Laser-raman study of solute-solvent interactions in aqueous solutions of d-fructose, d-glucose,and sucrose

The solute-solvent interactions of d-fructose, d-glucose, and sucrose in aqueous solution were studied by comparison of characteristic, Raman of the water and the sugar components. Shifts in frequency and intensity were observed in both the bending and the stretching regions of CH₂ and H₂O. The ratios of integrated, Raman intensities I(CH₂)/I(H₂O) of the CH₂ peak and the H₂O bending band, and I(CH)/I(OH) of the C-H stretching line to O-H stretching band were determined. Their evolutions in terms of mass-concentration display discontinuities at specific concentrations for each of the three sugars. These breaks were interpreted as changes in the hydrogen bonding of the various species.     

Low-Temperature conformation of Mg2+-Poly(U) in D2O as revealed by IR and Raman Spectroscopy and by normal-mode analysis treatment

Infrared and Raman spectra of the Mg²⁺ salt of poly(U) in D₂O were recorded in the 1600-1800 cm^?1 region and between 1 and 20C. The ir spectra showed a melting curve similar to the uv melting curves with a temperature of transition of about 6.5°C. This spectral change is assumed to be associated with the formation of the secondary structure of Mg²⁺-poly(U) in D₂O at this temperature. Three double-helical and two triple-helical structures were used as inputs to compute the normal modes of vibration. A double-helical structure was found to give the best agreement with the observations. Knowledge of the C=0 eigenvectors, and of the expression for transition probability from quantum mechanics, was used to explain the so far unanswered question of H. T. Miles [(1964) Proc. Natl. Acad. Sci. USA 51, 1104–1109; (1980) Biomolecular Structure, Conformation, Function and Evolution, Pergamon, Oxford, pp. 251–264] as to why there is an increase in the ir vibrational wave number of a carbonyl band when that group is H-bonded to another polynucleotide chain in a helix. Such considerations also explain why a predicted band at about 1648 cm^?1 is not to be seen in the ir spectra but is present in the Raman spectra. The model incorporating the C?O transition dipole-dipole coupling interaction is able to explain also the observed higher intensity of the higher wave-number ir band. The experimental results demonstrate that the complete picture of vibrational dynamics of Mg²⁺-poly(U) in D₂O is obtained only by looking simultaneously at ir and Raman spectra and not at only one of them. Weak ir bands were found to be as useful as the strong ones in understanding structure and vibrational dynamics. On the bases of our ir and Raman spectra, of the normal-mode analyses, and of the literature data, it is concluded that Mg²⁺-poly(U) in D₂O is present in a double-helical structure at temperatures below the temperature of transition, whereby the uracil residues are paired according to arrangement (a) (see Fig. 1). This structure is rodlike and arises by refolding of one poly(U) chain. The computations show that no normal mode is associated with a single C?O group vibration; all C?O group vibrations are heavily mixed motions of various C?O groups.     

Temperature dependence of amino acid side chain IR absorptions in the amide I' region

Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side‐chains that overlap the amide I' may significantly complicate the structural analyses. While the side‐chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side‐chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D₂O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side‐chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side‐chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN₃H₅⁺ bending signal, although a linear fit can account for this change to within ~1/3 cm^‐1. The applicability of the determined spectral parameters for estimations of temperature‐dependent side‐chain absorptions in peptides and proteins are discussed. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 536–548, 2014.     

