Study by (23)Na-NMR, (1)H-NMR, and ultraviolet spectroscopy of the thermal stability of an 11-basepair oligonucleotide

23Na-NMR, (1)H-NMR, and ultraviolet (UV) spectroscopy have been used to study the thermal stability of the double helix structure of an 11-basepair oligonucleotide. The denaturation curves obtained by (23)Na-NMR and UV are analyzed using a two-state model. The melting temperature and DeltaH(0) obtained are identical within experimental error, suggesting that modifications in the ionic atmosphere, probed by (23)Na-NMR, and the modifications in the basepair stacking, probed by UV, occur at the same temperature. Additional dynamical information on the denaturation process has been obtained by (1)H-NMR: slow exchange is observed between the thymine methyl resonances, and the disappearance of imino protons shows that a single basepair opening does not contribute significantly to proton exchange.     

Differential scanning calorimetric study of the effect of intercalators and other kinds of DNA-binding drugs on the stepwise melting of plasmid DNA.

The effect of intercalating drugs (the anthracycline group of antibiotics, ethidium bromide, actinomycin D) on stepwise melting of DNA was studied by differential scanning calorimetry (DSC). The DSC DNA melting profile of plasmid pJL3-TB5 DNA (5277 base-pairs in length) consists of seven peaks, and all the intercalators caused shifting of these peaks, particularly those formed at the high temperature ranges, to the higher temperature ranges in a characteristic manner depending upon the binding strength of the drug. The analysis of the anthracycline group of antibiotics, such as aclacinomycin A, daunomycin, adriamycin and pyrarubicin, indicates that the difference in binding is due to the sugar moiety at position O-7 of the chromophore in these antibiotics. Analysis on the basis of the helix-coil transition theory suggests that the anthracycline group of antibiotics interact preferentially with the 5'-CG-3' sequences. The effect of various DNA-binding drugs other than intercalators on stepwise melting of DNA was then studied by DSC. The representative drugs examined were distamycin A, peplomycin, cis-dichlorodiamine-platinum(II) (cis-DDP or cis-Platin) and mitomycin C, which differ in their mode of interaction with DNA; namely, minor groove binding, strand cleavage and intrastrand or interstrand cross-linking. Distamycin A caused shifting of the DSC peaks at the low temperature ranges to a higher temperature range, whereas peplomycin and cis-DDP caused shifting of all the DSC peaks to form a broad peak at a lower temperature range, suggesting that the DSC DNA melting profiles are affected in a characteristic manner depending upon the interaction mode of the drug.     

A scanning calorimetric study of natural DNA and antitumoral anthracycline antibiotic-DNA complexes

Thermal denaturation of natural DNA in the absence and presence of antitumor anthracycline antibiotics has been studied by adiabatic differential scanning calorimetry. The helix-coil transition is operationally irreversible as measured by DSC. Both the melting temperature and the overall molar transition enthalpy of the DNA samples was dependent on the percentage of GC base pairs. Calorimetric traces of anthracycline-DNA complexes have qualitatively similar features and the significance of this characteristic is discussed. The unsaturated drug-DNA complex melts through complex thermal transitions with one broad endotherm in the same temperature region as free DNA and the other at a higher temperature which is rf (mol ligand per mol DNA in base pairs) value dependent. Antibiotic binding at concentrations close to saturating conditions (rf = 0.2) reverts the melting range to a value near to its original one and increases the thermal stability of the duplex structure by around 30 degrees C. In addition, the calorimetric enthalpy is increased by between 64% and 150%, depending on which ligand was used.     

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.     

