The long-term goals of this project are the development of a new class of molecular reporters for biological systems, and their application to important biological and biomedical problems. The molecules under study are short DNA-like oligomers of fluorophores, in which fluorescent hydrocarbons and heterocycles are assembled on the natural deoxyribose-phosphate backbone, replacing DNA bases. These fluorescent glycoside oligomers, typically three or four monomers in length, are termed """"""""oligodeoxyfluorosides"""""""" (ODFs). This close interaction of potentially stacked pi- systems yields extensive electronic coupling and multiple forms of intramolecular energy transfer. As a result of this architecture, these molecules display a number of unusual and useful properties that are not available in commercial dyes. Among these properties are tunable excitation and emission, tunable Stokes shifts (leading to a wide range of emission colors with a single excitation wavelength), and the ability to act as color-changing sensors of molecular species. The DNA backbone makes these molecules water-soluble and makes it simple to conjugate them to nucleic acids, to affinity tags, and potentially to proteins. In addition, the modular synthesis makes it simple to create combinatorial libraries of ODFs on solid supports, and libraries of >14,000 members have been achieved. This property makes it possible to screen and discover new properties rapidly. In the initial funding period we succeeded in building more than sixteen new monomers for incorporation into ODFs, and characterized their photophysical properties. We assembled several new libraries, which were screened for a number of useful emission and sensing properties. A set of soluble blue, green, yellow and orange dyes, all excited by a single long-UV wavelength, was reported. We characterized a number of ODFs in which the emission spectrum was different than those of the components, establishing electronic coupling in these systems. We demonstrated highly efficient quenching (superquenching) of ODFs, which can lead to many useful applications. We showed that, like DNA, the emission of ODFs depends on sequence as much as on composition. Finally, we discovered sets of ODFs that act as fluorescence-changing sensors, including sensors of UV light exposure, and sensors of metal ions. In the near term covered by this proposal we have three main aims for both basic and applied development of ODF reporters: first, development of practical methods for biomedical applications, including methods for conjugation to proteins, and modulation of properties for intra- and extracellular applications;second, discovery of new excitation properties for multispectral biological application, and application to dynamic multicolor biological imaging;and third, large-scale development of molecular sensors for metal cations, and their application in solution and on microarrays. If successful, this work will lead to soluble organic reporters that can yield biological and biomedical information for systems where current fluorescent dyes are quite limited.

Public Health Relevance

We propose to develop and study a new class of oligomeric reporters and sensors for biologically relevant species, and to apply them to biomedically important problems. These oligomeric molecules resemble DNA, and include the natural sugar-phosphate backbone, but with all DNA bases replaced by fluorescent aromatic groups. Our molecular design leads to unusually rapid ways to make and discover molecules with new fluorescence properties, and the resulting molecules have several useful characteristics that are not available in commonly available fluorescent tags.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM067201-07
Application #
7827990
Study Section
Synthetic and Biological Chemistry A Study Section (SBCA)
Program Officer
Lewis, Catherine D
Project Start
2003-02-01
Project End
2012-04-30
Budget Start
2010-05-01
Budget End
2011-04-30
Support Year
7
Fiscal Year
2010
Total Cost
$287,168
Indirect Cost
Name
Stanford University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Kwon, Hyukin; Chan, Ke Min; Kool, Eric T (2017) DNA as an environmental sensor: detection and identification of pesticide contaminants in water with fluorescent nucleobases. Org Biomol Chem 15:1801-1809
Mohsen, Michael G; Kool, Eric T (2016) The Discovery of Rolling Circle Amplification and Rolling Circle Transcription. Acc Chem Res 49:2540-2550
Beharry, Andrew A; Lacoste, Sandrine; O'Connor, Timothy R et al. (2016) Fluorescence Monitoring of the Oxidative Repair of DNA Alkylation Damage by ALKBH3, a Prostate Cancer Marker. J Am Chem Soc 138:3647-50
Ji, Debin; Beharry, Andrew A; Ford, James M et al. (2016) A Chimeric ATP-Linked Nucleotide Enables Luminescence Signaling of Damage Surveillance by MTH1, a Cancer Target. J Am Chem Soc 138:9005-8
Roost, Caroline; Lynch, Stephen R; Batista, Pedro J et al. (2015) Structure and thermodynamics of N6-methyladenosine in RNA: a spring-loaded base modification. J Am Chem Soc 137:2107-15
Edwards, Sarah K; Ono, Toshikazu; Wang, Shenliang et al. (2015) In Vitro Fluorogenic Real-Time Assay of the Repair of Oxidative DNA Damage. Chembiochem 16:1637-46
Yuen, Lik Hang; Franzini, Raphael M; Tan, Samuel S et al. (2014) Large-scale detection of metals with a small set of fluorescent DNA-like chemosensors. J Am Chem Soc 136:14576-82
Kool, Eric T; Crisalli, Pete; Chan, Ke Min (2014) Fast alpha nucleophiles: structures that undergo rapid hydrazone/oxime formation at neutral pH. Org Lett 16:1454-7
Yuen, Lik Hang; Franzini, Raphael M; Wang, Shenliang et al. (2014) Pattern-based detection of toxic metals in surface water with DNA polyfluorophores. Angew Chem Int Ed Engl 53:5361-5
Crisalli, Pete; Kool, Eric T (2013) Importance of ortho proton donors in catalysis of hydrazone formation. Org Lett 15:1646-9

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