A Brillouin scattering study of the hydration of Li- and Na-DNA films

We have used Brillouin spectroscopy to study the velocities and attenuation of acoustic phonons in wet-spun films of Na-DNA and Li-DNA as a function of the degree of hydration at room temperature. Our data for the longitudinal acoustic (LA) phonon velocity vs water content display several interesting features and reveal effects that we can model at the atomic level as interhelical bond softening and relaxation of the hydration shell. The model for interhelical softening makes use of other physical parameters of these films, which we have determined by gravimetric, x-ray, and optical microscopy studies. We extract intrinsic elastic constants for hydrated Na-DNA molecules of c₁₁ ? 8.0 × 10¹⁰ dynes/cm² and c₃₃ ? 5.7 × 10¹⁰ dynes/cm², which corresponds to a Young's modulus, E ? 1.1 × 10¹⁰ dynes/cm² (with Poisson's ratio, σ = 0.44). The negative velocity anisotropy of the LA phonons indicates that neighboring DNA molecules are held together by strong interhelical bonds in the solid state. The LA phonon attenuation data can be understood by the relaxational model in which the acoustic phonon is coupled to a relaxation mode of the water molecules. Na-DNA undergoes the A to B phase transition at a relative humidity (rh) of 92% while Li-DNA (which remains in the B form in this range) decrystallizes at an rh of 84%. We find that our Brillouin results for Na- and Li-DNA are remarkably similar, indicating that the A to B phase transition does not play an important role in determining the acoustic properties of these two types of DNA.     

1H-NMR study of GM2 ganglioside: evidence that an interresidue amide-carboxyl hydrogen bond contributes to stabilization of a preferred conformation

Several properties of the exchangeable amide protons of the ganglioside G_M2 were studied in detail by¹H-NMR spectroscopy in fully deuterated dimethylsulfoxide [²H₆]DMSO/2% H₂O, and compared with data obtained for the simpler constituent glycosphingolipids G_A2 and G_M3. In addition to chemical shifts,³ J _2,HN coupling constants, and temperature shift coefficients, the kinetics of NH/²H chemical exchange were examined by following the disappearance of the amide resonances in [²H₆]DMSO/2%²H₂O. The results included observation of an increase in half-life of theN-acetylgalactosamine acetamido HN by more than an order of magnitude in G_M2 compared to G_A2, attributable to the presence of the additionalN-acetylneuraminic acid residue. Additional one-dimensional dipolar cross relaxation experiments were also performed on nonexchangeable protons of G_M2. The results of all of these experiments support a three-dimensional model for the terminal trisaccharide in which a hydrogen bond is formed between theN-acetylgalactosamine acetamido NH and theN-acetylneuraminic acid carboxyl group. The interaction is proposed to be of the -acceptor type, a possibility which has not yet been explored in the literature on carbohydrates. The proposed model is discussed in comparison with that of Sabesanet al. (1984,Can J Chem 62: 1034–45), and the models of G_M1 proposed more recently by Acquottiet al. (1990,J Am Chem Soc 112:7772–8) and Scarsdaleet al. (1990,Biochemistry 29:9843–55).     

1H-NMR study of the interaction of daunomycin with B-DNA helices of methylated oligodeoxynucleotides.

The interaction of daunomycin with B-DNA double helices of several methylated deoxynucleotides, d(C-G-m5C-G), d(m5C-G-C-G), d(C-G-m5C-G-C-G) and d(m5C-G-C-G-m5C-G) in solution was investigated by 1H-NMR spectroscopy at 500 MHz. At low temperature (t less than 20 degrees C for the tetramer and t less than 40 degrees C for the hexamers), several daunomycin-DNA complexes were observed in slow exchange with the drug-free DNA duplexes. The presence of daunomycin in a self-complementary double helix cancels the conformational symmetry of the two strands; the proton signals can split into several others owing to the difference between free and intercalated duplexes and to the many possible intercalation sites in a duplex (three for a tetramer, five for an hexamer). A model relating the chemical shifts of splitted proton signals to the various intercalated duplex conformations was given. The results show that one daunomycin molecule is associated with one duplex and that it can enter any intercalation site with equal probability; no side-effects were observed even for very short helices (of a tetramer). In the case of d(C-G-m5C-G) the association constant and the dissociation and association rates of the intercalated complex were evaluated.     

A new conformation-specific infrared band of A-DNA in films.