The diversity of the liquid ordered (Lo) phase of phosphatidylcholine/cholesterol membranes: a variable temperature multinuclear solid-state NMR and x-ray diffraction study

To investigate the properties of a pure liquid ordered (Lo) phase in a model membrane system, a series of saturated phosphatidylcholines combined with cholesterol were examined by variable temperature multinuclear (1H, 2H, 13C, 31P) solid-state NMR spectroscopy and x-ray scattering. Compositions with cholesterol concentrations>or=40 mol %, well within the Lo phase region, are shown to exhibit changes in properties as a function of temperature and cholesterol content. The 2H-NMR data of both cholesterol and phospholipids were used to more accurately map the Lo phase boundary. It has been established that the gel-Lo phase coexistence extends to 60 mol % cholesterol and a modified phase diagram is presented. Combined 1H-, 2H-, 13C-NMR, and x-ray scattering data indicate that there are large changes within the Lo phase region, in particular, 1H-magic angle spinning NMR and wide-angle x-ray scattering were used to examine the in-plane intermolecular spacing, which approaches that of a fluid Lalpha phase at high temperature and high cholesterol concentrations. Although it is well known for cholesterol to broaden the gel-to-fluid transition temperature, we have observed, from the 13C magic angle spinning NMR data, that the glycerol region can still undergo a "melting", though this is broadened with increasing cholesterol content and changes with phospholipid chain length. Also from 2H-NMR order parameter data it was observed that the effect of temperature on chain length became smaller with increasing cholesterol content. Finally, from the cholesterol order parameter, it has been previously suggested that it is possible to determine the degree to which cholesterol associates with different phospholipids. However, we have found that by taking into account the relative temperature above the phase boundary this relationship may not be correct.     

Studies on the interaction of human erythrocyte band 3 with membrane lipids using deuterium nuclear magnetic resonance and differential scanning calorimetry

Human erythrocyte band 3, reconstituted into large unilamellar phospholipid vesicles, has been used as a model system for studying the interactions between membrane lipids and large transmembrane glycoproteins. Both 2H-nuclear magnetic resonance (2H-NMR) and differential scanning calorimetric techniques have been used to probe dimyristoylphosphatidylcholine-band 3 interactions over the temperature range 4-32 degrees C. Analysis of 2H-NMR spectra allowed the assignment of liquid crystal, gel phase and two-phase regions for several protein/lipid mole fractions in the range (1-20) X 10(-4). Sample size was limited by the amount of available glycoprotein and this precluded exact determination of the phase boundaries for this system. The sharp discontinuity in the spectral first moment, M1, seen at the phase transition of the pure phospholipid is progressively diminished by addition of protein, and at the highest protein concentration the first moment varies smoothly between the two phases. For T greater than 26 degrees C or less than 16 degrees C, the moments are relatively insensitive to protein concentration, while between 20 and 26 degrees C the moments increase with protein concentration up to the boundary of the two-phase region. Beyond this boundary, they remain constant or decrease slightly with increasing amount of protein. A preliminary phase diagram for band 3 in this lipid system is presented, based on 2H-NMR data. Differential scanning calorimetry (DSC) showed that addition of glycoprotein dramatically alters the scan shape and tends to extend the coexistence of two phases to higher temperatures.     

Author index to volume 175

500 MHz ¹H-NMR and NOE measurements of d(GGATCC) and d(GGm⁶ATCC) show that both oligo-nucleotides assume a B-DNA conformation at low temperature. Around the melting temperature, however, the single and double strands of the N-methylated form are in slow exchange on the NMR time scale. The preferred conformation of the adenine methyl group, cis to N¹, retards base pairing and also destabilizes the double helix.     

Deuterium nuclear magnetic resonance study of the interaction of branched chain compounds (phytanic acid, phytol) with a phospholipid model membrane

