Interpretation of DNA vibration modes: III--The behaviour of the sugar pucker vibration modes as a function of its pseudorotation parameters

A systematic study of the sugar pucker characteristic vibration modes as a function of its geometrical conformations, has been performed. The present investigation is based on the Wilson GF method and a non-redundant valence force field. The calculated results allow to assign the modes arising mainly from the sugar motions and present in quasi whole vibrational spectra related to the right or left-handed double-helices (i.e., 1050 cm-1, 960 cm-1 and 890 cm-1). Moreover, the conformation dependent modes as those at 860 cm-1 and around 810 cm-1 (A form) as well as the one located around 830 cm-1 (B form) are interpreted by the present investigation. The possibility of the interaction of the latter modes with the phosphate group motions along the DNA double-helical chains are also discussed.     

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

Abstract

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.     

DNA-Carbohydrate Interaction. The Effects of Mono- and Disaccharides on the Solution Structure of Calf-Thymus DNA

Abstract

We report the interaction of calf-thymus DNA with D-glucose, D-fructose, D-galactose and sucrose in aqueous solution at physiological pH with sugar/DNA(P)(P=phosphate) molar ratios (r) of 1/10,1/5,1,5 and 10. FTIR difference spectroscopy was used to characterize the nature of sugar-DNA interaction and correlations between spectral changes and structural variations for both sugar and DNA complexes have been established.

FTIR difference spectroscopic results showed major sugar interaction (H-bonding) with the P0₂ groups of the backbone at low sugar concentrations (r= 1/10 and 1/5). Such interaction was characterized by the shift and the intensity variations of the backbone P0₂ antisymmetric stretch at 1222 cm^?1, which resulted in a major helical stability of DNA duplex. As sugar concentration increased, carbohydrate binding to DNA bases occurred. Evidence for this comes from major shiftings of the sugar O-H stretching vibrations at 3500–3200 cm^?1, and sugar C-O stretches and OH bending modes at 1450–1000 cm”. Similarly, shifting and intensity variations of several DNA in-plane vibrations at 1717 (G,T), 1663 (T,G,A,C) and 1492 cm^?1 (C,G) were observed, that are characterized by the presence of sugar-base interaction (via H₂0). The shiftings and the intensity changes of the sugar OH stretching modes at 35003200 cm^?1 are also indicative of the rearrangements of the sugar intermolecular H-bonding network, on DNA complex formation. A partial B to A conformational transition was observed for DNA molecule on sugar complexation, whereas carbohydrate binding occurred via both a- and β-anomeric structures.     

Interpretation of DNA vibration modes: I-The guanosine and cytidine residues involved in poly(dG-dC)·poly(dG-dC) and d(CG)3·d(CG)3

Abstract

A normal coordinate analysis has been carried out on guanosine and cytidine residues appearing in oligo and polynucleotides by using a simplified valence force field that allows the vibrational spectra of 5′-dGMP and 2′-deoxycytidine molecules to be reproduced. The role of both C2′-endo and C3′-endo conformations on sugar pucker, as well as that of glycosidic torsion angle (χ), on several characteristic vibration modes of these residues have been studied. The present calculations based on a non-redundant set of internal coordinates preserving the harmonic approximation of the potential field, allows us to explain quite satisfactorily the modifications of the vibrational spectra in the 1550-1250 cm^?1 and 785-500 cm^?1 regions, when the right → left-handed conformational transition occurs.     

Resonance raman spectroscopy of chemically modified and isotopically labelled purple membranes. I. A critical examination of the carbon-nitrogen vibrational modes

Resonance Raman spectra of bacteriorhodopsin are compared to the spectra of this protein modified in the following ways: (1) selective deuteration at the C-15 carbon atom of retinal, (2) full deuteration of the retinal, (3) the addition of a conjugated double bond in the β-ionone ring (3-dehydroretinal), (4) full deuteration of the protein and lipid components, (5) ¹⁵N enrichment of the entire membrane and (6) deuteration of the entire membrane (including the retinal). A detailed comparison of the ¹⁵N-enriched membrane and naturally occurring purple membrane from 800 cm^?1 to 1700 cm^?1 reveals that ¹⁵N enrichment affects the frequency of only two vibrational modes. These occur at 1642 cm^?1 and 1620 cm^?1 in naturally occurring purple membrane and at 1628 cm^?1 and 1615 cm^?1 in the ¹⁵N-enriched samples. Therefore, this pair of bands reflects the states of protonation of the Schiff base. However, our data also indicate that neither of these modes are simple, localized $\text{C}\text{=}\textcolor{red}{}\text{?}\text{H}$ or C=N stretching vibrations. In the case of the 1642 cm^?1 band motions of the retinal chain beyond C-15 are not significantly involved. On the other hand, in the 1620 cm^?1 band atomic motions in the isoprenoid chain beyond C-15 are involved.     