A band at 1185 cm-1 occurs in the infrared spectra of nucleic acids in their A-type conformation which has been reproduced in the literature, too. The absorbance of this band is proportional to the fraction of the A form of DNA samples containing a mixture of different forms. The 1185 cm-1 band has been assigned tentatively to a vibration of the sugar-phosphate backbone with a fairly high contribution from the sugar moiety. Drastic dehydration of the DNA films is accompanied by a continuous intensity decrease of the 1185 cm-1 band indicating a collapse of the A form.     

Vibrational modes of A-DNA,B-DNA,and A-RNA backbones: An application of a green-function refinement procedure

Normal vibrational analysis was carried out for DNA molecules in both A and B conformations as well as for A-RNA. A simplified backbone model was examined and expanded to include the backbone phosphate-group and the ribose ring. We applied the new force-constant refinement procedure discussed in the preceeding paper [Van Zandt, L. L., Lu, K.-C. & Prohofsky, E. W. (1977) Biopolymers, 16 , 2481–90] to fit some observed frequencies in the Raman spectra for all three nucleic acids with the same set of force constants. The results indicate that the observed frequency shift can be attributed to the conformational change solely. We ignored the second-order differences in force constants for the different geometries. The agreement between the observed and calculated frequencies derived from the final refined set of force constants is good and apparently justifies this assumption. Two modes previously assigned to the symmetric diester O-P-O stretch and the symmetric dioxy O‥P‥O stretch are actually fitted. They are mainly backbone phosphate-group modes. The refined ribose-ring force-constants were transferred to the calculation of the vibrational spectrum of tetrahydrofuran. The overall agreement is again good. We discuss these calculations and the resulting normal modes. We also discuss the application of the Green-function refinement scheme and several strategies adopted to bias the convergence of the procedure.     

2H-NMR comparative study of phosphocholine group conformation in bilayers composed of diacyl and dialkyl phosphatidylcholines

Model membranes formed from 1,2-dihexadecyl-, 1,2-dipalmitoyl-, 1,2-ditetradecyl- or 1,2-dimyristoyl-rac-glycero-3-phosphocholine, deuterium-labelled at choline groups, in an excess of water were compared using 2H-NMR spectroscopy. The dynamics and conformation of the labelled choline segments were estimated based on spin-lattice relaxation time and residual quadrupole splittings. The trimethylammonium group of dialkyl phosphatidylcholine was shown to be more distant from the bilayer surface as compared with that of the diacyl analogues.     

Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure

Molecular dynamics (MD) computer simulations have been carried out on four systems that correspond to an infinite array of parallel ordered B-DNA, mimicking the state in oriented DNA fibers and also being relevant for crystals of B-DNA oligonucleotides. The systems were all comprised of a periodical hexagonal cell with three identical DNA decamers, 15 water molecules per nucleotide, and counterions balancing the DNA charges. The sequence of the double helical DNA decamer was d(5'-ATGCAGTCAG)xd(5'-TGACTGCATC). The counterions were the two natural polyamines spermidine(3+) (Spd(3+)) and putrescine(2+) (Put(2+)), the synthetic polyamine diaminopropane(2+) (DAP(2+)), and the simple monovalent cation Na(+). This work compares the specific structures of the polyamine- and Na-DNA systems and how they are affected by counterion interactions. It also describes sequence-specific hydration and interaction of the cations with DNA. The local DNA structure is dependent on the nature of the counterion. Even the very similar polyamines, Put(2+) and DAP(2+), show clear differences in binding to DNA and in effect on hydration and local structure. Generally, the polyamines disorder the hydration of the DNA around their binding sites whereas Na(+) being bound to DNA attracts and organizes water in its vicinity. Cation binding at the selected sites in the minor and in the major groove is compared for the different polyamines and Na(+). We conclude that the synthetic polyamine (DAP(2+)) binds specifically to several structural and sequence-specific motifs on B-DNA, unlike the natural polyamines, Spd(3+) and Put(2+). This specificity of DAP(2+) compared to the more dynamic behavior of Spd(3+) and Put(2+) may explain why the latter polyamines are naturally occurring in cells.     

A 1H-NMR study of the solution conformation of secretin. Resonance assignment and secondary structure

The solution conformation of the 27 residue polypeptide hormone secretin has been investigated by 1H-NMR spectroscopy under conditions where it adopts a fully ordered structure as judged by circular dichroism spectroscopy, namely in an aqueous solution of 40% (v/v) trifluoroethanol. Using a combination of two-dimensional NMR techniques the 1H-NMR spectrum of secretin is completely assigned and its secondary structure is determined from a qualitative interpretation of the nuclear Overhauser enhancement data. It is shown that under these conditions secretin adopts a conformation consisting of an N-terminal irregular strand (residues 1-6) followed by two helices (residues 7-13 and 17-25) connected by a 'half-turn' (residues 14-16); the last two residues (26 and 27) are again irregular. This conformation is shown to be very similar to that of glucagon in perdeuterated dodecylphosphocholine micelles and to that of the active 1-29 fragment of growth hormone releasing factor in 30% (v/v) trifluoroethanol:     

Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics.

