Stacking interactions of nucleobases: NMR-Investigations II. Selfassociation of purine- and pyrimidine-derivatives

The selfassociation of various purine- and pyrimidine-derivatives in D₂O has been studied by means of NMR technique. The thermodynamic quantities have been calculated using an isodesmic NMR model. Among the nucleobases investigated, the adenine-derivatives were found to be most suitable for quantitative determination. A comparison of methylated adenine-derivatives and the pH-dependence of the selfassociation lead to the conclusion, that the stacking associates are stabilized by special van der Waals interactions based, essentially, on the polarizability of the π-electron-system of the associated molecules.     

Stacking interactions of nucleobases: NMR-investigations. I. Self association of N6, N9-dimethyladenine and N6-dimethyl-N9-ethyladenine.

The selfassociation of N6,N9-dimethyladenine and N6-dimethyl-N9-ethyladenine has been studied by means of NMR technique. The thermodynamic quantities have been calculated using an isodesmic NMR model with three NMR parameters (the monomer shift deltaM and two complex shifts delta2 and delta3). The dependence of the thermodynamic quantities on the NMR parameters is discussed. Special attention is given to the determination of deltaM and its temperature dependence. Calculations with delta3 = 2 - delta2 and deltaM taken independently of temperature result in an average entropy deltaS = - 17.9 +/- 1.8 e.u. for N6,N9-dimethyladenine and deltaS = - 16.7 +/- 1.7 e.u. for N6-dimethyl-N9-ethyladenine and in an average enthalpy deltaH = - 7.2 +/- 0.6 kcal - mol-1 for both substances investigated.     

Association of sexual hormones with nucleobases in water: NMR-investigations.

The mixed association of testosterone-sulfate and estradiol-sulfate with several derivatives of nucleobases in D2O has been investigated by means of nuclear magnetic resonnance spectroscopy. From the differences among the chemical shifts of the hormone-protons it is concluded, that the nucleobases in the complexes are located above the center of the steroid molecule. The beta-side of the steroid which is characterized by the axial methyl-groups is directed towards the bases. The enthalpies of mixed association of the hormones with a certain nucleobase of the same order of magnitude as the enthalpy of selfassociation of this nucleobase (Schimmack et al., to be published). It is suggested that the complexes are stabilized by van-der-Waals forces. This stacking-like interaction is not specific for the male or female sex hormones: no qualitative or quantitative differences have been observed among the complexes of the two hormone-sulfates with the nucleobases.     

Stacking interaction of nucleobases: NMR investigations

The stacking interaction between nucleic acid bases has been investigated by the determination of the self-association of 6-methylpurine in various mixtures of water and nonaqueous solvents in order to elucidate the solvent effect. The parameters of stacking association as well as of local solvent-solute interactions have been measured by means of NMR technique. The influences of local hydration and of solvent-solvent interactions on the stacking ability are discussed.Parts I and II see Schimmack 1975     

Theoretical calculations of base-base interactions in nucleic acids: II. Stacking interactions in polynucleotides.

Base-base interactions were computed for single- and double stranded poly,ucleotides, for all possible base sequences. In each case, both right and left stacking arrangements are energetically possible. The preference of one over the other depends upon the base-sequence and the orientation of the bases with respect to helix-axis. Inverted stacking arrangement is also energetically possible for both single- and double-stranded polynucleotides. Finally, interacting energies of a regular duplex and the alternative structures were compared. It was found that the type II model is energetically more favourable than the rest.     

Theoretical calculations of base-base interactions in nucleic acids: I. Stacking interactions in free bases.

Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both can be energetically favourable (ii) in both the types the stacking interaction is a combined effect of the overlap of the interacting bases and relative positions and orientations of the atomic centres of the two bases (iii) crystal symmetry and H-bonding interaction may influence stacking patterns.     

Stacking interactions in PUF-RNA complexes

Stacking interactions between amino acids and bases are common in RNA-protein interactions. Many proteins that regulate mRNAs interact with single-stranded RNA elements in the 3' UTR (3'-untranslated region) of their targets. PUF proteins are exemplary. Here we focus on complexes formed between a Caenorhabditis elegans PUF protein, FBF, and its cognate RNAs. Stacking interactions are particularly prominent and involve every RNA base in the recognition element. To assess the contribution of stacking interactions to formation of the RNA-protein complex, we combine in vivo selection experiments with site-directed mutagenesis, biochemistry, and structural analysis. Our results reveal that the identities of stacking amino acids in FBF affect both the affinity and specificity of the RNA-protein interaction. Substitutions in amino acid side chains can restrict or broaden RNA specificity. We conclude that the identities of stacking residues are important in achieving the natural specificities of PUF proteins. Similarly, in PUF proteins engineered to bind new RNA sequences, the identity of stacking residues may contribute to "target" versus "off-target" interactions, and thus be an important consideration in the design of proteins with new specificities.     