A Raman and calorimetric investigation of 3′, 5′ GpG

The Raman spectra of guanylyl (3′-5′) guanosine (GpG) in solution in H₂O and D₂O at pH 3–7 have been recorded at various temperatures between 0 and 80°C. The results are consistent with the existence in the lower temperature range of stable aggregates formed by the stacking of GpG tetramers. The aggregates melt cooperatively near 60°C, which results in important changes in the spectra. Among these, a large increase in intensity of some of the bands assigned to the guanine residues shows that unstacking of the bases occurs at the melting. Also apparent in the spectra are changes in the intensity and frequency of band attributable to molecular groups involved in intermolecular hydrogen bonding between adjacent molecules in the complex. The melting temperature of GpG decreases by approximately 15°C upon lowering the concentration from 5 × 10^?2 to 5 × 10^?4M, as shown by Raman, calorimetric, CD, and uv measurements. The experimentally determined ΔH and ΔS for the melting transition are 9 Kcal/mol and 28 e.u./mol, respectively. The aggregation of GpG in 1.5 × 10^?3M solutions was found to be very slow. The half-time of the process, which roughly follows first-order kinetics, is approximately 3 min at 10°C and 21 min at 35°C. The negative energy of activation associated with this reaction (?143 Kcal) indicated that the process involves intermediates whose concentrations decrease the temperatures raised, thus slowing down the overall process. The rate of disaggregation of GpG upon dilution to very low concentration is also extremely slow, indicating that the GpG aggregates, once formed, are very stable.     

Conformational properties of poly[d(G-T)].poly[d(C-A)] and poly[d(A-T)] in low- and high-salt solutions: NMR and laser Raman analysis

³¹P- and ¹H-nmr and laser Raman spectra have been obtained for poly[d(G-T)]·[d(C-A)] and poly[d(A-T)] as a function of both temperature and salt. The ³¹P spectrum of poly[d(G-T)]·[d(C-A)] appears as a quadruplet whose resonances undergo separation upon addition of CsCl to 5.5M. ¹H-nmr measurements are assigned and reported as a function of temperature and CsCl concentration. One dimensional nuclear Overhauser effect (NOE) difference spectra are also reported for poly[d(G-T)]·[d(C-A)] at low salt. NOE enhancements between the H8 protons of the purines and the C5 protons of the pyrimidines, (H and CH₃) and between the base and H-2′,2″ protons indicate a right-handed B-DNA conformation for this polymer. The NOE patterns for the TH3 and GH1 protons in H₂O indicate a Watson–Crick hydrogen-bonding scheme. At high CsCl concentrations there are upfield shifts for selected sugar protons and the AH2 proton. In addition, laser Raman spectra for poly[d(A-T)] and poly[d(G-T)]·[d(C-A)] indicate B-type conformations in low and high CsCl, with predominantly C2′-endo sugar conformations for both polymers. Also, changes in base-ring vibrations indicate that Cs⁺ binds to O2 of thymine and possibly N3 of adenine in poly[d(G-T)]·[d(C-A)] but not in poly[d(A-T)]. Further, ¹H measurements are reported for poly[d(A-T)] as a function of temperature in high CsCl concentrations. On going to high CsCl there are selective upfield shifts, with the most dramatic being observed for TH1′. At high temperature some of the protons undergo severe changes in linewidths. Those protons that undergo the largest upfield shifts also undergo the most dramatic changes in linewidths. In particular TH1′, TCH₃, AH1′, AH2, and TH6 all undergo large changes in linewidths, whereas AH8 and all the H-2′,2″ protons remain essentially constant. The maximum linewidth occurs at the same temperature for all protons (65°C). This transition does not occur for d(G-T)·d(C-A) at 65°C or at any other temperature studied. These changes are cooperative in nature and can be rationalized as a temperature-induced equilibrium between bound and unbound Cs⁺, with duplex and single-stranded DNA. NOE measurements for poly[d(A-T)] indicate that at high Cs⁺ the polymer is in a right-handed B-conformation. Assignments and NOE effects for the low-salt ¹H spectra of poly[d(A-T)] agree with those of Assa-Munt and Kearns [(1984) Biochemistry 23 , 791–796] and provide a basis for analysis of the high Cs⁺ spectra. These results indicate that both polymers adopt a B-type conformation in both low and high salt. However, a significant variation is the ability of the phosphate backbone to adopt a repeat dependent upon the base sequence. This feature is common to poly[d(G-T)]·[d(C-A)], poly[d(A-T)], and some other pyr–pur polymers [J. S. Cohen, J. B. Wouten & C. L Chatterjee (1981) Biochemistry 20 , 3049–3055] but not poly[d(G-C)].     