Deuterium nuclear magnetic resonance (2H-NMR) spectra have been determined for 50 wt% aqueous dispersions of 1-palmitoyl(stearoyl)-2-[2H31]palmitoyl-sn-glycero-3-phosphocho lin e (PC-d31) containing 20 mol% of the isoprenoid compounds phytol or phytanic acid over the temperature range -5-55 degrees C. Concentration effects of the isoprenoid compounds are also reported. First moments (M1) and order parameters were calculated from the spectra. 20 Mol% of either branched chain compound causes an approximate 9% increase in the mean order parameter SCD. Significant effects are seen on the PC-d31 phase behavior. 20 Mol% of either branched chain compound causes the gel to liquid crystalline onset temperature (Ts) to drop to 28 degrees C from 38 degrees C for PC-d31 alone, as seen from the temperature dependent M1 values. The melting range ([Tl--Ts]) is congruent to 1.5 degrees C for PC-d31 and congruent to 11 degrees C for PC-d31 containing 20 mol% of the branched chain compounds. This is in direct contrast to their straight chain analogues, hexadecanol and palmitic acid, which have been shown to elevate the phase transition temperature. The isoprenoid compounds cause significant disruption of the gel phase, forcing nearest neighbor phospholipid chains apart. Transverse relaxation times (T2e, the time constant for decay of the quandrupolar echo) have been determined over the temperature range -5-50 degrees C. Possible explanation for the effect of the isoprenoid compounds on the dynamic structure of phospholipids in the bilayer are proffered.     

Role of peptide structure in lipid-peptide interactions: nuclear magnetic resonance study of the interaction of pentagastrin and [Arg4]pentagastrin with dimyristoylphosphatidylcholine

Complexes formed between dimyristoylphosphatidylcholine (DMPC) and the peptide pentagastrin or [Arg4]pentagastrin were examined by 31P- and 2H-NMR. The cationic [Arg4]pentagastrin produces larger changes in the lipid NMR spectra than does the anionic pentagastrin. 31P-NMR spectra of DMPC with [Arg4]pentagastrin below the phase transition exhibits two components one of which is motionally restricted compared with the pure lipid. The exchange between these two lipid domains is slow on the millisecond time scale. The interactions between this peptide and phospholipid are diminished above the melting temperature of the complex. The 2H-NMR spectra of DMPC which had been labelled in a choline methylene group is also affected more by the [Arg4]pentagastrin than by pentagastrin. In the presence of [Arg4]pentagastrin, even above the lipid phase transition, an additional doublet with a smaller quadrupole splitting is observed. These results clearly demonstrate the importance of peptide charge in determining the effects of peptides on lipid bilayers.     

Thermal behaviour,phase diagram,and spectroscopic properties of rac-indobufen and its enantiomers

The binary phase diagram of the enantiomers of indobufen, 1 (Ibustrin), an antithrombotic drug, has been investigated by differential scanning calorimetry (DSC); 1 is a racemic compound (racemate) with melting point lower than that of the enantiomers. Its thermal behaviour (DSC) has been examined and is discussed in comparison with other physical methods (IR spectroscopy and X-ray powder diffraction). Absolute configuration has been assigned to the enantiomers by ¹H-NMR correlations. © 1995 Wiley-Liss, Inc.     

Assignments of the iminoproton resonances of Bombyx mori tRNA(UCCGly) and the comparison of its structure and stability with those of tRNA(GCCGly)

Most of the iminoproton resonances in the 1H-NMR spectrum of Bombyx mori tRNA(UCCGly) have been assigned by the sequential NOEs. Any peak which indicates the presence of the tertiary GC base pair between the D and T loops could not be detected. The effects of temperature and the addition of magnesium ions and spermine on the 1H-NMR spectrum of this tRNA were examined. From the temperature change, it was found that the acceptor stem and the D stem in Bombyx mori tRNA(UCCGly) are equally stable even in the absence of magnesium, which is different from tRNA(GCCGly) where the D stem is not so stable.     

The ionic strength dependence of the cooperativity factor for DNA melting

The melting temperature for the d(AT)24.d(AT)24 stretch, located inside the DNA helix and terminally, have been determined in a wide range of ionic strength values (0.01 - 1 M Na+). The cooperativity factor was calculated from the shifts in the melting temperature of the stretch due to its different boundary conditions. With the sodium concentration decreasing from 1 M to 0.01 M the cooperativity factor dropped by three orders of magnitude, its change being less marked at high than at low ionic strength.     

A bunch-oligonucleotide forming stable monomolecular quadruplex containing a T-tetrad

The chemical synthesis of bunch-ODN I and II prone to form quadruplex structures containing G-and T-tetrads has been reported. Structural studies were performed by 1H-NMR and CD melting experiments.     

