2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields. The nucleotide 2-aminopurine (2AP) has been used as a site-specific probe of nucleic acid structure and dynamics (1-11) because it base pairs with cytosine in a wobble configuration (4,5,12) or with thymine in a Watson-Crick geometry (7,11). Thermodynamic measurements of DNAs containing 2AP:C or 2AP:T show that the former pairing is more destabilizing (11,12). Incorporating 2AP into DNA quenches its fluorescence (2, 8, 11), reducing its quantum yield from that of the free nucleoside (0.65 in aqueous solution). This reduction is attributed to stacking interactions with nearest neighbor nucleobases, and, therefore, fluorescence properties of 2AP have been used to probe the equilibrium stacking properties of DNA duplexes containing these mismatched pairs (2,8,10). Although the fluorescence decay of 2AP in solution is single exponential, with a lifetime of Ϸ10 ns, in the context of a DNA molecule, four decay components, from 50 ps to 8 ns, are typically needed to describe its lifetime (2). The short decay time observed for 2AP in a duplex is attributed to the fully stacked state, whereas the longest lifetime comes from unstacked 2AP (2, 7). The distribution of stacked states can be altered by temperature, solvent, flanking bases, and bound protein, and so all of these conditions can be probed by using 2AP fluorescence. Dynamics of stacked bases adjacent to a mutagenic mismatch in DNA (such as 2AP:C and 2AP:T) may be part of the recognition mechanism by replication͞repair enzymes (3, 13), so interpretation of 2AP fluorescence data is critical for describing these environments.To understand the effect of base stacking on fluorescent properties of 2AP, we have used time-dependent density functional theory (TDDFT) (14, 15) to calculate the excited-state properties of 2AP alone and in stacked B-and A-form dinucleotides (dimers). Analysis of monomer calculations indicates the accuracy with which TDDFT describes spectral properties: excited-state transition energies, transition dipole directions, and oscillator strengths for 2AP, thymine, cytosine, adenine, and guanine (see figures) are in excellent agreement w...

A quantum mechanical theory of photoinduced electron transfer, based on the Redfield theory of relaxation, is developed and applied to the standard two state-one mode system interacting with a thermal bath. Quantum mechanical treatment of the reaction coordinate allows incorporation of both finite vibrational dephasing and energy flow rates into the description of electron transfer dynamics. The field-matter interaction is treated explicitly to properly incorporate the total energy and magnitude of the vibrational coherence present in the initially prepared state. Calculation of the reduced density matrix of the system is carried out in a vibronic basis that diagonalizes the electron exchange coupling so that the method is valid for arbitrarily large coupling strength. For weak electronic coupling, we demonstrate the equivalence between the results from Redfield theory and those obtained from the standard perturbative expression (golden rule) for nonadiabatic electron transfer. We then discuss quantitatively the breakdown of the Fermi golden rule with increasing electronic coupling strength. The failure of the golden rule is seen to result from either slow energy equilibration in the reactant or product well or from quantum interference effects resulting from finite dephasing rates. For cases where the reorganization energy is large compared to the frequency of reactive motion, such that we may ignore nuclear tunneling, results from the theory show good agreement with those from the semiclassical Landau-Zener theory when motion of the reaction coordinate through the surface crossing region can be considered to be ballistic. Finally results are shown in the weak damping (coherent) limit that demonstrate interference effects between phase coherences involving states in both wells.

2-Aminopurine (2AP) fluorescence intensity and decay lifetimes have been used as indicators of nucleic acid geometry and dynamics. To characterize 2AP photophysics in the context of a DNA strand, time-dependent density functional theory is applied to 2AP stacked with two flanking nucleobases. Calculations show that 2AP in the trimers suffers a reduction in the oscillator strength of its low-lying pi-pi* 2AP-like allowed transition, manifested in a reduction of its radiative rate. Trimers also exhibit two or three lower-energy excited states (charge transfer states) that are predicted to facilitate nonradiative transitions from the fluorescent excited state.

We present results from simulations of vibrational energy and phase relaxation and electronic curve crossing using a multilevel formulation of Redfield theory, which demonstrate the shortcomings of the optical Bloch approximation and the importance of coherence transfer processes in the relaxation dynamics of multilevel systems. Specifically, we show that for a harmonic well, energy relaxation can occur with retention of vibrational phase, and that for sufficiently strong electronic coupling, the product of an electronic curve crossing process can be formed vibrationally coherent even when no coherence is present in the initially excited state.

The structure and dynamics of DNA trimers are experimentally assessed using the fluorescent purine analogue 2-aminopurine (2AP), incorporating 2AP between purine and pyrimidine bases to form 5'dXp2APpY3' molecules. Circular dichroism and fluorescence quenching of the 2AP show that the bases are stacked; at the same time, fluorescence decay lifetimes are heterogeneous, indicative of conformational sampling. 2AP does not exhibit the long fluorescence decay time characteristic of the free nucleoside, suggesting that its motions in the trimers bring it into proximity of the neighboring bases, resulting in efficient charge transfer and average fluorescence lifetimes on the order of 1-2 ns.