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Fluorescent Base Modified Oligonucleotides

The large selection of fluorescent probes has revolutioninzed many studies of biochemical reactions and interactions. Although, the usage of conventional fluorecent probes tagging methods are widely applied in many area of research, they have limited usefulness for the study of base-pairing interaction, or subtle changes in DNA structure, binding and composition. Conventional strategies for preparing fluorescent probes are often large in size and structurally dissimilar to purine and pyrimidines, they must be attached through the use a linker arm at some distance from the site of the interest on the DNA. Although this design permits them to be used without perturbing the detecting system, study shown it removes them from the ability to detect subtle interaction changes which are often the goal of such studies.

Fluorescent nucleoside analogue probse resembles the natural bases and exhibit dramatic fluorescent changes when base-stacking or base pairing interactions occurs1-4 . These probes has been used in integrase assay to study endonucleolytic cleavage activity of a protein from HIV-11. It also use as bulge hybridization probes to measure the porducts of polymerase chain reactions (PCR) without the need for separation techniques (Hawkins et al.,)

Bio-Synthesis provides DNA fluorescent probes using modified fluorescent base analogues. Those bases can be incorporate into an oligonucleotide through a deoxyribose linkage during chemical synthesis and allow site-selective insertion.

Contact Bio-Synthesis for Probing DNA Structures with Fluorescent Nucleosides.

All oligonucleotide synthesized at Bio-Synthesis is quality check by using either MALDI-TOF mass spectrometry, analytical HPLC,or polyacrylamide gel electrophoresis (PAGE) analysis. Final yields are determined using UV absorbance at OD260 In addition, we perform custom formulation and quality control tailored to meet your specific requirements.

Fluorescent Bases Analogues Modification Code 5' Prime Internal 3' Prime
Pyrrolo-2'-deoxycytidine Pyrrolo dC Y Y Y
Pyrrolo-C Pyrollo C Y Y Y
Fluorescent dC Analogus dF Y Y Y
Zebularine Zeb Y Y Y
8-Vinyl-dA 8vdA Y Y Y
8-Oxo-G Clamp 8-oxo-dG Clamp Y Y Y
AP-dC G Clamp Y Y Y
Etheno-2'-deoxyadenosine Ethno-dA Y Y Y
5-(1-Pyrenylethynyl)-2'-deoxyuridine Pyrene-dU Y Y Y
5-(3-Perylenylethynyl)-2'-deoxyurindine Perylene-dU Y Y Y
1,3-diaza-2-oxophenothiazine tC Y Y Y
1,3-diaza-2-oxophenoxazine tCo Y Y Y
7-nitro-1,3-diaza-2-oxophenothiazine tCnitro Y Y Y
2-aminopurine 2-Amino-A 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 :
  • Hawkins, M. E., Pfleiderer, W., Mazumder, A., Pommier, Y. G., and Balis, F. M. Nucleic Acids Res. 23 , 2872–2880, 1995.
  • Hochstrasser, R. A., Carver, T. E., Sowers, L. C. and Millar, D. P. Biochemistry, 33 , 11971–11979, 1994.
  • Raney, K. D., Sowers, L. C., Millar, D. P., and Benkovic, S. J. Proc. Natl. Acad. Sci. USA 91, 6644–6648, 1994.
  • Nordlund, T. M., Wu, P., Andersson, S., Nilsson, L., Rigler, R., Graslund, A., McLaughlin, L. W., and Gildea, B. SPIE Time- Resolved Laser Spectrosc. Biochem. II 1204 , 344–353, 1990.

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