Study of hydrogen bonds in cyrstalline monosaccharides the spectra of monosaccharides derivatives in the middle-and far-infrared regions

The spectra of a series of monosaccharide derivatives in the middle- and far-infrared region were investigated. An explanation is provided for the band shifts in the OH stretching region at 3100–3400 cm^?1 and in the region of hydrogen-bond vibrations at 180–120 cm^?1 under effect of low temperatures. A comparison of i.r., X-ray, and neutronographic data indicates the absence of intramolecular hydrogen-bonds in the crystalline monosaccharide derivatives investigated.     

Changes in Raman vibrational bands of calf thymus DNA during the B-to-A transition

The B -to-A conformational transition of calf thymus DNA fibers was followed employing Raman spectroscopy. The transition was induced by soaking DNA fibers in water/ethanol mixtures increasing from 60 to 85% ethanol (v/v). Intensity changes of 17 Raman vibrational bands were quantified in the region from 400 to 860 cm^?1. Two bands at 500 and 784 cm^?1 were employed as internal standards. These bands do not appear to change in intensity with ethanol concentration. Large intensity changes relative to these two bands are observed between 70 and 74% ethanol for backbone vibrations at 708, 808, and 835 cm^?1, and base vibrations at 682, 730, and 750 cm^?1. These results indicate that a highly cooperative conformational change takes place between different portions of DNA in the B -to-A transition. Relative intensity changes preceding the onset of the major transition are observed in only two bands; at 835 cm^?1, assigned to a ribose–phosphate vibration, and at 750 cm^?1, assigned to thymine. The implications of these pretransition changes are discussed.     

Far-infrared Bands of Amino-acid Residues with α-Helical and β-Form Conformations

INFRARED spectra in the far-infrared region are very sensitive to the conformational changes of polypeptide backbones^1–6. We have measured the infrared spectra of sequential polypeptides in the region from 700 to 200 cm^?1 and have found several far-infrared bands characteristic of component amino-acid residues with α-helical and β-form conformations.     

Conformational dependence of the Raman scattering intensities from polynucleotides. 3. Order-disorder changes in helical structures

Raman spectra are presented on ordered and presumably helical structures of DNA and RNA as well as the poly A·poly U helical complex, polydAT, and the helical aggregates of 5′-GMP and 3′-GMP. The changes in the frequency and the intensity of the Raman bands as these structures undergo order-disorder transitions have been measured. In general the changes we have found can be placed into three categories: (1) A reduction in the intensities of certain ring vibrations of the polynucleotide bases is observed when stacking or ordering occurs (Raman hypochromism). Since the ring vibrational frequencies are different for each type of base, we have been able to obtain some estimate of average amount of order of each type of base in partially ordered helical systems. (2) A very large increase in the intensity of a sharp, strongly polarized band at about 815 cm^?1 is observed when polyriboA and polyriboU are formed into a helical complex. Although this band is not present in the separated chains at high temperature, a broad diffuse band at about 800 cm^?1 is present. The 815 cm^?1 band undoubtedly arises from the vibrations of the phosphate-sugar portions of the molecule and provides a sensitive handle to the back-bone conformation of the polymer. This band also appears upon ordering of RNA, formation of the helical aggregate of 5′-riboGMP, and to some extent in the selfstacking of the polyribonucleotides polyA, polyU in the presence of Mg⁺⁺, PolyC, and polyG. No such intense, polarized band is found, however, in ordered DNA, polydAT, or the 3′-riboGMP aggregate, although there is a conformationally independent band at about 795 cm^?1 in DNA and polydAT. (3) Numerous frequency changes occur during Conformational changes. In particular the 1600–1700 cm^?1 region in D₂O shows significant conformationally dependent changes in the C?O stretching region analogous to the changes in this region which have been observed in these substances in the infrared. Thus, Raman scattering appears to provide a technique for simultaneously observing the effects of base stacking, backbone conformation and carbonyl hydrogen bonding in nucleic acids in moderately dilute (10–25 mg/ml) aqueous solutions.     

Far-infrared spectra of some globular proteins

The far-infrared absorption spectrum (40–400 cm^?1) of solid pellets and films of several globular proteins (lysozyme, myoglobin, hemoglobin, serum albumin, ribonuclease, chymotrypsinogen, subtilisin) and of some representative polypeptides [nylon 66, poly (γ-benzyl L -glutamate)] have been investigated by using a Michelson interferometer. While polypeptides are known to present several peaks which can be assigned mostly to hydrogen-bond modes, all the investigated globular proteins display only one broad, intense baud in the 100–200 cm^?1 region. The origin of this band, which persists even after denaturation or partial digestion, is discussed.     