One of the truly challenging problems for molecular dynamics (MD) simulations is demonstrating that the trajectories can sample not only in the vicinity of an experimentally determined structure, but also that the trajectories can find the correct experimental structure starting from some other structure. Frequently these transitions to the correct structure require that the simulations overcome energetic barriers to conformational change. Here we present unrestrained molecular dynamics simulations of the DNA analogs of the RNA 5'-GGACUUCGGUCC-3' hairpin tetraloop. In one simulation we have used deoxyuracil residues, and in the other we have used the native DNA deoxythymine residues. We demonstrate that, on a nanosecond time scale, MD is able to simulate the transitions of both of the A-DNA stems to B-DNA stems within the constraints imposed by the four-base loop that caps the helix. These results suggest that we are now in a position to use MD to address the nature of sequence-dependent structural effects in nonduplex DNA structures.     

Farnesol-DMPC phase behaviour: a (2)H-NMR study

Involved in a number of diverse metabolic and functional contexts, farnesol is a central component of the mevalonate pathway, post-translationally attaches to proteins, and affects a number of other membrane-associated events. Despite farnesol's biological implications, a detailed analysis of how farnesol affects the physical properties and phase behaviour of lipid membranes is lacking. As (2)H-NMR spectra are sensitive to molecular motions and acyl chain orientation, they can be used to measure the degree of molecular order present in the system. Also, since the (2)H-NMR spectra of fluid and gel phase lipids are very different, they are sensitive probes of membrane phase equilibrium and can be used to determine fluid-gel phase boundaries. In this study, dimyristoyl phosphatidylcholine-d(54) (DMPC-d(54)) bilayers containing varying concentrations of trans-trans farnesol (2.5-20.0 mol%) are investigated over a range of temperatures (8-30 degrees C). Analysis of these spectra has led to the construction of a farnesol-DMPC-d(54) temperature-composition plot. We show that increasing concentrations of farnesol induce a decrease in the fluid-gel phase transition temperature and promote fluid-gel coexistence. Interestingly, farnesol does not seem to affect the quadrupolar splittings (Delta v(Q)) in the fluid phase, i.e., the organization of farnesol within the bilayer and its interaction with phospholipids does not appreciably influence acyl chain order in the fluid phase.     

Ordered water structure around a B-DNA dodecamer: A quantitative study

The crystal structure of the double-helical B-DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved and refined independently in three forms: (1) the parent sequence at room temperature; (2) the same sequence at 16 K; and (3) the 9-bromo variant C-G-C-G-A-A-T-T^BrC-G-C-G at 7 °C in 60% (v/v) 2-methyl-2.4-pentanediol. The latter two structures show extensive hydration along the phosphate backbone, a feature that was invisible in the native structure because of high temperature factors (indicating thermal or static disorder) of the backbone atoms. Sixty-five solvent peaks are associated with the phosphate backbone, or an average of three per phosphate group. Nineteen other molecules form a first shell of hydration to base edge N and O atoms within the major groove, and 36 more are found in upper hydration layers. The latter tend to occur in strings or clusters spanning the major groove from one phosphate group to another. A single spermine molecule also spans the major groove. In the minor groove, the zig-zag spine of hydration that we believe to be principally responsible for stabilizing the B form of DNA is found in all three structures. Upper level hydration in the minor groove is relatively sparse, and consists mainly of strings of water molecules extending across the groove, with few contacts to the spine below. Sugar O-1′ atoms are closely associated with water molecules, but these are chiefly molecules in the spine, so the association may reflect the geometry of the minor groove rather than any intrinsic attraction of O-1′ atoms for hydration. The phosphate O-3′ and O-5′ atoms within the backbone chain are least hydrated of all, although no physical or steric impediment seems to exist that would deny access to these oxygen atoms by water molecules.     

A 1H-NMR study of the solution conformation of cyclo(GRGDSPA): conformational effects on the physiological activity.

Solution conformations of cyclo(GRGDSPA) have been analyzed by the use of two-dimensional proton nuclear magnetic resonance spectroscopy and the dynamical simulated annealing calculation. It has been shown that the RGDS segment in cyclo(GRGDSPA) takes a beta-turn conformation. We have concluded that this beta-turn conformation is essential for the physiological activity of cyclo(GRGDSPA).     

