5′-DMT-5-Fluoro-2′-deoxyuridine Phosphoramidite provides a fluorinated nucleoside building block for modified DNA synthesis and nucleic acid research and specifically combines a 5-fluoro substitution on the uracil base with a 2′-deoxyribose sugar, a 5′-O-dimethoxytrityl (DMT) protecting group, and phosphoramidite functionality for solid-phase oligonucleotide synthesis. This reagent supports site-specific incorporation of 5-fluoro-2′-deoxyuridine into synthetic DNA specifically for investigating nucleic acid structure, hybridization, and molecular recognition.
Key Features and Benefits
- 5-Fluoro Modification: Introduces a fluorine atom at the 5-position of the uracil base specifically for investigating the effects of halogen substitution on nucleic acid properties.
- 2′-Deoxyuridine Structure: Provides a deoxyribonucleoside framework compatible with modified DNA synthesis and nucleotide analog research.
- 5′-DMT Protection: Protects the 5′-hydroxyl group during stepwise oligonucleotide assembly and specifically supports controlled acid-mediated detritylation.
- Phosphoramidite Functionality: Enables incorporation into synthetic oligonucleotides specifically through established phosphoramidite coupling chemistry.
- Site-Specific Fluorination: Supports precise placement of fluorinated uracil residues within synthetic DNA sequences.
- Modified Base Recognition: Enables investigation of how fluorine substitution influences base pairing, molecular recognition, and interactions with nucleic acid-binding proteins.
- DNA Duplex Research: Supports studies of hybridization behavior, duplex stability, and sequence-dependent structural properties.
- Automated Synthesis Compatibility: Supports incorporation using compatible solid-phase DNA synthesizers and optimized phosphoramidite coupling protocols.
- Versatile Nucleotide Analog: Provides a specialized building block for modified DNA probes, biochemical assays, and nucleic acid structure-function investigations.
Applications
- Modified DNA Synthesis: Enables incorporation of 5-fluoro-2′-deoxyuridine residues into synthetic DNA oligonucleotides for biochemical research.
- Fluorinated Oligonucleotide Development: Supports preparation of DNA sequences containing site-specific fluorinated nucleobases.
- DNA Hybridization Studies: Enables evaluation of how 5-fluoro substitution influences complementary strand recognition and duplex formation.
- Nucleic Acid Structure Research: Supports investigation of modified DNA conformation, base stacking, and sequence-dependent structural behavior.
- DNA-Protein Interaction Studies: Enables exploration of how fluorinated nucleobases affect interactions with DNA-binding proteins and enzymes.
- Oligonucleotide Probe Development: Supports synthesis of modified DNA probes for molecular recognition and nucleic acid detection research.
- Nucleotide Analog Research: Facilitates investigation of fluorinated pyrimidine nucleosides and their incorporation into synthetic nucleic acids.
- DNA Stability Studies: Enables comparative analysis of modified and unmodified oligonucleotides under controlled experimental conditions.
- Solid-Phase Oligonucleotide Synthesis: Serves as a specialized nucleotide building block for automated phosphoramidite-based DNA synthesis.
Storage and Handling
- Storage: Store at −20°C in a tightly sealed container under dry, inert conditions, unless otherwise specified. Protect from moisture, excessive 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 synthesis protocol. Maintain anhydrous conditions during reagent preparation and automated synthesis to support coupling efficiency.
- Apply validated cleavage and deprotection procedures compatible with the 5-fluoro-2′-deoxyuridine modification and other protecting groups present in the synthesized oligonucleotide. Avoid unnecessarily harsh conditions that could compromise the integrity of modified nucleic acids.
- Confirm successful incorporation and product purity using appropriate analytical methods, such as HPLC and mass spectrometry.
5′-DMT-5-Fluoro-2′-deoxyuridine Phosphoramidite combines fluorinated pyrimidine chemistry with protected nucleoside functionality for modified DNA synthesis and specifically supports fluorinated oligonucleotide development, DNA hybridization studies, nucleic acid structure research, DNA-protein interaction studies, and molecular probe preparation.
AxisPharm offers 5000+ PEG Linkers with high purity. Different kinds of PEG Reagents may be available by custom synthesis.