A new approach to the characterization of the B and A forms of DNA by I.R. spectroscopy

The RNA conformational changes of B, A and C forms are reflected in the infrared absorption spectra in the region of 800 cm^?1 to 900 cm^?1 and allow one to investigate unoriented samples. The transition to the A form is characterized by the appearence of bands at about 870 cm^?1 and at 813 cm^?1 whereas the B and the C forms exhibit a band at 837 cm^?1, these bands undoubtedly arise from phosphate diester stretching vibrations and yield information about backbone conformation. The presence of these infrared bands provides a criterion for testing the simultaneous presence of two coexisting forms of DNA. It represents a useful method for structural studies of nucleic acid complexes such as protein-DNA for which it is difficult to obtain orientation.     

Low-frequency vibrations in α-helices: Helicoidal analysis of polyalanine and deoxymyoglobin molecular dynamics trajectories

We present an approach to the analysis of low-frequency (0-200 cm^?1) α-helix vibrations in molecular dynamics simulation. The approach employs the P-Curves algorithm [H. Sklenar, C. Etchebest, and R. Lavery, (1989) Proteins: Structure, Function and Genetics, Vol. 6. pp. 46–60] to determine the helical axis and a set of helicoidal parameters describing the axis curvature and the position of the repealing units with respect to the axis and each other. The vibrations are analyzed in terms of time correlation functions of the fluctuations of P-Curves parameters and their Fourier transforms. Simulations of polyalanine and myoglobin are analyzed. For polyalanine, global twisting, bending, and stretching vibrations are found at 11, 20, and 40 cm^?1, respectively. In myoglobin, the spectra of the global helix vibrations are qualitatively different from those of polyalanine and considerably more complicated. Local vibrations of individual amino acid units in the helix backbones are also analyzed with P-Curves and compared. © 1995 John Wiley & Sons, Inc.     

Far-infrared spectra of poly(-α-amino acids) with basic alkyl group side chains

Far-infrared spectra in the region from 700 to 60 cm^?1 have been measured for the α-helix structures of poly(L -α-amino-n-butyric acid), poly-L -norvaline, poly-L -norleucine, and poly-L -leucine and for the β-form structures of poly(L -α-amino-n-butyric acid), poly-L -valine, poly(DL -amino-n-butyric acid), poly-DL -norvaline, and poly-DL -norleucine. The changes of the spectra on N-deuteration have been measured in the region between 700 and 400 cm^?1. It is concluded that, the α-helix has characteristic bauds near 690, 650, 610, 380, 150, and 100 cm^?1, and that the β-form has characteristic bands near 700, 240, and 120 cm^?1. The main-chain vibrations in the region from 600 to 200 cm^?1 are strongly coupled with the side-chain deformation vibrations.     

Laser Raman scattering of cobramine B, a basic protein from cobra venom

Cobramine B, a small basic protein from cobra venom, is selected as a model for studying the scattering intensity of tyrosyl ring vibrations in the Raman spectra of proteins. All three tyrosines in this protein appear to be “buried” in the interior of the molecule and probably involved in interactions which are similar to those of the three “buried” tyrosines in RNase A when it is dissolved in water. Spectral evidence is presented and discussed. The Raman spectra in the 300–1800 cm^?1 region of cobramine B in the solid and solution are compared quantitatively. Several differences exist between the two spectra and may be interpreted in terms of difference in conformation. In the amide I region, a strong single line was observed at 1672 cm^?1 both in the solid and solution spectra, suggesting that this protein may contain a large fraction of antiparallel-β structure. This is supported by the presence of a line at 1235 cm^?1 in the amide III region, which is also characteristic of β-structure. The resolved peaks at 1254 and 1270 cm^?1 indicate the coexistence of some hydrogen-bonded random-coil and some α-helix with the β-structure.     

Infrared absorption and raman scattering of sulfate groups of heparin and related glycosaminoglycans in aqueous solution

The i.r. spectra for aqueous solutions of sulfated glycosaminoglycans and model compounds in the transmittance “window” region of the solvent (1400-950 cm^?1) are dominated by the strong and complex absorption centered at ～1230 cm^?1 and associated with the antisymmetric stretching vibrations of the SO groups. Primary and secondary O-sulfate groups absorb at somewhat higher frequencies (1260-1200 cm^?1) than N-sulfates (～1185 cm^?1). Each sulfate band lends itself to quantitative applications, especially within a given class of sulfated polysaccharide. Laser-Raman spectra of heparin and model compounds have been obtained in aqueous solution and in the solid state. The most-prominent Raman peak (at ～1060 cm^?1) is attributable to the symmetrical vibration of the SO groups, with N-sulfates emitting at somewhat lower frequencies (～1040 cm^?1) than O-sulfates. The Raman pattern in the 950-800 cm^?1 region (currently used in the i.r. for distinguishing between types of sulfate groups) also involves vibrations that are not localized only in the COS bonds.     

