160107-15-3

Basic information

• Product Name: N4-Benzoyl-5-methylcytidine
• Synonyms: N4-Benzoyl-5-methylcytidine
• CAS NO: 160107-15-3
• Molecular Formula: C₁₇H₁₉N₃O₆
• Molecular Weight: 361.34926
• Mol File: 160107-15-3.mol

Chemical Properties

• Appearance: /
• Density: 1.55±0.1 g/cm3(Predicted)
• PKA: 8.63±0.40(Predicted)
• CAS DataBase Reference: N4-Benzoyl-5-methylcytidine(CAS DataBase Reference)
• NIST Chemistry Reference: N4-Benzoyl-5-methylcytidine(160107-15-3)
• EPA Substance Registry System: N4-Benzoyl-5-methylcytidine(160107-15-3)

Safety Data

• Hazardous Substances Data: 160107-15-3(Hazardous Substances Data)

Upstream product

• 98-88-4 benzoyl chloride 
• 2140-61-6 5-methylcytidine 
• 93-97-0 benzoic acid anhydride 
• 554-01-8 5-methylcytosin 
• 32865-88-6 2'-O,N⁴-bis-trimethylsilyl-5-methylcytosine 
• 59237-68-2 2',3',5'-tri-O-benzoyl-5-methylcytidine 

Downstream Products

• 160107-17-5 N-(1-{(2R,3R,4S,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3,4-dihydroxy-tetrahydro-furan-2-yl}-5-methyl-2-oxo-1,2-dihydro-pyrimidin-4-yl)-benzamide 
• 160107-13-1 N-{1-[(2R,3R,4R,5R)-5-[Bis-(4-methoxy-phenyl)-phenyl-methoxymethyl]-3-(tert-butyl-dimethyl-silanyloxy)-4-hydroxy-tetrahydro-furan-2-yl]-5-methyl-2-oxo-1,2-dihydro-pyrimidin-4-yl}-benzamide 

Relevant articles and documents

Oligonucleotides comprising a modified or non-natural nucleobase

One aspect of the present invention relates to a double-stranded oligonucleotide comprising at least one non-natural nucleobase. In certain embodiments, the non-natural nucleobase is difluorotolyl, nitroindolyl, nitropyrrolyl, or nitroimidazolyl. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, only one of the two oligonucleotide strands comprising the double-stranded oligonucleotide contains a non-natural nucleobase. In certain embodiments, both of the oligonucleotide strands comprising the double-stranded oligonucleotide independently contain a non-natural nucleobase. In certain embodiments, the oligonucleotide strands comprise at least one modified sugar moiety. Another aspect of the present invention relates to a single-stranded oligonucleotide comprising at least one non-natural nucleobase. In a preferred embodiment, the non-natural nucleobase is difluorotolyl. In certain embodiments, the ribose sugar moiety that occurs naturally in nucleosides is replaced with a hexose sugar, polycyclic heteroalkyl ring, or cyclohexenyl group. In certain embodiments, at least one phosphate linkage in the oligonucleotide has been replaced with a phosphorothioate linkage.

Recognition of RNA by tripler formation: Divergent effects of pyrimidine C-5 methylation

In DNA triple helices, methylation at C-5 of thymine or cytosine is reported to have similar stabilizing effects for both bases. Here we show, however, that methylation of the same positions in RNA triplexes has distinctly different effects than in DNA. We have previously described the use of circular triplex-forming RNA oligonucleotides to recognize RNA sequences. Here it is shown that addition of C-5 methyl groups to uracils in these compounds very significantly increases not only affinity but also sequence selectivity in binding a purine-rich RNA target, as measured by thermal denaturation with various target RNAs. Surprisingly, however, addition of C-5 methyl groups to cytosines actually decreases affinity in binding RNA, while the same substitution in DNB is thermally stabilizing. Possible sources of this divergent behavior are discussed. A synthesis of 5-methylcytidine ribonucleoside 2'-O-silyl-3'-O-phosphoramidite is also described.