Intensity Changes of Base and Backbone Raman Modes in the B to Z Transition of poly(dG-dm5C)

Abstract

Raman spectroscopy was employed to investigate the temperature-induced B to Z transition of poly(dG-dm-⁵C). The transition midpoint was about 37°C for a solvent containing 20 mM Mg²⁺. A 10-fold change in Mg²⁺ concentration altered the transition midpoint by at least 60°C. Raman spectra of the B and Z forms of poly(dG-dm⁵C) exhibited characteristics similar to those observed with poly(dG-dC). The 682 cm^?1 guanine mode and 835 cm^?1 backbone mode were present in the B conformation. In the Z form the intensities of these two bands decrease substantially and new peaks were observed at 621 cm^?1, 805 and 819 cm¹. Several bands unique to poly(dG-dm⁵C) were also observed. Transition profiles of band intensity vs. temperature were determined for fourteen Raman bands. The curves of all of the base vibrations and one backbone mode had the same slope and midpoint. This indicates that conformational changes in the guanine and methycytosine bases occur concurrently.     

Low-frequency infrared bands and chain conformations of polypeptides

Infrared spectra of polypeptides were measured in the region of 1800–400 cm^?1. For the α-helical form, disordered form, and antiparallel-chain β-form, amide V band- arising from N-H out-of-plane bending models were observed at 610–620, around 650, and 700–705 cm^?1, respectively, and amide V′ bands arising from N-D out-of-plane bending modes were observed at 455–465, around 510, and a 515–530 cm^?1, respectively. These correlations are useful for conformation diagnoses, particularly for copolyamino-acids or proteins which are not oriented. The nature of low-frequency amide bands are discussed with reference to potential energy distributions calculated for the α-helical form and β form.     

Direct Measurement of Hydration-Related Dynamic Changes in Lysozyme using Inelastic Neutron Scattering Spectroscopy

Abstract

Inelastic neutron scattering spectroscopy is used to investigate dynamic changes in lysozyme powder at two different low D,0 hydrations (0.07g D²,O/g protein and 0,20 g D²,O/g protein). In the higher hydration sample, the inelastic scattering between 0.8 and 4.0 cm^?1 energy transfer is increased and the elastic scattering is decreased. The decreased elastic scattering suggests increased atomic amplitudes of motion and the increased 0.8 to 4.0 cm^?1 scattering suggests increased motions in this frequency range. Comparison with normal mode models of lysozyme dynamics shows that the inelastic difference occurs in the frequency region predicted for the lowest frequency, largest amplitude, global modes of the molccule[M. Levitt, C. Sanderand P. S. Stern, J. Mol. Biol. 181. 423 (1985). B.Brooks and M.Karplus.Prot. Natl Acad. Sci (U.S.A) 82. 4995 (1985), R.E. Bruccoleri, M. Karplus and J.A. McCammon, Biopolymers 25 1767 (1986)]. Our results are consistent with a model in which an increased number of low frequency global modes are present in the higher hydrated sample.     

Contribution of the Resonance Raman Spectroscopy to the Identification of Z DNA

Abstract

Poly(dG-dC)?poly(dG-dC) at low salt concentration (0.1 M NaCl) and at high salt concentration (4.5 M NaCl) has been studied by Raman resonance spectroscopy using two excitation wavelengths: 257 nm and 295 nm. As resonance enhances the intensity of the lines in a proportion corresponding to the square of the molar absorption coefficient, the intensities of the lines with 295 nm wavelength excitation are enhanced about sevenfold during the B to Z transition.

With 257 nm excitation wavelength the 1580 cm^?1 line of guanosine is greatly enhanced in the Z form whereas with 295 nm excitation several lines are sensitive to the modifications of the conformation: the guanine band around 650 cm^?1 and at 1193 cm^?1 and the bands of the cytosines at 780 cm^?1, 1242 cm^?1 and 1268 cm^?1.

