Fluorescent DNA base replacements: reporters and sensors for biological systems

Abstract

We describe the design, synthesis, and properties of nucleoside monomers in which the DNA base is replaced by fluorescent hydrocarbons and heterocycles, and the assembly of these monomers into DNA-like molecules in which the all bases are fluorescent. As monomers, such molecules have useful applications as reporters in the DNA context. The use of fluorescent DNA bases, rather than more traditional fluorophores tethered to the DNA strand, gives a more predictable location and orientation, and yields a more direct response to changes that occur within the helix. In addition to uses as monomers, such compounds can be assembled into polychromophoric oligomers ("oligodeoxyfluorosides" or ODFs). ODFs are water soluble, discrete molecules and are easily arranged into specific sequences by use of a DNA synthesizer. They have displayed a number of properties not readily available in commercial fluorophores, including large Stokes shifts, tunable excitation and emission wavelengths, and sensing responses to physical changes or molecular species in solution. We describe an approach to assembling and screening large sets of oligofluorosides for rapid identification of molecules with desirable properties. Such compounds show promise for applications in biochemistry, biology, environmental and materials applications.

Differential Fluorescence Quenching of Fluorescent Nucleic Acid Base Analogues by Native Nucleic Acid Monophosphates

“…1,2 In the best cases, these fluorescent base analogues (FBAs) alter the native structure of helical DNA minimally, while allowing for selective optical excitation and detection. In many FBAs, the fluorescence quantum yield can be very sensitive to changes in base stacking, [3][4][5][6][7][8][9][10][11] making them uniquely suited to studying helical structure and dynamics.…”

8‐Vinyl‐2′‐deoxyguanosine as a Fluorescent 2′‐Deoxyguanosine Mimic for Investigating DNA Hybridization and Topology

“…[1] Typical approaches are fluorophore-base conjugates [2] in which common fluorophores are tethered to the nucleobases, or expanded nucleobases [3] or nucleotides bearing a fluorescent aromatic moiety instead of a natural nucleobase.…”

Controlling the Fluorescence of Benzofuran‐Modified Uracil Residues in Oligonucleotides by Triple‐Helix Formation

“…DNA and RNA were purchased from Sigma-Aldrich. Dry solvents were purchased and stored over molecular sieves (4 5-(Benzofuran-2-yl)-5'-O-(4,4'-dimethoxytrityl)deoxyuridine (4 a): 3 a (200 mg, 0.58 mmol) was coevaporated three times with pyridine and dissolved in pyridine (2.9 mL). 4, 4'-Dimethoxytrityl chloride (288 mg, 0.64 mmol) was added to the reaction mixture and stirred for 3 h at room temperature.…”