Infrared spectrum of deoxyribonucleic acid. Effects of base composition and of N15-substitution

tRNA as a stabilizing matrix for fluorescent silver clusters: photophysical properties and IR study

In this experimental study fluorescent silver clusters on a tRNA matrix were synthesized for the first time. Two types of fluorescent complexes emitting in the green (550 nm) and red (635 nm) regions of the visible spectrum were obtained. Using FTIR spectroscopy, we identified possible binding sites for the clusters, which appeared to be within the helical regions of tRNA. It was also shown that tRNA retained its double helical structure after the cluster formation, which is essential for its functionality.

Interpreting DNA Vibrational Circular Dichroism Spectra Using a Coupling Model from Two-Dimensional Infrared Spectroscopy

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.

Infrared spectroscopy: a new frontier in medicine

As we enter the second half of the nineties, one of the major challenges for biological infrared spectroscopists is to transfer the knowledge we have gained from studies on isolated molecules to the complex world of medicine. That it is possible to meet this challenge is suggested by comparison with the development of other biophysical techniques, such as magnetic resonance spectroscopy and imaging, which have already found their place in medical research and practice. The Spectroscopy Group in Winnipeg is developing and evaluating a variety of new IR techniques for the analysis of body fluids and tissues, both in vitro and in vivo. Herein, we review these methodologies, which comprise both instrumental (imaging and spatially localized IR spectroscopy) and interpretational procedures aimed at optimizing the measurements and their conversion to biodiagnostic information.

Interpretation of DNA vibration modes: IV--A single-helical approach to assign the phosphate-backbone contribution to the vibrational spectra in A and B conformations

A calculated approach based on the Higgs method for assigning the vibration modes of an infinite helicoidal polymeric chain has been performed on the basis of a reliable valence force field. The calculated results allowed the phosphate-backbone marker modes of the A and B forms, to be interpreted. In the dynamic models used, the bases have been omitted and no interchain interaction was considered. The calculation can also interprete quite satisfactorily the characteristic Raman peaks and infrared bands in the 1250-700 cm-1 spectral region arising from the sugar or sugar-phosphate association and reproduce their evolution upon the B----A DNA conformational transition. They clearly show that the phosphate-backbone modes in the above mentioned spectral region constitute the optical branches of the phonon dispersion curves with no detectable variation in the first Brillouin-zone.

F.t.-i.r. and laser-Raman spectra of cytosine and cytidine

Fourier-transform infrared (F.t.-i.r.) and laser-Raman spectra of cytosine and cytidine in the solid state have been recorded and assignments of the frequencies made. Comparison of the observed frequencies for cytosine with those for cytidine permits identification of the bands characteristic of the sugar on the one hand, and of the pyrimidine base on the other.

Raman pH profiles for nucleic acid constituents I. Cytidine and uridine ribonucleosides

Raman spectra of aqueous solutions of uridine and cytidine have been recorded as a function of pH with the band intensities and vibrational frequencies monitored to determine bands which may be considered as diagnostic of the concentration of the various species. Quantitative band intensity measurements indicate that not all pH-sensitive bands can be considered as diagnostic of the pK value for the acid form of the nucleoside, and for the percent species in solution. Although the accuracy of the Raman band intensity method is inherently less than that of the titrimetric or visible-ultraviolet spectrophotometric methods, the pK values and percent species agree well with those obtained from these methods. The utility of the results obtained from the pH profiles for cytidine is discussed in terms of the effect of acidification on the structural and conformational characteristics of polycytidylic acid in solution.

Raman ph profiles for nucleic acid constituents. II. 5'-AMP and 5'-GMP ribonucleotides

Raman spectra of aqueous solutions of 5'-AMP and 5'-GMP have been recorded as a function of pH. Band intensities and frequencies have been monitored to determine bands which may be considered as diagnostic for the concentration and the pK of the solution species. Quantitative band intensity measurements indicate only a selected number of bands can be considered as diagnostic of the base or the secondary phosphate proton dissociation. The utility of the pH profiles derived from specific band intensity variations for 5'-AMP is discussed in terms of the effect of acidification on solution characteristics of polyadenylic acid.

Proton dispersion forces. Secondary-structure stabilizing forces between the hydrogen bonds of the polynucleotides

In the double helix formed by the semiprotonated polycytidylic acid (poly C), both strands are linked via NH(+)...N hydrogen bonds. It is a known fact that such symmetrical hydrogen bonds with a double minimum potential well are extremely polarizable. This polarizability causes interaction effects, in particular the proton dispersion forces between such hydrogen bonds. These forces result in a shift of the energy levels and a continuum is observed in the infrared (IR) spectra of solutions in which such hydrogen bonds are present. The continuum occurs in the IR spectrum of the semiprotonated poly C, when the former is present in coiled state. If the double helix forms, an extremely broad band of the NH stretching vibration is observed instead of the continuum, since in the double helix all hydrogen bonds are oriented equally to one another and polarize each other mutually to a strong degree. The proton dispersion forces between the hydrogen bonds balance a considerable part of the electrostatic repulsion of the protons and hence enable the double helix to form. It is conceivable that an unsymmetrical double minimum potential well is present in the NH...N bonds in the DNA and RNA. Such bonds may likewise be considerably more polarizable than electron systems and thus, in this case too, proton dispersion forces would contribute to helix stabilization.