Head-group conformation in phospholipids: a phosphorus-31 nuclear magnetic resonance study of oriented monodomain dipalmitoylphosphatidylcholine bilayers

Angular-dependent 31P NMR spectra of oriented biaxial monodomain DPPC.H2O multilayers are employed to study head-group conformation in this phospholipid. The results indicate that the O-P-O plane of the phosphate, where the O's are the nonesterified oxygens of the phosphodiester, is tilted at 47 +/- 5 degrees with respect to the bilayer normal. This PO4 orientation could result in the choline moiety being extended parallel to the bilayer plane, and it will explain the breadth of the axially symmetric 31P powder spectrum observed for DPPC in excess water. This work is the first direct observation of this conformation for lecithins and it illustrates the utility of high-resolution solid-state NMR in structural studies of disordered systems.     

Phospholipid/cholesterol membranes containing n-alkanols: a 2H-NMR study

The influences of 1-octanol and 1-decanol on aqueous multilamellar dispersions of 1-hexadecanoyl(octadecanoyl)-2-[2H31]hexadecanoyl-sn-glycero -3-phosphorylcholine (PC-d31)/cholesterol (3:1) have been examined using 2H-NMR. The gel to liquid crystalline phase transition of the PC-d31/cholesterol dispersion is modulated by the addition of 1-alkanol, which reduces the onset temperature and increases the width of the transition. 1-Octanol has a greater effect on the transition onset and completion temperatures than does 1-decanol, as determined from analysis of the temperature-dependent 2H-NMR spectra. 2H-NMR C-2H bond order parameters as a function of phospholipid acyl chain position at 60 degrees C, where all dispersions are fully liquid crystalline, have been calculated from the depaked spectra. 1-Decanol reduces the phospholipid order by only 2%. This can be attributed to the lower effective cholesterol concentration in the 1-alkanol/PC-d31/cholesterol dispersions. 1-Octanol, however, reduces the phospholipid order by 10% at 60 degrees C. Correlations between the effects of 1-octanol and 1-decanol on phospholipid order parameters and phospholipid/cholesterol phase transitions are discussed.     

Interactions of the local anesthetic tetracaine with glyceroglycolipid bilayers: a 2H-NMR study

We have examined the effects of the local anesthetic tetracaine on the orientational and dynamic properties of glycolipid model membranes. We elected to study the interactions of tetracaine with the pure glycolipid 1,2-di-O-tetradecyl-3-O-(beta-D-glucopyranosyl)-sn-glycerol (beta-DTGL) and a mixture of beta-DTGL (20 mol%) in dimyristoylphosphatidylcholine (DMPC) by deuterium NMR (2H-NMR) spectroscopy. 2H-NMR spectra of beta-DTGL have been measured as a function of temperature in the presence of both the charged (pH 5.5) and uncharged forms (pH 9.5) of tetracaine. The results indicate that the anesthetic induces the formation of non-lamellar phases. Specifically, the incorporation of uncharged tetracaine results in the formation of a hexagonal phase which is stable from 52 to 60 degrees C. At lower pH, the spectrum at 52 degrees C is very reminescent of that of the beta-glucolipid alone in a bilayer environment, while as the temperature is elevated to 60 degrees C, a transition from a spectrum indicative of axial symmetry to one due to nearly isotropic motion or symmetry occurs, which may result from the formation of a cubic phase. Although it leads to an alteration in the phase behavior, the presence of tetracaine does not induce large changes in the headgroup orientation of beta-DTGL. In contrast to the pure glycolipid situation, the interaction of tetracaine with beta-DTGL (20 mol%) in DMPC does not trigger the formation of non-lamellar phases, but leads to a slight reduction in molecular ordering. The presence of the charged form of the local anesthetic near the aqueous interface of the bilayer appears to induce a small change in the conformation about the C2-C3 bond of the glycerol backbone of beta-DTGL in the mixed lipid system. Thus, the major influence of the local anesthetic on glycolipids is a change in the stability of the lamellar phase, facilitating conversion to phases with hexagonal or isotropic environments for the lipid molecules.     