Fourier-transform infrared spectroscopy of Pediastrum duplex: characterization of a micro-population isolated from a eutrophic lake

Fourier-transform infrared (FTIR) spectroscopy was carried out on single colonies of Pediastrum duplex present in air-dried preparations of mixed phytoplankton samples isolated from a eutrophic freshwater lake. FTIR absorption spectra had 12 distinct bands over the wavenumber range 3300–900?cm^?1 which were tentatively assigned to a range of chemical groups, including –OH (residual water, wavenumber 3299?cm^?1), –CH2 (lipid, 2924), –C=O (cellulose, 1739), amide (protein, 1650 and 1542), >P=O (nucleic acid, 1077) and –C–O (starch, 1151 and 1077). Measurement of band areas identified residual water, protein and starch as the major detectable constituents. Areas of single bands and combined bands of –CH₂, –C–O and >P=O species normalized to protein (to correct for differences in specimen hydration and thickness) showed wide variation between colonies, indicating environmental heterogeneity. Correlation analysis demonstrated close statistical associations between different molecular species. Particularly high levels of correlation between bands 3/4 (CH₂), 6/7 (amide) and 8/9 (–CH₃) was consistent with their joint origin from the same molecular species. The isolation of bands 11 and 12 in the correlation pattern was confirmed by factor analysis, suggesting that variation in the level of starch is statistically unrelated to other macromolecules being monitored. The use of FTIR spectroscopy to characterize an algal micro-population within mixed phytoplankton has potential for future studies on biodiversity and environmental interactions at the species level.     

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.     

Vibrational analysis of nucleic acids. IV. normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Raman and ir spectra are reported for diethyl phosphate [(CH₃CH₂O)₂PO^-₂] and diethyl phosphate isotopomers incorporating carbon-13 at methylene group sites [(CH¹³₃CH₂O)₂PO^-₂] and deuterium substituents on methyl and methylene carbons [(CH₃CD₂O)₂PO^-₂, (CD₃CH₂O)₂PO^-₂ (CD₃CD₂O)₂PO^-₂]. The vibrational spectra are analyzed to develop a consistent set of assignments for the C-C-O-P(O^-₂)-O-C-C network, which serves as a model for the nucleic acid phosphodiester backbone. The present study resolves previously conflicting vibrational assignments for the phosphodiester skeleton and provides a firm empirical basis for interpreting conformationally sensitive modes of DNA and RNA. Ab initio vibrational analyses have also been conducted on the above isotopomers of diethyl phosphate in the trans-gauche-gauche-trans conformation, optimized using the 3-21+G^* basis set at the restricted Hartree-Fock level. The ab initio calculations are in good agreement with the empirical results, thus strengthening the proposed assignment scheme for Raman and infrared spectra. The present study provides a basis for improvement of empirical force fields utilized in previous normal coordinate analyses of the nucleic acid phosphodiester group. © 1996 John Wiley & Sons, Inc.     

Vitamin E Decreases the Order of the Phospholipid Model Membranes in the Gel Phase: An FTIR Study

The effect of -tocopherol on the frequency of the CH₂ stretching bands of infrared spectra of dipalmitoylphosphotidylcholine multibilayers has been investigated, both in H₂O and ²H₂O buffer, to determine the reason for the discrepancy in the literature between the results of different spectroscopic techniques relating to the effect of -tocopherol on membrane order in the gel phase. In contrast to previous FTIR studies, the present FTIR results indicate that T increases the frequencies of the CH₂ stretching bands in the gel phase, which implies an increase in the number of gauche conformers (increase in disordering), which is in agreement with other ESR and NMR spectroscopic studies.     