By comparison with the U.V. resonance Raman spectra of DNA, we conclude that resonance Raman spectroscopy allows one to characterize the B to Z transition from one line with 257 nm excitation wavelength and from three lines with 295 nm excitation. The conjoined study of these four lines should permit to observe a few base pairs being in Z form in a DNA.     

Excited-State Lifetimes of Far-Infrared Collective Modes in Proteins

Vibrational excitations of low frequency collective modes are essential for functionally important conformational transitions in proteins. Here we report the first direct measurement on the lifetime of vibrational excitations of the collective modes at 87 pm (115 cm^-1) in bacteriorhodopsin, a transmembrane protein. The data show that these modes have extremely long lifetime of vibrational excitations, over 500 picoseconds, accommodating 1500vibrations. We suggest that there is a connection between this relativelyslow anharmonic relaxation rate of approximately 10 g sec^-1 and thesimilar observed rate of conformational transitions in proteins, which require require multi-level vibrational excitations and energy exchanges with othervibrational modes and collisional motions of solvent molecules.     

Vibrational Analysis of Phosphorothioate DNA: II. The POS Group in the Model Compound Dimethyl Phosphorothioate [(CH3O)2(POS)]-

Abstract

The results of Raman and Infrared (IR) spectroscopic investigations on the vibrational modes of dimethyl phosphorothioate (DMPS) anion, [(CH₃O)₂(POS)]^?, are reported. Ab initio calculations of the vibrational modes, the IR and Raman spectra and the interatomic force constants of DMPS were performed. A normal mode calculation was performed and the results were used to calculate the potential energy distribution for the vibrational modes. This analysis shows that in DMPS the P-S stretching mode has a frequency of about 630 cm^?1 and an angle bending mode involving the sulfur atom has a frequency of about 440 cm^?1. The proposed vibrational mode assignments will serve as marker bands in the conformational studies of phosphorothioate oligonucleotides which play a central role in the novel antisense therapeutic paradigm.     

Zwitterion l-cysteine adsorbed on the Au20 cluster: enhancement of infrared active normal modes

The study reported herein addressed the structure, adsorption energy and normal modes of zwitterion l-cysteine (Z-cys) adsorbed on the Au₂₀ cluster by using density functional theory (DFT). It was found that four Z-cys are bound to the Au₂₀ apexes preferentially through S atoms. Regarding normal modes, after adsorption of four Z-cys molecules, a more intense infrared (IR) peak is maintained around 1,631.4 cm^?1 corresponding with a C=O stretching mode, but its intensity is enhanced approximately six times. The enhancement in the intensity of modes between 0 to 300 cm^?1 is around 4.5 to 5.0 times for normal modes that involve O–C=O and C-S bending modes. Other two normal modes in the range from 300 to 3,500 cm^?1 show enhancements of 6.0 and 7.4 times. In general, four peaks show major intensities and they are related with normal modes of carboxyl and NH₃ groups of Z-cys.     

Internal DNA Modes Below 25 cm−1: A Resonance Raman Spectroscopy Observation

Abstract

The first resonance Raman scattering observation of the low-frequency (LF) region (below 40 up to 12 cm^?1) of DNA motions is presented. Since the concentration of the studied DNA solution was very low (1 mg/ml), the spectra features reflect internal vibrations of the macro-molecule. The decomposition of the spectra into Lorentzians clearly indicate three intrahelical DNA modes: the corresponding peaks are located at the frequencies 16,19, and 23 (±1) cm^?1. This result is in agreement with our quasi-continuity model of the LF B-form DNA dynamics (V. Lisy, P. Miskovsky and P. Schreiber, J. Biomol. Struct. Dyn. 13, 707 (1996)). The fit of the experimental frequencies to the theory, using the Genetic Algorithms approach, allowed us to make some conclusions about the model force constants which could be found by independent conformational energy calculations. Possible positions of five lowest-frequency DNA peaks, predicted by the model, are discussed.     

Lattice vibrational modes of poly(rU)-poly(rA). A coupled single-helical approach

The eigenvalues and eigenvectors of 11-fold double-helical poly(rU)·poly(rA) have been calculated. The vibrational potential energy of the double-helical structure is initially considered to be a sum of the vibrational potential energy of the single-helical structures poly(rU) and poly(rA). Coupling between the single helices is introduced by including a stretch force constant for each hydrogen bond between the uracil and adenine base residues. In addition, a model is presented for nonbonded interactions between nearest neighbor base pairs, which is consistent with a previous model for such interactions in the single helices. Because of the simple structural relationship between the uncoupled single helices and the double helix we are able to cast the secular equation for poly(rU)·poly(rA) in a form suitable for the use of perturbation theory using the previously calculated normal modes for the single helices as the unperturbed modes. Perturbation theory was found to be inapplicable for the region of the spectrum ?450 cm^?1. In this region an exact Green function technique is used to calculate the strongly coupled modes. We explicitly display one aspect of these double-helical normal modes. The stretching motions of the hydrogen bonds in the region of the spectrum <450 cm^?1 have been plotted as bar graphs for each mode.     

