Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue

Abstract

The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson–Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay.

Fluorescence Quenching in BODIPY Dyes: The Role of Intramolecular Interactions and Charge Transfer

“…Here we use the ADC(2) method which is closely related, and has a similar accuracy as CC2 . ADC(2) was recently applied to various organic molecules, typically providing the results consistent with experiments. The method can also be used for optimizing conical intersections, although it does not provide a correct dimensionality of the crossing seam (for S 1 /S 0 crossing) .…”

“…Conical intersections, i.e ., the crossings between the electronic states of the same multiplicity are of key importance to rationalize the fluorescence properties of many organic molecules (see for instance recent applications in Ref. ). In the illustrative vinyl‐BODIPY compound, the crossing between the lowest excited singlet state (S 1 ) and the ground state (S 0 ) lies energetically below the initial vertical excitation, the so‐called Franck‐Condon (FC) point, thus explaining the high nonradiative rates.…”

Development of Fluorescent Aptasensors Based on G-Quadruplex Quenching Ability for Ochratoxin A and Potassium Ions Detection

“…The prerequisite for the occurrence of fluorescence resonance energy transfer is that both the fluorescent donor and acceptor molecules can fluoresce [ 26 ]. However, the G-quadruplex absorbs approximately 260 nm and shows very low fluorescence quantum yields [ 27 ].…”

Mechanistic insights into excited state intramolecular proton transfer in isolated and metal chelated supramolecular chemosensors

“…In these cases, the excited state population may be trapped in a metastable CS state, which then decays to the ground state by an alternative route, by interacting with surrounding solvent molecules or, in extreme cases, by fluorescing. The fluorescence from such constrained systems can be exploited when designing effective supramolecular fluorescent probes 22,23,26 as we illustrate here. The class of (supra-)molecular sensors known to function via PCET is still rather small but, as shown in a recent review, 27 is growing fast.…”