Intrinsic protein-lipid interactions. Infrared spectroscopic studies of gramicidin A, bacteriorhodopsin and Ca2+-ATPase in biomembranes and reconstituted systems

Infrared spectroscopy has been applied to the study of a number of aqueous systems of model and natural biomembranes. The absorption bands arising from water and buffer solutions were eliminated by means of an infrared spectrometer data station. Spectra were examined using H₂O and ²H₂O aqueous buffer systems. Pure lecithin-water systems, and various model biomembranes containing cholesterol, gramicidin A, bacteriorhodopsin or Ca²⁺-ATPase were examined. The infrared spectra of the reconstituted biomembranes were compared with those of the corresponding natural biomembranes, i.e. the purple membrane of Halobacterium halobium and also sarcoplasmic reticulum membranes, respectively.Changes in lipid chain conformation caused by the various intrinsic molecules incorporated within the model lipid bilayer structures were monitored by studying the shifts in frequency (cm^?1) of the CH₂ symmetric and asymmetric absorption bands arising from the lipid chains. The effect of gramicidin A and also the intrinsic proteins, as indicated by the shift of band frequencies, are quite different from that of cholesterol at temperatures above the main lipid transition temperature t_c. Cholesterol causes a reduction in gauche isomers which increases with concentration of cholesterol within the lipid bilayer. Whilst gramicidin A and the intrinsic proteins at low concentration cause a reduction of gauche isomers, at higher concentrations of these molecules, however, there is little difference in gauche isomer content when the intrinsic molecule is present compared with that of the fluid lipid alone. These results are considered and compared with previously published studies using deuterium nuclear magnetic resonance spectroscopy on similar model biomembrane systems. Below the lipid t_c value, all the intrinsic molecules produce an increase in gauche isomers presumably by disturbing the lipid chain packing in the crystalline lipid arrangement.Information about the polypeptide structure within gramicidin A. the reconstituted proteins and also the proteins in the natural biomembranes was obtained by examining the region of the infrared spectrum between 1600 and 1700 cm^?1 associated with the amide I and amide II bands. An examination of the infrared band frequencies of the different systems in this region leads to the conclusions: (1) that gramicidin A within a phospholipid bilayer structure probably has a single helix rather than a double helix structure; (2) that there are differences in band widths of the reconstituted Ca²⁺-ATPase and bacteriorhodopsin compared with the spectra of the corresponding sarcoplasmic reticulum and purple membrane; (3) different membrane proteins adopt different conformations as evinced by a comparison of the spectra of the sarcoplasmic reticulum and purple membrane; (4) the polypeptide arrangement in the purple membrane is mainly helical but the abnormal frequency of the amide I band suggests that some distortion of the helix occurs: and (5) the sarcoplasmic reticulum membrane contains unordered as well as α-helix polypeptide arrangements.     

Sedimentation and viscosity of bacteriophage T7 DNA in presence of CH3HgOH

The effects of increasing concentartions of methylmercuric hydroxide (CH₃HgOH) on the rate of sedimentation, S⁰, and intrinsic viscosity, [η], of T7 DNA have been studied at 20°C in 0.005, 0.05, and 0.5M Na₂SO₄, respectively, whereby each salt solvent conatined, in addition, 0.005M sodium borate, pH 9.18, as a buffer. Both S⁰ and [η] are independent of organomercurial concentration as long as DNA remains native. Denaturation, brought about by the complexing of CH₃HgOH with the polymer, produces large changes in S⁰ as wll as [η]. The sedimentation coefficient increases strongly with increasing oragnomercurial concentration once strand separation has occured. Experimental difficulties prevented measuring of [η] in the posttransition region. The data on S⁰ have been used, in combination with available information on the so-called density increment (?ρ/?c₂), to obtain information on the frictional properties of single-stranded and methylmercurated T7 DNA. The frictional coefficient, defined as f′₂ = M₂(?p/?c₂)/S⁰ηN_A, where M₂ is the molecular wieght of T7 DNA, c₂ is the concentration of DNA in g/ml of solution, η_r the realtive viscosity of the salt solvents, and N_A is Avogadro's number, was evaluated for all three salt media as a function of organomercurial concentration. f′₂ of native T7 DNA was found not to be sensitive to changes in ionic strngth; but f′₂ of single-stranded and methylmercurated T7 DNA varied strongly with salt concentration. Since f′₂ of single-stranded T7 DNA was barely affected by organomercurial concentration at a given ionic strength, it is concluded that the dramatic variations of S⁰ with pM (pM ≡ -log[CH₃HgOH]) observed in the posttransition zone reflect only changes in the thermodynamic interactions (“preferential interactions”) existing between DNA and the vatious other solution components, but not changes in the coil dimensions of the polymer.     

