J. Phys. Chem. B 2003, 107, 9165-9169
9165
Inter and Intrastrand Vibrational Coupling in DNA Studied with Heterodyned 2D-IR Spectroscopy Amber T. Krummel, Prabuddha Mukherjee, and Martin T. Zanni* Department of Chemistry, UniVersity of WisconsinsMadison, Madison, Wisconsin 53706-1396 ReceiVed: May 27, 2003; In Final Form: July 7, 2003
Heterodyned 2D-IR, frequency resolved photon echo, and pump-probe spectroscopies were collected to study the couplings and anharmonicities of cytidine and guanosine bases in DNA. Cytidine and guanosine anharmonicities were measured to be 9 and 14 cm-1, respectively. Strong cross-peaks were observed between the guanosine (G) and cytosine (C) carbonyl stretches in the 2D-IR spectra of the self-complementary oligonucleotide dG5C5 (5′-GGGGGCCCCC-3′). The spectra are interpreted in terms of inter- and intrastrand couplings between the carbonyl modes, and an excitonic Hamiltonian, based on transition dipole coupling, was used to fit the 2D-IR spectra. The accuracy of this model is discussed in light of observed couplings to the ring modes.
New multidimensional laser spectroscopies are beginning to be developed that are capable of measuring the anharmonic terms in the potential energy surface not readily accessible to linear spectroscopies.1-11 These terms are the result of mechanical and electrostatic couplings between the normal modes of the molecule, and are thus sensitive to the molecular structure. In the case where the anharmonicities are dominated by mechanical coupling mechanisms, deducing the molecular structure from the frequencies and anharmonicities is difficult, because the potential is a complicated function of nuclear coordinates.12 However, in the case where electrostatic coupling dominates, it is more likely that the higher order terms can be described by a simple model, such as a transition dipole or transition charge model.13 In this Letter, we report the first application of 2D-IR spectroscopy to DNA and present a preliminary interpretation of the spectra with regard to mechanical and electrostatic coupling mechanisms. The infrared spectra of DNA oligomers in the region of the base carbonyl stretches are known to be sensitive to the 3D structure of DNA.14 Each of the four bases of DNA has a unique vibrational frequency that shifts upon duplex formation.15 For example, in poly(dG)‚poly(dC), the guanosine (G) and cytidine (C) carbonyl frequencies shift +21 and -2 cm-1, respectively, suggesting strong vibrational coupling,16 although the origin of the coupling is unknown. Transition dipole coupling has been proposed to explain shifts in poly(adenosine)‚poly(uridine) helices,17 but in neither case has a model been developed that accounts for both the intrastrand coupling among stacked bases and the interstrand coupling between hydrogen-bonded bases. We use heterodyned 2D-IR spectroscopy to measure the coupling between the carbonyl stretch bands of G and C bases (structure I) in double-stranded dG5C5. Using additional information from frequency resolved photon echo and pump-probe spectroscopies, we simulate the spectra using an exciton model and transition dipole coupling. A detailed description of the methods will be given elsewhere.18 Briefly, a difference frequency optical parametric amplifier generates ∼6 µm, 120 fs, 2 µJ pulses that are split into four beams, three of which (k1, k2, and k3) generate a photon echo and the fourth overlaps the echo in the kLO ) -k1 + k2 +
k3 phase matching direction. The four pulses are separated by time t1, t2, and t3 and have polarizations 〈p1,p2,p3,pLO〉. The time delays t1 and t3 were scanned with t2 ) 0 and the signal Fourier transformed to generate the 2D-IR spectra.19 The frequency axes of the spectra were calibrated using the linear spectrum along ω1 and the frequency resolved photon echo along ω3. Pumpprobe and frequency resolved echo signals were obtained by dispersing the third-order signal in a monochromator. The samples dCMP (2′-deoxycytidine-5′-monophosphate, 50 mM), dGMP (2′-deoxyguanosine-5′-monophosphate, 50 mM), and self-complementary dG5C5 (5′-GGGGGCCCCC-3′, 500 µM) were buffered in 50 mM NaCl/50 mM potassium phosphate in D2O with pD ) 6.9.20 dG5C5 was annealed to induce helix formation and is in the A-form.21 Linear and absolute value 2D-IR spectra of dG5C5 are shown in Figure 1a-d.22 Four diagonal peaks are observed in the 2D-IR spectra, labeled A-D, corresponding to the G and C ring modes at 1584 and 1621 cm-1, respectively, and the carbonyl stretches of C and G at 1650 and 1682 cm-1, respectively. In dG5C5, G is 18 cm-1 higher than in dGMP, and C has the same frequency as dCMP. Peaks E and F are cross-peaks between the carbonyl modes, and peaks G-J are cross-peaks between the carbonyl and ring modes. The diagonal peaks obscure some of the cross-peaks, which might be improved with appropriate window functions.8,23 The relative intensities of the cross-peaks change in 〈0°,90°,90°,0°〉 due to nonzero angles between their transition dipoles.8,24 Peaks E and F are more clearly observed for 〈45°,-45°,90°,0°〉, which removes the diagonal peaks.25 Cross-peaks also contribute to D that cause the residual “diagonal” peak in Figure 1d. To interpret and simulate the spectra, we use an excitonic Hamiltonian that has previously been used to describe the
10.1021/jp035473h CCC: $25.00 © 2003 American Chemical Society Published on Web 08/12/2003
9166 J. Phys. Chem. B, Vol. 107, No. 35, 2003
Letters amide-I band of peptides.1 In the limit that the carbonyl group vibrations are completely separable from all other molecular modes, the vibrational Hamiltonian for the one-quantum exciton system of dGn‚dCn can be written 1
H)
C βij|Ci〉〈Cj| + ∑i Gi|Gi〉〈Gi| + ∑i Ci|Ci〉〈Ci| + ∑ i