Far-infrared spectra of polyalanines with alpha-helical and beta-form structures

Far-infrared spectra of poly-L -alanines having the α-helical conformation and the β-form structure were measured. The spectra of glycine–L -alanine copolymer, silk fibroin, and copoly-D ,L -alanines with different D :L compositions were also measured. In addition to the bands so far reported, four bands at 190, 107, 120, and 90 cm^?1were found for the α-helix conformation and the two bands at 442 and 247 cm^?1 were found for the β form. The 442 cm^?1 band consists of the parallel 432 cm^?1 and perpendicular 445 cm^?1 bands. The 247 cm^?1 band is well defined and has strong dichroism parallel to the direction of stretching. These two bands appear also for silk fibroin and glycine–L -alanine copolymer. All the far-infrared bands of copoly-D ,L -alanines can be interpreted as α-helix bands, the three peaks at 580, 478, and 420 cm^?1 being ascribed to the D -residue incorporated into the right-handed α-helix or to the L -residue in the left-handed α-helix.     

A vitrational study of poly (L-proline) I and II in the far infrared.

The far infrared spectra of poly(L -proline) I (190–35 cm^?1) and II (400–35 cm^?1) were obtained in the solid state at both 300° and 110°K. A significant difference in the region below 100 cm^?1 was observed. A very intense band located at 60 cm^?1 in the infrared spectrum of form II has no counterpart in form I. This indicates the sensitivity of low-frequency vibrations to the difference in conformation assumed by both forms in the solid state. Additional bands observed in this study are correlated with ir and Raman data previously reported and tentative assignments are made using the results of normal mode calculations (in the single-chain approximation) which have been reported.     

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.     

Far-infrared absorption of nucleotides and poly(I)·poly(C) RNA

We have measured the ir absorption of 5′CMP, 5′IMP, and poly(I)·poly(C) from ～25 to ～500 cm^?1. From a comparison of the data with the previously measured absorption of the corresponding nucleosides and bases we can identify several “lines” associated with the deformation of the ribose ring. Out-of-plane deformation of the bases contributes strongly to vibrations near 200 cm^?1. The same ribose vibrations observed in the nucleotides are found in poly(I)·poly(C). They sharpen with increasing water absorption. A study of the spectra of poly(I)·poly(C) as a function of the adsorbed water indicates that water does not contribute in a purely additive fashion to the polynucleotide spectrum but depends on the conformation of the helix. However, the only spectral feature that shifts drastically with conformation is near 45 cm^?1. Measurements at cryogenic temperatures indicate some sharpening of the spectrum of poly(I)·poly(C). Instead, no sharpening is observed in the spectrum of the nucleotides. Shear degradation of poly(I)·poly(C) produces significant spectral changes in the 200-cm^?1 region and sharpening of the features assigned to the low-frequency ribose-ring vibrations.     

RNA Binding Efficacy of Theophylline,Theobromine and Caffeine

Abstract

The binding of naturally occurring methylxanthines such as theophylline, theobromine and caffeine to nucleic acids are reckoned to be pivotal as they are able to modulate the cellular activities. We explore the interaction of yeast RNA binding efficacy of the above xanthine derivatives by using UV absorption differential spectroscopy and Fourier Transform Infrared (FTIR) spectroscopy. Both the analyses show discrimination in their binding affinity to RNA. The differential UV-spectrum at P/D 3.3 reveals the greater RNA binding activity for theophylline (85 ± 5%), whereas moderate and comparatively less binding activity for theobromine (45 ± 5%) and caffeine (30 ± 5%) and the binding activity was found to depend on concentration of the drugs. In FTIR analysis we observed changes in the amino group (NH) of RNA complexed by drugs, where the NH band is found to become very broad, indicating hydrogen bonding (H-bonding) with theophylline (3343.4 cm^?1), theobromine (3379.8 cm^{? 1}) and caffeine (3343 cm^?1) as compared to the free RNA (3341.6 cm^?1). Furthermore in RNA-theophylline complex, it is observed that the carbonyl (C=O) vibration frequency (υC=O) of both drug (υC=O=1718, 1666 cm^?1) as well as RNA (υC=O=1699, 1658 cm^?1) disappeared and a new vibration band appeared around 1703 cm^?1, indicating that the C=O and NH groups of drug and RNA are effectively involved in H-bonding. Whereas in RNA-theo- bromine and RNA-caffeine complexes, we found very little changes in C=O frequency and only broadening of the NH band of RNA due to complexation is observed in these groups. The changes in the vibrations of G-C/A-U bands and other bending frequencies are discussed. Thus the discrimination in the binding affinity of methylxanthines with RNA molecule shows that strong RNA binding drugs like theophylline can selectively be delivered to RNA targets of microbial pathogens having the mechanism of RNA catalysis.     