Beta-turns in bridged proline-containing cyclic peptide models

The synthesis, CD, ir spectroscopic, and conformational studies of a series of bridged cyclic peptides of the general formula, cyclo[NH-(CH₂)_n-CO-Gly-Pro-Y-Gly] (2a–d, Y = Gly or Ser(OBu^t), n = 4 or 2) is reported. As indicated by difference nuclear Overhauser enhancement and Fourier transform ir experiments, the tetrapeptide sequence of cyclo[NH-(CH₂)₄-CO-Gly-Pro-Gly-Gly] (2a) and cyclo[NH-(CH₂)₂-CO-Gly-Pro-Gly-Gly] (2b) adopts a 1 ← 4 hydrogenbonded type II β-turn conformation in solution, while cyclo[NH-(CH₂)₄-CO-Gly-Pro-Ser(OBu^t) -Gly] (2c) features a type I β-turn, fixed by 1 ← 4 and O^γ … NH intramolecular H bonds. In aqueous solution 2a and 2c show class B and class C CD spectra, respectively. This is the first case reported of a typical class C CD pattern in aqueous solution for a conformationally mobile system having a type I β-turn. Based on the comparison of the band intensities of the bridged models with those of linear and cyclic model systems reported earlier, a set of subspectra with reduced band intensities is suggested for use in the CD analysis of the conformation of polypeptides in solution.     

Changes of aliphatic C–H bonds in cyanobacteria during experimental thermal maturation in the presence or absence of silica as evaluated by FTIR microspectroscopy

Aliphatic C–H bonds are one of the major organic signatures detected in Proterozoic organic microfossils, and their origin is a topic of interest. To investigate the influence of the presence of silica on the thermal alteration of aliphatic C–H bonds in prokaryotic cells during diagenesis, cyanobacteria Synechocystis sp. PCC6803 were heated at temperatures of 250–450°C. Changes in the infrared (IR) signals were monitored by micro‐Fourier transform infrared (FTIR) spectroscopy. Micro‐FTIR shows that absorbances at 2,925 cm^?1 band (aliphatic CH₂) and 2,960 cm^?1 band (aliphatic CH₃) decrease during heating, indicating loss of the C–H bonds, which was delayed by the presence of silica. A theoretical approach using solid‐state kinetics indicates that the most probable process for the aliphatic C–H decrease is three‐dimensional diffusion of alteration products under both non‐embedded and silica‐embedded conditions. The extrapolation of the experimental results obtained at 250–450°C to lower temperatures implies that the rate constant for CH₃ (k_CH3) is similar to or lower than that for CH₂ (k_CH2; i.e., CH₃ decreases at a similar rate or more slowly than CH₂). The peak height ratio of 2,960 cm^?1 band (CH₃)/2,925 cm^?1 band (CH₂; R_3/2 values) either increased or remained constant during the heating. These results reveal that the presence of silica does affect the decreasing rate of the aliphatic C–H bonds in cyanobacteria during thermal maturation, but that it does not significantly decrease the R_3/2 values. Meanwhile, studies of microfossils suggest that the R_3/2 values of Proterozoic prokaryotic fossils from the Bitter Springs Group and Gunflint Formation have decreased during fossilization, which is inconsistent with the prediction from our experimental results that R_3/2 values did not decrease after silicification. Some process other than thermal degradation, possibly preservation of specific classes of biomolecules with low R_3/2 values, might have occurred during fossilization.     

