Comparison of Py^•+/dU^•- Charge Transfer State Dynamics in 5-(1-pyrenyl)-2‘-deoxyuridine Nucleoside Conjugates with Amido-, Ethylenyl-, and Ethynyl Linkers

Abstract

Femtosecond, picosecond, and nanosecond transient absorbance (TA) and picosecond emission kinetics results are presented for three 5-(1-pyrenyl)-2'-deoxyuridine nucleosides each with a different two-atom linker joining pyrenyl C-1 to uracil C-5. The linkers are respectively -NHCO-, -(CH(2))(2)-, and -C[triple bond]C- for PAdU, PEdU, and PYdU. For all three nucleoside conjugates, most conformers undergo intramolecular charge transfer (CT) from their pyrenyl (1)(pi,pi) excited states to form Py(*+)/dU(*-) CT products in ultrashort times: <or=0.6 ps for PAdU, <or=30 ps for PEdU, and <or=100 ps for PYdU (instrumentally limited times). Additionally for all three nucleosides, a small fraction of conformers also undergoes slower intramolecular CT from their pyrenyl (1)(pi,pi) states in times as long as tens of nanoseconds. Importantly, for use of these nucleosides in studies of excess electron transport in DNA, the lifetimes the CT products in MeOH lengthen significantly in the above series: 6.0 ps for PAdU, 560 ps for PEdU (the shortest of three TA lifetime components), and 1.06 ns for PYdU. The effects on pyrenyl-dU nucleoside CT state dynamics due to adding oxygen via both aeration and oxygen saturation are also examined for the PEdU nucleoside in MeOH.

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

“…pyrene and its derivatives incorporated into nucleic acids, display low quantum yields due to interactions with quenchers of fluorescence, e.g. solvent molecules and nucleobases 43 Representative target titration curve for duplex of ON5 and complementary DNA. Spectra were obtained in a medium salt phosphate buffer at 19°C using an excitation wavelength of 425 nm and 500 nM concentration of the probe a structure shielding the fluorophore from the quenchers (i.e.…”

Efficient synthesis of pyrene-1-carbothioamides and carboxamides. Tunable solid-state fluorescence of pyrene-1-carboxamides

“…12,[14][15][16] Moreover, these compounds were used in the synthesis of polymers with tunable luminescent properties 17 and in the labelling of nucleosides. 7,8,[18][19][20][21][22] In contrast to amides, pyrene-1-carbothioamides are only weakly uorescent 23,24 because of the internal quenching effect of the thiocarbonyl group. Since some chemical species desulfurize thioamides (e.g.…”

Highly Fluorescent Conjugated Pyrenes in Nucleic Acid Probes: (Phenylethynyl)pyrenecarbonyl‐Functionalized Locked Nucleic Acids

“…It is also worth noting that the fluorescence spectrum of single‐stranded ON4 is entirely redshifted by 19 nm with regard to ON4 :DNA/RNA. At the same time, the fluorescence quantum yields of ONs and duplexes with single incorporations of M 1 or M 2 are remarkably higher than typical quantum yields23 of pyrene on DNA (Table 3; data for ON1 , ON6 , and the corresponding duplexes). The high quantum yields measured for PEPyc–LNAs can be explained by the decreased lifetime of the excited state accompanied by the direction of the functionalities attached to 2′‐amino‐LNA by an amide linker to the minor groove of the nucleic acid helix, thus reducing the quenching of fluorescence 3.…”