Steric structure of L-proline oligopeptides. I. Infrared absorption spectra of the oligopeptides and poly-L-proline

Poly-L -prolines I and II were differentiated by the characteristic bands in the far infrared region. Form I showed two broad bands at about 280 and 160 cm^?1 and form II two bands at, 400 and 670 cm.^?1. Furthermore, three broad bands at about 250, 200, and 100 cm.^?1 were observed in the spectrum for form II. Infrared absorption bands of the pentamer, hexamer, and octamer of tert-amyloxycarbonyl-L -proline were almost similar to those of poly-L -proline II in the 1800–75 cm.^?1 region. In the far-infrared region, especially, the absorption bands of these three oligopeptides were in good agreement with that of poly–L –proline II. Accordingly we concluded that the molecules of pentamer, hexamer, and octamer had a helical structure of a left-handed threefold screw axis. The tetrapeptide of tert-amyloxycarbonyl-L -proline might also have a left-handed helix, probably one turn, since the tetramer clearly showed an absorption band at about 400 cm.^?-1 characteristic of poly–L –proline II.     

Low-frequency Raman scattering study of six nucleosides

Raman spectroscopy was used to study the low-frequency (?200?cm^?1) vibrations in crystalline samples of six naturally occurring nucleosides: deoxythymidine (dT), deoxycytidine (dC), deoxyadenosine (dA), uridine (rU), cytidine (rC), and adenosine (rA). Such low-frequency vibrations are important for biological processes in which the conformation of a nucleic acid molecule changes. These experiments also provide a test for the low-frequency vibrational modes of dT, dC, and dA predicted by Shishkin et al.     

Raman intensities of carbon-carbon stretching modes in a model membrane

Laser-Raman spectra of L-α-dimyristoylphosphatidylcholine (DMPC) liposomes in the spectral range 1000–1200 cm^?1 were obtained as a function of temperature from ?80 to +50°C. The triplet found in this spectral region was resolved into Lorentzian components by means of an iterative computer program. The peak intensities, band widths, and band areas of the resolved 1062 cm^?1 and 1130 cm^?1 bands, assigned to CC stretching vibrations of trans segments, were evaluated as a function of temperature. While the peak intensities of the bands decrease substantially with temperature, the band widths show a considerable increase. The change in band areas is therefore smaller than the change in peak heights. Experiments with all trans carboxylic acids showed that in these compounds the area of the Raman bands at 1062 cm^?1 and 1130 cm^?1 is proportional to the number of trans bonds. The variation with temperature of the number of trans and gauche bonds in the studied phospholipid is reflected by the change of the area of the 1130 cm^?1 Raman band.     

Pre-resonance Raman spectra of adriamycin

Pre-resonance Raman spectra have been obtained for aqueous solutions of adriamycin. All bands are attributable to the anthracycline chromophore and are vibrations coupled to the first (20,800 cm^?1) electronic transition of the molecule. Both ring modes and vibrations of the carbonyl, hydroxy and methoxy substituents are observed.     

Far-infrared spectroscopy of salt penetration into a collagen fiber scaffold

We employed far-infrared spectroscopy to observe the amount of salt that penetrates into collagen fiber masses. The absorption properties of collagen sheets prepared from tilapia skin, bovine skin, rat tail, and sea cucumber dermis were measured using a transmission Fourier transform spectrometer in a band from approximately 100 to 700 cm⁻¹. We confirmed that the absorbance spectra of the four types of dried collagen sheet show good agreement, even though the amino acid compositions differed. The absorbance peaks observed in the band corresponded to collective vibrations of plural functional groups such as methylene and imino groups in collagen. When salt solution was added to the collagen sheets and then dried, the spectral shapes of the sheets at approximately 166 cm⁻¹ were clearly different from those of the plain collagen sheets. The differential absorbance between wavenumbers 166 cm⁻¹ and 250 cm⁻¹ sensitively reflected the difference between higher-order structures, and the salt diffusion (crystallization) depended on the collagen fiber condition. From these results, we consider that spectral changes can be used for the numerical evaluation of salt penetration into a collagen fiber scaffold.