the 88% formic acid treatment from radiation-induced 5,6-saturated pyrimidine precursors. It is likely that cytosine and uracil diols are involved in this reaction. The radiochemical yields of formation (in μmol · J-1) for the products studied are in the following decreasing order: 5-ForUra (0.0083) > 5-OHCyt (0.0046) > 5-HMUra (0.0039) > 5-OHUra (0.0035).