Ultrafast IR spectroscopy of the short-lived transients formed by UV excitation of cytosine derivatives

Abstract

A strong infrared band at 1574 cm 21 is observed following 267 nm excitation of 29-deoxycytidine (t = 37 ¡ 4 ps) or 29-deoxycytidine 59-monophosphate (t = 33 ¡ 4 ps); this band is provisionally attributed to an 1 n N p* state and is absent for cytosine.The nature of the electronic excited states of DNA continues to be a focus of significant interest because of their role in UV-light induced modifications that could potentially be mutagenic. 1 The nucleobases fluoresce extremely weakly and this has led to the conclusion that their excited states must be very short-lived. 2 This is supported by femtosecond transient visible absorption 3 and fluorescence upconversion 4 measurements that reveal that the bases and mononucleotides possess sub-picosecond excited state lifetimes. However, the reasons for the short lifetimes are still a matter of debate, with theoretical studies emphasising the importance of ultrafast non-radiative processes. 5 IR methods, including 2D-IR, are proving an increasingly valuable tool for the study of DNA systems. 6,7 Time-resolved IR (TRIR) absorption spectroscopy 8 can provide structural as well as kinetic information on the ultrafast processes in DNA and our first paper in this area allowed the observation of the vibrationally excited ground states formed from nucleotides excited at 267 nm. 9 Subsequently the method has been used to identify the products of the photoionisation of GMP after excitation at 200 nm 10 and very recently the formation of thymine dimers. 11 In this paper we probe the transient species formed from 29-deoxycytidine 59-monophosphate (dCMP), 29-deoxycytidine (dCyd) and cytosine (Cyt) using vibrational spectroscopy. The presence of a new short-lived species is shown for both dCyd and dCMP but not for the nucleobase Cyt. Fig. 1 shows the transient IR difference spectra recorded between 2 ps and 1000 ps after 267 nm (150 fs) excitation of the mononucleotide dCyd in neutral (buffered pH 6.9) solution. (Identical spectra were also recorded at pH 8.5). The spectrum shows areas corresponding to ground state depletion (bands at 1505, 1524, 1617 and 1652 cm 21 as found in the FTIR) and ones where the transient absorbs more strongly. Similar behaviour is observed for dCMP (see ESI).The transient decay (and the ground state recovery) is essentially complete over the 1000 ps time scale of the experiment. However, in contrast to the results for other nucleotides such as dAMP and dGMP, 9 the kinetics are distinctly biphasic (see Fig. 2). At short times (2-8 ps -shown in red in Fig. 1) the transient absorption bands are observed to shift to higher wavenumber, behaviour which is consistent with relaxation of vibrationally excited ground states, as previously proposed. 9 The time constant for this is determined to be 2.6 ¡ 0.3 ps for dCyd.After this cooling process is complete a strong transient absorption at 1574 cm 21 persists. This band is the only one observable in the IR absorption spectrum in the region 1450-1750 cm 21 (assuming that there is no accidental overlap of other band...

A study of the pH dependence of electronically excited guanosine compounds by picosecond time-resolved infrared spectroscopy

“…1, 3 However, it is known that very simple modifications of nucleic acids, such as chemical substitution or the presence of a ribose group or protonation, may significantly change the excited state lifetimes. 17 In this light the protonation of 5¢-GMP to form 5¢-GMPH + (2) (pK a = 2.3) is known to have a dramatic effect on the lifetime of the electronic excited state. The protonated form is significantly more fluorescent than the neutral base.…”

A Comparative Picosecond Transient Infrared Study of 1-Methylcytosine and 5′-dCMP That Sheds Further Light on the Excited States of Cytosine Derivatives

“…This is in good agreement with that measured for the parent nucleobase cytosine, which undergoes rapid single exponential decay with a lifetime of 4.4  0.4 ps. 5 The similarity in kinetics between cytosine and 1-mCyt leads us to assign the observed TRIR activity to rapid crossing from the electronic excited potential energy surface (PES) to the ground-state PES (via internal conversion from the 1 ππ* state) creating vibrationally hot ground state molecules, formed with up to 34,000 cm -1 excess energy. Turning our attention to 5'-dCMP, we see that the TRIR spectra ( Figure 2a) are clearly different from that of 1-mCyt.…”

“…;Evidence of the non-emissive decay route for electronically excited cytosine derivatives has been obtained from both transient UV/vis 4 and time-resolved infrared (dCyd and 5'-dCMP) spectroscopies. 5 The relatively long-lived (34-37 ps) species has been assigned as a 1 nπ* state and is formed in moderate yields. 4 In our TRIR study a strong transient absorption band centred at 1574 cm -1 was observed.…”

Picosecond infrared probing of the vibrational spectra of transients formed upon UV excitation of stacked G-tetrad structures

“…4 To fully understand the nature of the molecular specific interactions, it is essential to employ techniques that can interrogate the structural modifications underpinning these processes, and here we apply ultrafast time-resolved infrared spectroscopy (TRIR) for this purpose. ps-TRIR is now being demonstrated as a powerful technique for probing the photophysical properties of DNA, [5][6][7][8] and its strength stems from its ability to yield kinetic and structural information that goes beyond that obtainable from fluorescence or transient UV/visible absorption techniques.In this communication, we describe how ps-TRIR can be employed to investigate conformationally dependent photophysical properties of base-base interactions. Guanine is known to aggregate to form stacked species at high concentrations.…”