Ultrafast excited-state dynamics of RNA and DNA C tracts

Abstract

The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC) 18 were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC) 18 at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common basestacked structure, which may be identical with that of i-motif DNA.

Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

“…Notably, long-lived excited states are still observed at low pH in poly(A) [27] and poly(dC) [81], conditions under which the polymers adopt higher-order structures which retain base stacking. This suggests that it is not protonation of the nucleobases per se that quenches long-lived excited states, but rather the loss of base stacking.…”

“…3. Excited-state dynamics in novel DNA structures such as these will not be discussed here, but can be read about elsewhere [81][82][83][84][85][86]. Knowledge of the many ways that DNA can self-assemble into higher-order structures is clearly needed to interpret spectroscopic experiments correctly, which putatively investigate 'standard' single and double strands.…”

“…Non-WC base pairing motifs are also important, particularly in RNA. Two non-WC motifs, important in model systems which have been the subject of photophysical investigations [81][82][83][84][85][86], are shown in Fig. 3.…”

Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state

“…This species was assigned to an excimer on the basis that it was unlikely that the transient band at 570 nm could be due to a 1 nπ* state. 9 The role of excimers was challenged by recent transient fluorescence experiments by 60 Schwalb and Temps who found the lifetimes for ss-dC 20 were similar to those of the monomer with no emissive species observed at longer times. However, transient fluorescence measurements convey a fraction of the story as they are blind to long-lived dark states such as 1 nπ* states.…”

“…Long-lived species observed in polynucleotides are typically attributed to either an 50 excimeric or charge-transfer (CT) state. 8,9 However, in the case of polymeric dC systems, ultrafast studies have yielded differing interpretations of the excited states. Early studies by Plessow et al interpreted ps-fluorescence data as showing evidence for an excimer in dCpdC and dC 15 .…”