DMT-2′-OME-dC(Bz)-CE-Phosphoramidite provides a protected 2′-O-methylcytidine building block for automated oligonucleotide synthesis and modified RNA research and specifically features a 5′-O-dimethoxytrityl (DMT) protecting group, N4-benzoyl (Bz) base protection, and a 3′-O-(2-cyanoethyl) phosphoramidite group. This reagent specifically supports site-specific incorporation of 2′-O-methylcytidine into synthetic oligonucleotides for studying nuclease resistance, hybridization, and RNA-based molecular interactions.
Key Features and Benefits
- 2′-O-Methyl Modification: Introduces a methyl group at the ribose 2′-oxygen to specifically support research on oligonucleotide stability, structural properties, and enzymatic resistance.
- 5′-DMT Protection: Provides acid-labile protection of the 5′-hydroxyl group specifically for controlled, stepwise oligonucleotide chain assembly.
- N4-Benzoyl Base Protection: Protects the cytosine exocyclic amino group during synthesis and is removed during appropriate post-synthesis deprotection.
- 2-Cyanoethyl Phosphoramidite: Enables coupling through established phosphoramidite chemistry for automated solid-phase oligonucleotide synthesis.
- Site-Specific Incorporation: Supports precise placement of modified cytidine residues within synthetic RNA and other compatible oligonucleotide sequences.
- Enhanced Nuclease Resistance: Enables investigation of how 2′-O-methyl modifications influence resistance to nuclease-mediated degradation.
- RNA Structural Studies: Supports research on sugar conformation, duplex stability, and hybridization behavior in modified oligonucleotides.
- Automated Synthesis Compatibility: Designed for use with suitable DNA/RNA synthesizers and validated phosphoramidite coupling protocols.
- Versatile Modification Chemistry: Provides a building block specifically for preparing modified RNA probes, antisense oligonucleotides, and other research oligonucleotides.
Applications
- Modified RNA Synthesis: Enables incorporation of 2′-O-methylcytidine into synthetic RNA sequences for biochemical and structural research.
- Antisense Oligonucleotide Research: Supports development of chemically modified antisense sequences for investigating hybridization and target recognition.
- siRNA Modification Studies: Enables evaluation of 2′-O-methylcytidine substitutions in synthetic small interfering RNA sequences.
- Nuclease Stability Studies: Supports comparative analysis of modified and unmodified oligonucleotide degradation under controlled experimental conditions.
- RNA Hybridization Research: Enables investigation of duplex formation, melting behavior, and sequence-dependent interactions.
- Oligonucleotide Probe Development: Supports synthesis of modified probes for nucleic acid detection, binding studies, and molecular assays.
- RNA Structure and Function Studies: Facilitates research on the effects of 2′-O-methyl substitutions on RNA conformation and molecular recognition.
- Solid-Phase Oligonucleotide Synthesis: Serves as a protected nucleotide building block for automated phosphoramidite-based synthesis workflows.
- Nucleic Acid Chemistry Research: Supports exploration of chemical modifications that influence oligonucleotide properties, stability, and biological interactions.
Storage and Handling
- Storage: Store at −20°C in a tightly sealed container under dry, inert conditions, unless otherwise specified. Protect from moisture, heat, and prolonged exposure to light. Allow the sealed container to reach room temperature before opening to minimize condensation.
- Handling: Prepare solutions using anhydrous acetonitrile or another validated solvent compatible with phosphoramidite synthesis. Minimize exposure to atmospheric moisture because phosphoramidite groups are susceptible to hydrolysis.
- Use appropriate activators and coupling conditions according to the oligonucleotide synthesizer protocol. Maintain anhydrous conditions throughout preparation and coupling. Apply validated deprotection procedures suitable for the N4-benzoyl group and other protecting groups present in the synthesized oligonucleotide.
- Confirm product identity and purity using appropriate analytical techniques before critical synthesis applications. Optimize coupling and deprotection conditions for the intended sequence and modification pattern.
DMT-2′-OME-dC(Bz)-CE-Phosphoramidite combines 2′-O-methyl sugar modification with established nucleotide protecting-group chemistry for controlled oligonucleotide synthesis and specifically supports modified RNA preparation, antisense research, siRNA modification studies, nucleic acid probe development, and investigations of oligonucleotide stability and hybridization.
AxisPharm offers 5000+ PEG Linkers with high purity. Different kinds of PEG Reagents may be available by custom synthesis.
