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Fluorescent labels with tunable properties - New Fluorescent Deoxyribosides and their Incorporation into Combinatorial Fluorophore Arrays


Stanford Reference:

01-226


Abstract


This invention consists of combinatorial arrays of fluorophores (CFAs) built on a repeating oligomeric (e.g.,DNA) backbone. With the DNA backbone, the invention starts with a number of synthesized new fluorescent monomer molecules in which the fluorescent part replaces a DNA base (termed "fluorosides"). By assembling oligomers in various combinations, hundreds or thousands of different fluorescent assemblies can be created from a small number of monomers that make them up. Thus one can generate many tunable fluorescence properties (emission wavelength, emission intensity, Stokes shift) by assembling molecules from a small library of individual molecules off the shelf.




Advantages of a DNA backbone over other organic backbones


  • The DNA backbone is highly water soluble, offering great utility in aqueous buffers.

  • It is easily and rapidly constructed in automated fashion on commercial synthesizers.

  • DNA bases are arranged so as to be stacked directly on one another; thus, fluorophores that replace the bases will be in intimate contact with one another, offering optimum chances for energy transfer.

  • The application to labeling of DNA and RNA is direct, since the synthesizer is already being used for the construction of the label.

  • Conjugation to peptides, antibodies, small molecules should be simple using commercial reagents.

Completion of a successful prototype combinatorial library

The Kool lab recently completed the synthesis of a high-yield library consisting of 256 different tetrafluors on polymer beads (J. Am. Chem. Soc. 2002,124:11590-1). There were four individual fluorosides (D,Y,E,Q) used in all possible combinations in strings four units long. The tetrafluors were examined on the beads under a fluorescence microscope. Remarkably, approximately 50-100 different hues and intensities were visible by the naked eye, giving a very wide range of outcomes, and yet only four dyes make up this set. Several examples of polyfluors were selected and re-synthesized on preparative scale, and useful properties were observed. For example, a set of multiply-colored dyes with a single wavelength of excitation was found. In addition, dyes with exceptionally long Stokes shifts were found.

AVAILABLE RIGHTS: co-exclusive research use

Applications


  • Creation of hundreds or thousands of fluorescent molecules from a small number of monomers, allowing generation of many selectable types of fluorescence properties.
  • Fluorescent labels with tunable properties (desired excitation, emission, brightness).
  • Creation of sets of different-color labels with a single excitation.
  • Most currently available applications that employ standard labels.
  • Obtaining information about distance and geometry in biomolecular systems using interactions between fluorophores (e.g., FRET).
  • Use of energy transfer between two fluorophores in sequencing DNA and other genomics methods.

Advantages


  • A single excitation can yield widely varied emission wavelengths, simplifying instrumentation needed to use fluorescence in diagnostics applications and experiments. Similar to quantum dots in this respect, but much simpler to conjugate.
  • Multiple energy transfer leading to very large Stokes shifts (avoiding background interference in fluorescence).
  • Very high localized fluorescence intensity resulting from very high total molar absorptivities.
  • Choice of using various types of modified backbones for aqueous or organic solubility.
  • Replacement of more traditional reporting methods such as radioactivity because of greater safety and greater utility.

Publications



Kool Lab Web Pages


Eric Kool's Stanford Faculty Page. Home Page of the Kool laboratory.

Innovators & Portfolio



Patent Status



Date Released

 7/12/2012
 

Licensing Contact


Chu Chang, Licensing Associate
650-723-0652 (Direct)
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biological and chemical sensors   research tool: DNA/RNA sequencing   fluorescence   dye   fluorescent agent   fluorogenic molecules   Fluorophores   nucleic acid labeling   research tool: reagent   research tool   cell sorter   cell sorting   FACS (Fluorescent Activated Cell Sorting)   flow cytometry   fluorescence imaging   fluorescence microscopy   fluorescence sensor   fluorescent proteins   fluorochemicals   Immunofluorescence Microscopy   
 

   

  

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S01-226 Fluorescent labels with tunable properties - New Fluorescent Deoxyribosides and their Incorporation into Combinatorial Fluorophore Arrays