Projection Methods for the Analysis of Complex Motions in Macromolecules

Abstract

In studies of macromolecular dynamics it is often desirable to analyze complex motions in terms of a small number of coordinates. Only for simple types of motion, e.g., rigid-body motions, these coordinates can be easily constructed from the Cartesian atomic coordinates. This article presents an approach that is applicable to infinitesimal or approximately infinitesimal motions, e.g., Cartesian velocities, normal modes, or atomic fluctuations. The basic idea is to characterize the subspace of interesting motions by a set of (possibly linearly dependent) vectors describing elementary displacements, and then project the dynamics onto this subspace. Often the elementary displacements can be found by physical intuition. The restriction to small displacements facilitates the study of complicated coupled motions and permits the construction of collective-motion subspaces that do not correspond to any set of generalized coordinates.

As an example for this technique, we analyze the low-frequency normal modes of proteins up to ≈ 20 THz (600 cm^?1) in order to see what kinds of motions occupy which frequency range. This kind of analysis is useful for the interpretation of spectroscopic measurements on proteins, e.g., inelastic neutron scattering experiments.     

An FT-IR Study of DNA and RNA Conformational Transitions at Low Temperatures

Abstract

Fourier Transform Infrared (FT-IR) spectra of solid samples of DNA and RNA obtained from freeze-drying at solid CO₂ and liquid nitrogen temperatures, have been recorded and correlation between the conformational transitions and spectral changes is proposed. It is concluded that an equilibrium exists between A, B and Z conformations at low temperatures for the DNA molecule, which is temperature dependent, whereas the RNA molecule exhibits only the A conformation. The results have been compared with the metal-adducts of DNA and RNA, where one of the conformations is predominant.

Marker infrared bands for the B conformer have been found to be the strong band at 825 cm^?1 (sugar conformer mode) and a band with medium intensity at 690 cm^?1 (guanine breathing mode). The A conformation showed characteristic bands at 810 and 675 cm^?1. The B to Z conformational transition was characterized by the strong absorption bands near 820-810 cm^?1 and at 665-600 cm^?1.     

Far-Infrared Study of the Vibrational Modes of 5′-GMP Gels and Crystals of Na+ and K+

Abstract

Five Far-Infrared (50–600 cm^?1) spectra are presented: the sodium and potassium salts of 5′ Guanosine Monophosphate (GMP), each salt in both the gel and crystal conformations, and poly(rG). Measurements were performed at a sample temperature of 10 Kunder vacuum with a liquid He-cooled bolometer. The spectra were fit with Lorentzians and assignments are suggested. There are noteworthy differences in oscillator strengths and frequencies of the bands between all spectra. We report the tentative observation of a 100 cm^?1 mode which is in the neighborhood of a mode observed by Raman spectroscopy in solution (1) and dried gels (2).     

Flexibility of DNA and RNA upon Binding to Different Metal Cations. An Investigation of the B to A to Z Conformational Transition by Fourier Transform Infrared Spectroscopy

Abstract

The interaction of DNA and RNA with Cu(II), Mg(II), [Co(NH₃)₆]³⁺ [Co(NH₃)₅Cl]²⁺ chlorides and, cis- and trans-Pt(NH₃)₂Cl₂ (CIS-DDP, trans-DDP) has been studied by Fourier Transform Infrared (FT-IR) spectroscopy and a correlation between metal-base binding and conformational transitions in the sugar pucker has been established. It has been found that RNA did not change from A-form on complexation with metals, whereas DNA exhibited a B to Z transition. The marker bands for the A-form (C′₃-endo-anti conformation) were found to be near 810–816 cm^?1, while the bands at 825 and 690 cm^?1 are marker bands for the B- conformation (C′₂-endo, anti), The B to Z (C₃′-endo, syn conformation) transition is characterized by the shift of the band at 825 cm^?1 to 810–816 cm^?1 and the shift of the guanine band at 690 cm^?1 to about 600–624 cm^?1.