Photoinduced short-range electron transfer in DNA with fluorescent DNA bases: lessons from ethidium and thiazole orange as charge donors.

Charge transfer processes through the double helix of DNA cover a broad range of mechanistic models ranging from superexchange to hopping mechanisms. Over the last decade, these processes were studied by our group in a photoinduced fashion since (i) the starting time for the charge transfer is clearly defined by the absorption of the photon and (ii) photoexcitation delivers the necessary driving force to the DNA system. It is a prerequisite to modify oligonucleotides synthetically with suitable organic fluorophores that serve as photoinducable charge donors.

BODIPY-modified uridines as potential fluorescent probes for nucleic acids that are recognized by DNA-polymerases.

A new type of BODIPY-modified uridines that contain the fluorophore attached to the 5-position of uridine via a short phenylene bridge have been prepared and characterized by methods of the optical spectroscopy and electrochemistry. The spectroscopic and redox properties can be manipulated by substituent and ligand exchange. After synthetic incorporation into DNA via phosphoramidite chemistry the canonical base pairing is maintained due to the rigid phenylene bridge.

Nucleotide insertion and bypass synthesis of pyrene- and BODIPY-modified oligonucleotides by DNA polymerases.

The chromophores pyrene and bordipyrromethenylbenzene directly linked to the 5-position of uridine are tolerated and recognized as thymine derivatives by DNA polymerases in primer extension experiments.

Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer.

8-(Pyren-1-yl)-2'-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods.