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Caged Oligonucleotides

Bio-Synthesis offer caged oligonucleotide synthesis and labeling. Photocaging has developed into an attractive and simple procedure for achieving exquisite control over complex biological processes through photoactivation by UV light. The term ‘caging’ refers to the attachment of a photolabile protecting group to a biologically active molecule at specific locations, effectively rendering the molecule inactive. After irradiation by light at the wavelength required to remove the protecting group, the biological properties of the ‘uncaged’ molecule are restored. Caged oligonucleotide has been used in PCR and polymerase activity1, antisense and gene silencing2, regulartion of restriction endonuclease activity3, and enzyme-free mutagenesis4 . Caged oligonucleotide also been used to activation and deactivation of DNAzyme and antisense activity controlling gene expression in mammalian cells5, and photochemical control of DNA decoy function to regulate gene transcription6. Contact Contact Bio-Synthesis for Fluorescent base modified oligonucleotides.

Bio-Synthesis caged modified bases can be incorporate at any position of an oligonucleotide . Every oligo synthesized is strictly controlled for quality by using either MALDI-TOF mass spectrometry or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform QC methods tailored to specific modifications, such as OD ratio measurement where appropriate.

Fluorescent Base Analogues Function 5' Prime Internal 3' Prime
NPOM-Caged-dT Uncaged at 365 nm Y Y Y
DEACM dG Photo cross-linker
Uncaged between 365 to 505 nm 		Y Y Y
Abberior Cage 500 Uncage at 360 — 440 nm, use as single-molecule photoswitching and also can act as a FRET donor Y Y Y
Abberior Cage 532 Uncaged at 360 — 440 nm, design for single-molecule photoswitching, useful for tracking experiments Y Y Y
Abberior Cage 552 Uncaged at 360−440 nm and readily transforms into the deeply red and highly fluorescent dye. It absorbs around 552 nm and emits around 575 nm. After uncaging it can be effectively used as a STED dye at ~660nm. Design for single-molecule photoswitching Y Y Y
Abberior Cage 590 Uncage at 360 — 440 nm, design for single-molecule photoswitching, useful for tracking experiments Y Y Y
Abberior Cage 635 Uncage at 360-440nm and releases a highly fluorescent dye far into the red. It can most effectively be excited from 620 to 645nm. Y Y Y

Quality Control: Analytical HPLC, Gel eletrophoresis, and  MALDI-TOF Mass Spectrometry

Delivery times: 5-7 Working days

Packaging:    Dried

Shipping conditions: Room temperature

Storage conditions: -20 oC to -70 oC

Oligonucleotides are stable in solution at 4 oC for up to 2 weeks. Properly reconstituted material stored at -20 oC should be stable for at least 6 months. Dried DNA (when kept at -20 oC) in a nuclease-free environment should be stable for years.

References:

  1. D.D. Young, W.F. Edwards, H. Lusic, M.O. Lively, and A. Deiters, Chem Commun, 2008, 462-4.
  2. D.D. Young, H. Lusic, M.O. Lively, J.A. Yoder, and A. Deiters, ChemBioChem, 2008, 9, 2937-40.
  3. D.D. Young, J.M. Govan, M.O. Lively, and A. Deiters, ChemBioChem, 2009, 10, 1612-6.
  4. D.D. Young, H. Lusic, M.O. Lively, and A. Deiters, Nucleic Acids Res, 2009, 37, e58.
  5. D.D. Young, M.O. Lively, and A. Deiters, J Am Chem Soc, 2010, 132, 6183-93.
  6. J.M. Govan, M.O. Lively, and A. Deiters, J Am Chem Soc, 2011, 133, 13176-82.

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