Raman studies of conformational changes in model membrane systems

Laser Raman spectra of concentrated samples of phosphatidyl choline and phosphatidyl ethanolamine were taken at approximately 10° intervals over a temperature range of 90°–19°C. The spectral region from 30 to 3300 cm^?1 was investigated. Several new spectral features were discovered which are correlated to phospholipid liquid crystalline structure. It is shown that 1) frequency shifts occur in the $\text{PO}{}_2{}^{\mathrm{?}}$ symmetric stretch band which suggest a change in exposure of the PO₂ group to the solvent upon melting, 2) the frequency of the translational hydrocarbon mode around 150 cm^?1 appears to indicate the degree to which the hydrocarbon chain is extended, 3) the methyl and methylene stretch bands at 2890 and 2850 cm^?1 very clearly demonstrate hydrocarbon chain melting, and 4) the 720 cm^?1 band, previously assigned to the symmetric OPO diester stretch, appears to be due instead to the symmetric CN stretch of choline.     

Fatty acids,part X. Raman spectra of all dimethylene interrupted methyl cis,cis-octadecadienoates and octadecadiynoates

The Raman spectra of all the dimethylene interrupted methyl cis, cis-octadecadienoates and octadecadiynoates have been studied. The Raman band positions and their relative intensities for the ν(CC), ν(CC), ν(CO), ν(CH) and δ(CH₂) modes are recorded. The height intensity of the bands arising from ν(CC) relative to ν(CO) provides a means of determining the number of cis-ethylenic bonds in a mono-ester. In the acetylenic series, the intensity of the bands arising from ν(CC) relative to ν(CO) failed to indicate with certainty the number of acetylenic bonds in the mono-esters studied, due to the weak intensity of the band due to ν(CO). However a better correlation between the relative intensities of the ν(CC) and δ(CH₂) bands is established instead. An attempt to correlate the areas under the bands due to ν(CC), (CC), (CO) and δ(CH₂) failed to produce any significant results. The Raman spectra of the methyl octadec-cis-10-en-5-ynoate and methyl octadeca-5, 10-diynoate are also recorded.     

Changes of Raman scattering in the CU-stretching region during thermally induced unfolding of ribonuclease

Thermally induced unfolding of ribonuclease at low pH produces a large increase of Raman scattering intensity at ～ 2930cm^?1 (CH₃-stretching region). Comparisons of the CH₃-stretching spectra of various model compounds in the presence or absence of H₂O (²H₂O), indicate that the changes observed with ribonuclease arise from the insertion of previously buried, aliphatic amino acid residues into water.     

曼地亚红豆杉对甲醛胁迫的生理响应

以一年生曼地亚红豆杉(Taxus media cv.hicksii)扦插苗为材料,采用密闭箱静态熏气法,研究不同甲醛（CH₂O）浓度(0、5、10、20和40 mg·m^-3)和熏气时间（1、3、5、7 d）对曼地亚红豆杉的生理响应。结果显示:（1）在5~20 mg·m^-3CH₂O浓度下,曼地亚红豆杉叶片均无受害症状,在40 mg·m^-3CH₂O熏气1 d时,叶片开始出现受害症状,并随时间的延长逐渐加重;（2）随着CH₂O浓度的增加和熏气时间的延长,叶片MDA、Pro含量和相对电导率皆呈增加趋势,SS含量表现为先升后降,但仍显著高于对照;（3）在5 mg·m^-3CH₂O处理下,叶片SOD、CAT、PPO和GR作为第一道防线共同作用以清除过多的活性氧,其中PPO最为敏感;在10、20 mg·m^-3CH₂O处理下,SOD、POD、CAT、PPO、APX和GR共同作用加快对活性氧的清理;在40 mg·m^-3CH₂O浓度下,各酶的活性均受到抑制,其中APX、PPO和GR活性显著低于对照,而SOD、POD和CAT活性仍显著高于对照。研究表明,在中低CH₂O浓度（5~20 mg·m^-3）处理下,曼地亚红豆杉主要通过合成渗透调节物质和活性氧自由基的酶促清除机制共同作用来适应逆境,在40 mg·m^-3CH₂O浓度下,APX、PPO、GR活性受到显著抑制,细胞膜过氧化程度加剧,植物叶片受到伤害;在CH₂O浓度低于20 mg·m^-3时,曼地亚红豆杉通过自身的应激保护系统来维持正常的生理活动,表现出较强的CH₂O耐受性。     