1H-NMR investigation of the interaction of the amino terminal domain of the LexA repressor with a synthetic half-operator.

A synthetic half-operator DNA-duplex, d(GCTACTGTATGT), containing a portion of the proposed recognition sequence (CTGT) of several "SOS" genes, has been synthesized. The dodecamer has been characterized through 1H-NMR spectroscopy. Complete assignment of exchangeable hydrogen bonded imino protons has been achieved by applying 1D NOE techniques and an analysis of the temperature dependence of the chemical shifts. In order to determine the specific role of the CTGT consensus sequence in the overall recognition process, the oligonucleotide duplex has been titrated with the amino terminal DNA binding domain of the LexA repressor. The observation of substantial changes of 1H-NMR chemical shifts in the imino proton region upon interaction with the protein strongly suggests that the protein binds specifically to the operator DNA. The largest deviations of 1H-NMR chemical shifts upon protein binding have been observed for protons assigned to the CTGT segment, thus strongly suggesting a direct involvement of this sequence in the binding process. At high potassium chloride concentrations the 1H-NMR chemical shift deviations are reverted which is consistent with the known drop in the affinity constant of LexA for operator DNA at high salt concentrations.     

Interaction between aromatic antibiotics and vitamins: 1H NMR analysis of the heteroassociation of nicotinamide and anthracycline antitumor antibiotics

The interaction between anthracycline antitumor antibiotics daunomycin and novatrone and the vitamin nicotinamide has been investigated by one- and two-dimensional 1H NMR spectroscopy (500 MHz). Due to significant differences in structures of the chromophores of interacting molecules, a two-site heteroassociation model has been developed, allowing the arrangement of one and two nicotinamide molecules on the chromophore of the antibiotic. The equilibrium association constant, thermodynamical parameters (deltaH, deltaS) of the heteroassociation of nicotinamide with daunomycin and novatrone and the induced proton chemical shifts in the heterocomplexes have been determined from the concentration and temperature dependences of proton chemical shifts of interacting molecules. The most favorable structures of 1:1 nicotinamide--daunomycin and nicotinamide-novatrone heteroassociation complexes have been determined using both the molecular mechanics methods (X-PLOR software) and the calculated values of induced proton chemical shifts. Analysis of the results obtained allows one to conclude that two nicotinamide molecules cannot simultaneously bind on one side of the chromophore of antibiotic. Heterocomplexes of the vitamin with the antibiotics with a stoichiometry 1:1 are mainly stabilized by the stacking of aromatic chromophores.     

Anthracycline antibiotic, beromycin. The formation of complexes with DNA and the suppresion of nucleic acid biosynthesis]

Beromycin, an antitumor anthracycline antibiotic formed in vitro complexes with native and denaturated DNA and ribosomal RNA. Beromycin had a comparatively low constant of DNA binding and to a less extent increased the melting temperature and viscosity of DNA than the other anthracycline antibiotics. A peculiar property of beromycin was very slow binding with DNA, the complex formation was completed in 60 minutes. Beromycin had a selective inhibitory effect on synthesis of nucleic acids in bacterial and tumor cells. Beromycin inhibited synthesis of RNA in the DNA-dependent RNA-polymerase reaction when both the native and denaturated DNA were used as the template. A lower biological activity of beromycin as compared to the other anthracycline antibiotics, such as rubomycin or carminomycin may be explained by lower affinity of this antibiotic to DNA.     

Calorimetric study of the polyG-polyC complex

Heat effects of polyG-polyC melting in neutral aqueous solutions have been measured using differential scanning microcalorimeter with an extended temperature range. The limiting value of melting enthalpy is 53 +/- 4 kJ per mole of base pairs and melting temperature dependence on the sodium concentration can be expressed by the empiric relation Tm = 13.2 log(Na+) + 420 K.     

Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 2. The hairpin form

The solution conformations of the oligonucleotides d(C-C-G-A-A-T-T-C-G-G) and d(C-C-G-A-m6A-T-T-C-G-G) as a function of temperature and sample concentration were investigated by means of 1H-NMR spectroscopy. The NMR spectra revealed that, at certain combinations of temperature and low sample and salt concentration, both compounds exist as a B-DNA-type duplex slowly (on the 1H-NMR time scale) interconverting with a monomeric species. From chemical shift data and imino-proton spectra, it is concluded that the monomeric species consists of a mixture of a hairpin form in rapid equilibrium with the random-coil form. The double-helical stem of the hairpin is formed by the six terminal cytidine and guanine residues, whereas the four core residues, -A-(m6)A-T-T-, partake in the loop. Thermodynamic analysis of the chemical shift of the resonances of the monomeric species vs temperature profiles of the two decamers and mutual comparison of these profiles indicate the following: the influence of N6-methylation of residue A(5) upon the local structure of the hairpin must be small; methylation decreases the stability of the duplex relative to the monomeric species: the temperature at which the fraction duplex equals 0.5 was found to be 312 K for the parent compound and 305 K for the methylated decamer at 2 mM sample concentration; methylation does not significantly alter the stability of the hairpin form relative to the random coil form: the Tm of the hairp----n equilibrium random-coil equilibrium is 308 K for the parent compound and 306 K for the methylated decamer. A higher fraction hairpin-like structure for the N6-methylated compound is observed under identical conditions of temperature and sample concentration: at 300 K, 2 mM sample concentration, the fraction hairpin form is 0.12 for d(C-C-G-A-A-T-T-C-G-G) and 0.20 for d(C-C-G-A-m6A-T-T-C-G-G). This finding appears to be a consequence of the reduced stability of the methylated dimeric species relative to the monomeric species, and to depend upon the sodium-ion concentration: it becomes more pronounced under low-salt conditions.     

Intracomplex alkylation of octanucleotide pd(TGTTTGGC) by a 5'-(4-N-methyl-N-(2-chloroethyl)-amino)benzylphosphamide derivative of heptanucleotide pd(CCAAACA). Preparation of a covalent adduct and study of its spatial structure in an aqueous solution by two-dimensional (1)H-NMR spectroscopy]

Covalent adduct--the product of intracomplex alkylation at N-3-position of dC-8-nucleoside residue of target octanucleotide pd[TGTTTGGC] was completely synthesized by means of 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5'-phosphamido derivative of heptanucleotide pd[CCAAACA]. Its melting temperature was shown to be 70 degrees C. Tm did not depend on covalent adduct concentration and was by 40 degrees C higher than that for unmodified duplex pd[TGTTTGGC].pd[CCAAACA] at concentration of 0.5 x 10(-4) M. The spatial structure of the covalent adduct in aqueous solution was investigated by two-dimensional 3H-NMR spectroscopy. The assignment of oligonucleotide protons as well as protons of a modifying group was carried out using COSY, COSY-DQF and NOESY experiments. Conformational analysis of proton-proton coupling constants for H1', H2'a, H2'b and H3' protons showed the sugar residues to be in 2'-endo conformation. Analysis of NOE connectivities observed between the protons of the alkylating group and oligonucleotide protons yielded conclusion, regarding the 4-[N-methyl-N-(2-chloroethyl)amino]benzylamido 5'-residue being localized in the region of the lacked nucleoside residue of the heptanucleotide chain about 5 A apart from the dC-1 residue and from cytosine base of the alkylated dC-8 residue.     

The use of neocarrabiose oligosaccharides with different length and sulphate substitution as model compounds for 1H-NMR spectroscopy.

The high-field 1H-NMR spectra of various carrageenan oligosaccharides at room temperature are given. The assignments were faciliated by the use of proton double-quantum coherence (DQCOSY) and 1H-13C chemical shift correlation 2D NMR spectroscopy, and by comparing high-field 1H-NMR spectra of various 4-sulphated oligosaccharides of the neocarrabiose type. The effects of anomeric configuration on the 1H resonances on the same or neighbouring units are discussed. The 13C-NMR shift data are given for the tetrasaccharide of kappa-carrageenan.