A 2H-NMR study of the DNA hydration water in solid Li-DNA assembles

High-resolution ²H-nmr is employed to monitor the D₂O in hydrated solids of Li-DNA prepared from solution by three different methods: lyophilization, slow evaporation of the water, and wet spinning in alcohol. From the spectral shapes and spin–spin relaxation measurements, the DNA in the lyophilized samples is found to be locally ordered with a domain size of ～ 0.4 μm. Much longer range macrosopic ordering is found in samples prepared by slow evaporation of the water. Here the DNA spontaneously assembles into a structure that is probably cholesteric, in which the pitch axis is perpendicular to the plane on which the DNA dried. The wet-spinning method produces macroscopically, uniaxially oriented DNA molecules with a maximum helix axis disorder of 12°. To aid in the comparison between calculated and experimental line shapes, a two-dimensional technique is employed to separate the contributions to the line width arising from DNA static disorder, magnetic inhomogeneities, and spin–spin relaxation.     

Study of bradykinin conformation in a dimethylsulfoxide solution by two-dimensional 1H-NMR spectroscopy

The role of charged groups of the nonapeptide bradykinin in stabilization of its spatial structure in dimethyl sulfoxide solution was investigated. The signal assignment in the 1H-NMR spectra was achieved by means of two dimensional correlated spectroscopy (COSY) and nuclear Overhauser enhancement spectroscopy (NOESY). The changes in the NH and C alpha H proton chemical shifts of the Arg1 and Arg9 residues, variations both in temperature coefficients of chemical shifts of NH-resonances and coupling constants, as well as the appearance of additional NOE cross-peaks in NOESY spectra for d alpha N and d beta N 1H-1H distances were revealed by comparing the NMR spectra for two states--with the protonated C-terminal carboxyl group and deprotonated one. The experimental results are in agreement with the assumption that the conformation of the peptide in (CD3)2SO is stabilized by electrostatic interaction between the oppositely charged N- and C-terminal groups. The conformation with deprotonated alpha-carboxyl group is characterized by two beta-turns in the sequences Pro2-Pro-Gly-Phe5 and Ser6-Pro-Phe-Arg9.     

The interaction of n-alkanols with lipid bilayer membranes: a 2H-NMR study

The interaction of eight n-alkanols with bilayers of dimyristoylphosphatidylcholine (DMPC) has been studied by deuterium nuclear magnetic resonance (2H-NMR). At comparable temperatures and concentrations of solute in the bilayer, order parameters measured at the 1-methylene segment of the n-alkanols show a maximum for n-dodecanol. For both n-dodecanol and n-tetradecanol, orientational ordering shows a maximum at the C-4 to C-7 methylene segments, with labels at both ends of the n-alkanol exhibiting reduced order. These observations are consistent with earlier findings for n-octanol and n-decanol. Unlike the longer chain n-alkanols, ordering in n-butanol decreases from the hydroxyl group end to the methyl group end of the molecule. Orientational ordering at nine inequivalent sites in DMPC, has also been measured as a function of temperature, for bilayers containing n-butanol, n-octanol, n-dodecanol and n-tetradecanol. At the 3R,S sites on the glycerol backbone, for comparable temperatures and solute concentrations, n-butanol produces a larger disordering than the other n-alkanols. This result probably reflects the greater fraction of time spent by the hydroxyl group of n-butanol in the vicinity of the lipid polar head group compared with the hydroxyl group in longer chain n-alkanols. It was found that n-octanol orders the acyl chains of DMPC, unlike n-butanol which disorders them, and the longer chain n-alkanols which have little effect. Within experimental error, the effect of n-dodecanol on order at all sites in DMPC is the same as n-tetradecanol. The influence of n-alkanols on DMPC ordering at twelve sites has been compared with that of cholesterol which is shown to interact with DMPC bilayers in a distinctly different manner from the n-alkanols.     

Pilin C-terminal peptide binds asialo-GM1 in liposomes: a 2H-NMR study.

Wideline 2H-NMR observations are described demonstrating the interaction of a synthetic peptide (PAK), representing residues 128-144 of the binding domain of pilin surface protein from Pseudomonas aeruginosa, with a complex glycosphingolipid thought to be its natural receptor. The receptor glycolipid (asialo-GM1) carried 2H probe nuclei on the terminal and next-to-terminal carbohydrate residues and was present as a minor component in fluid phosphatidylcholine liposomes. The peptide induced spectral changes that could be understood as arising from receptor motional changes, without receptor immobilization on the NMR time scale of 10(4) s-1. Spectral effects were reversed by reduction of the single peptide disulfide bond--a structural feature previously shown to be a determinant of PAK conformation (Campbell AP, McInnes C, Hodges RS, Sykes BD. 1995. Biochemistry 34:16255-16268). This is the first demonstration of PAK interaction with its epithelial cell receptor in liposomes.