Conformational properties of the sequential polyproline analogs poly(Pro-Aze-Pro) and poly(Aze-Pro-Aze)

The lack of the positive band at around 226 nm in the CD spectra of poly(prolyl-azetidine-2-carbonyl-proline) in trifluoroethanol and of poly(azetidine-2-carbonyl-prolyl-azetidine-2-carboxylic) acid in F₃EtOH and water, the hyperchromism of the absorption maximum at about 202 nm, and the extremely small intensity of the C^β-Pro, C^γ-Pro, and C^β-Aze signals for the cis peptide bonds in the ¹³C nmr spectrum of poly(Pro-Aze-Pro) in F₃EtOH indicate that both polyproline analogs exist as disordered chains in this solvent, the trans peptide group being maintained. The disordering of the chains is attributed to an increase in the accessible range of ψ due to the reduced dimensions of the square ring of L -azetidine-2-carboxylic acid residue relative to the pyrrolidine ring of proline and to strong interactions of the haloalcohol with the peptide groups of the chains.     

Conformational geometry and vibrational frequencies of nucleic acid chains.

Normal coordinate analysis of diethyl phosphate has been made, which predicts all observed Raman frequencies in the range 170–1300 cm^?1. The force constants from this calculation have been transferred to a vibrational calculation for a simplified model of the backbone of nucleic acids, which also involves the ? O? PO₂^?? O phosphate group and the ? C₅′? C₄′? C₃′? linkage of the ribose. The coordinates of these atoms are those recently given by Arnott and Hukins, which place the ribose ring of B-DNA in a C₃′-exo conformation. This simple polymer model appears to be able to describe adequately the frequency-dependent changes observed in the Raman spectra arising from the backbone vibrations of nucleic acid in going from the B- to A-form. The symmetric ? O? P? O? diester stretch increases in frequency from about 787 cm^?1 in the B-form to 807 cm^?1 in the A-form. The increased frequency characteristic of the A-form is due to the combining of the diester stretch with vibrations involving the C₅′, C₄′, and C₃′ nuclei. The frequency of the symmetric ? O? P? O? diester stretch is shown to be very dependent on the conformation of the ribose ring, indicating that in polynucleotides the ribose ring takes on one of two rigid conformations: C₃′-endo for A-form or C₃′-exo for B-form and “disordered” polynucleotides. The calculation lends confirmation to the atomic coordinates of Arnott and Hukins since the use of other geometries with the same force constants failed to give results in agreement with experimental evidence. The calculations also demonstrate the lowering effect of hydration on the anionic PO stretching frequencies. Experimental results show that the 814-cm^?1 band observed in the spectra of 5′GMP gel arises from a different vibrational mode than that of the 814-cm^?1 band of A-DNA.     

Conformational evaluation of labeled C3′‐O‐P‐13CH2‐O‐C4″ phosphonate internucleotide linkage,a phosphodiester isostere

Modified internucleotide linkage featuring the C3′‐O‐P‐CH₂‐O‐C4″ phosphonate grouping as an isosteric alternative to the phosphodiester C3′‐O‐P‐O‐CH₂‐C4″ bond was studied in order to learn more on its stereochemical arrangement, which we showed earlier to be of prime importance for the properties of the respective oligonucleotide analogues. Two approaches were pursued: First, the attempt to prepare the model dinucleoside phosphonate with ¹³C‐labeled CH₂ group present in the modified internucleotide linkage that would allow for a more detailed evaluation of the linkage conformation by NMR spectroscopy. Second, the use of ab initio calculations along with molecular dynamics (MD) simulations in order to observe the most populated conformations and specify main structural elements governing the conformational preferences. To deal with the former aim, a novel synthesis of key labeled reagent (CH₃O)₂P(O)¹³CH₂OH for dimer preparation had to be elaborated using aqueous ¹³C‐formaldehyde. The results from both approaches were compared and found consistent. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 514–529, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com