| Pyrene-dU-CE Phosphoramidite |
Catalog Number: 10-1590-xx
Description: Pyrene-dU-CE Phosphoramidite
5'-Dimethoxytrityl-5-(pyren-1-yl-ethynyl)-2'-deoxyUridine,
3'-[(2-cyanoethyl)-(N,N-diisopropyl)]-phosphoramidite |
| Formula: C57H55N4O8P |
M.W.: 955.04 |
F.W.: 514.42 |
Diluent: Anhydrous Acetonitrile/Dichloromethane 1:1 (v/v) |
| Coupling: 6 minute coupling time recommended. |
| Deprotection: No changes needed from standard method recommended by synthesizer manufacturer. |
| Storage: Freezer storage, -10 to -30°C, dry |
| Stability in Solution: 1-2days |
FLUORESCENT NUCLEOSIDES
Etheno-dA is a fluorescent nucleoside which is especially useful in observing the transition between DNA structural types. It is quite base labile and should be deprotected with ammonium hydroxide at room temperature for 24 hours. Alternatively, UltraMild chemistry can be used. 2-Aminopurine and AP-dC (G-Clamp) are also useful fluorescent nucleosides.
Pyrrolo-dC is a fluorescent deoxycytidine analog that is an ideal probe of DNA structure and dynamics. It base-pairs as a normal dC nucleotide. An oligo fully substituted with pyrrolo-dC has the same ™ as the control dC oligo with the same specificity for dG. Its small size does not perturb the structure of the DNA helix and it is well tolerated by a number of DNA and RNA polymerases. It is highly fluorescent and its excitation and emission are well to the red of most fluorescent nucleotide analogs, which eliminates or reduces background fluorescence from proteins. Pyrrolo-dCTP has potential uses in biological assay development.
When a benzylcarbamoyl analogue of AP-dC (G-Clamp) was synthesized, it was found that, when incorporated into an oligo, it exhibited similar fluorescence to AP-dC. However, when base-paired against the 8-oxo-dG, its fluorescence was severely quenched. Rather remarkably, however, when base paired with dG or any of the other bases, A, C or T, there was no change in fluorescence – making it a specific probe for 8-oxo-dG.
By attaching pyrene or perylene to the 5 position of deoxyuridine through a triple bond, the fluorophore is electronically coupled to the deoxyuridine base. This electronic coupling of the base and the fluorophore makes the fluorescence sensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.
The base analogue tCnitro is a FRET-acceptor together with tCO (or tC) as the donor molecule. This constitutes the first ever description of a nucleobase FRET-pair. This novel FRET-pair provides a unique tool for investigations of nucleic acid containing systems. tCnitro is virtually non-fluorescent under normal conditions.
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