The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. Quantum mechanical methods, such as configuration interaction singles (CIS) corrected with second-order perturbation theory (CIS(D)), are able to provide theoretical insight into electronic excitations and charge-transfer characters of the fluorescent probe after exposure to light. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similarly to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. Our results calculated at the CIS(D)/aug-cc-PVDZ level revealed that the nonradiative relaxation pathway of PC from the lowest p-p* state  is hindered by the high energy of the conical intersections relative to the minimum. Consequently, 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 complex. 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. However, the mechanism is not well known. To examine the origin of quenching, we studied the photophysical properties for complexes where PC is base-stacked with guanine at either the 3' or 5' terminus as it would be in B-form DNA, PC is hydrogen-bonded to guanine, and PC is stacked between two guanines. Our calculated values for the fluorescence rate constants, lifetimes, and wavelengths for all systems are consistent with the experimental results. Calculations also predicted charge-transfer states, which may contribute to the quenching mechanisms of the systems that are under investigation.

Fluorescent properties of DNA/RNA base analog pyrrolocytosine

247th National Meeting (2014)

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