Self-association of troponin.

Ox muscle troponin was shown by equilibrium- and velocity-sedimentation studies to undergo concentration-dependent dissociation into its constituent subunits as well as self-association in imidazole buffers, pH 6.9. The extent of troponin association was found to be strongly dependent on ionic strength and also to exhibit a dependence on pH and temperature; under conditions physiological in regard to pH, temperature and ionic strength the extent of polymerization of troponin is considerable in 2 mg/ml solutions. The ability of polymeric troponin to bind to tropomyosin has been inferred from studies of mixtures containing actin-tropomyosin and an excess of troponin over the amount required for the normal 7:1:1 actin-tropomyosin-troponin complex. These findings should be relevant to studies of reconstituted actin-tropomyosin-troponin preparations, since they signify possible chemical as well as physical differences between the gel, paracrystalline and filamentous states of the complex that result from adoption of different preparative procedures for analogues of the native thin filament.     

Stacking Interactions of nucleobases: NMR-Investigations I. Selfassociation of N6,N9-Dimethyladenine and N6-Dimethyl-N9-Ethyladenine

The selfassociation of N⁶,N⁹-dimethyladenine and N⁶-dimethyl-N⁹-ethyladenine has been studied by means of NMR technique. The thermodynamic quantities have been calculated using an isodesmic NMR model with three NMR parameters (the monomer shift _M and two complex shifts ₂ and ₃).The dependence of the thermodynamic quantities on the NMR parameters is discussed. Special attention is given to the determination of _M and its temperature dependence.Calculations with ₃=2· ₂ and _M taken independently of temperature result in an average entropy _S =–17.9±1.8 e.u. for N⁶,N⁹-dimethyladenine and _S =–16.7±1.7 e.u. for N⁶-dimethyl-N⁹-ethyladenine and in an average enthalpy _H=–7.2±0.6 kcal· mol^–1 for both substances investigated.Part of the Ph.D. Theses of W. Schimmack and H. Sapper.Dedicated to Professor Dr. A. Schraub on the occasion of his 65th birthday.     

Stacking interactions of ApA analogues with modified backbones

CD spectra have been measured as a function of temperature for a number of ApA analogues with modified backbones. Oligonucleotides with these modified backbones are being used as antisense agents having potential as viral therapeutics. Results of these studies show that when a carbonyl is substituted for the phosphate to produce an uncharged backbone, the analogues that have either sugar or morpholino substitution do not stack. In contrast, when a morpholino group is substituted for the sugar and the phosphate is modified so as to be uncharged, there is strong base stacking. Stacking interactions in the phosphorus-linked morpholino analogues are at least as strong as those found in d (ApA). The stacking interactions in ApA are weak by comparison. Singular value decomposition demonstrates that the stacking is two state, and Taylor series decomposition yields a coefficient that measures base stacking interactions. The van't Hoff equation is applied to the base stacking coefficient from the Taylor series fitting to give thermodynamic parameters. © 1992 John Wiley & Sons, Inc.     

Self-association and stability of the ApoE isoforms at low pH: implications for ApoE-lipid interactions

Apolipoprotein E (apoE) isoforms are known to differentially accumulate in the lysosomes of neuronal cells, and the deleterious effects of the apoE4 isoform in Alzheimer's disease may relate to its properties at the low lysosomal pH. However, the effect of pH on the molecular properties of full-length apoE is unclear. Here we examine the pH dependence of the monomer-dimer-tetramer reaction, of lipid binding, and of the stability of the three major apoE isoforms. Using FRET measurements, we find that the association-dissociation behavior of apoE proteins changes dramatically with changes in pH. At pH 4.5, approximating the pH of the lysosome, rate constants for association and dissociation are 2-10 times faster than those at pH 7.4. Aggregation beyond the tetrameric form is also more evident at lower pH values. Stability, as measured by urea denaturation at pH 4.5, is found to be considerably greater than that at neutral pH and to be isoform dependent. Lipid binding, as measured by turbidity clearance of unilamellar vesicles of DMPC, is faster at acidic pH values and consistent with our previous hypothesis that it is only the monomeric form of apoE that binds lipid tightly. Since apoE is more stable at pH 4.5 than at neutral pH, the more rapid apoE-lipid interactions at low pH are not correlated with the stability of the apoE isoforms, but rather to the faster association-dissociation behavior. Our results indicate that pathological behavior of apoE4 may arise from altered molecular properties of this protein at the acidic pH of the lysosome.     

Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals

Non-additivity of base-base interactions in all ten possible model dinucleotide steps were analyzed on MP2/aug-cc-pvDZ quantum chemistry level. Conformations of four nucleobases exactly matched to ones occurring in B-DNA crystals. In most of thw 162 analyzed tetramers both three- and four-body contributions are negligible except for d(GpG) steps. However, in these dinucleotides both contributions are always of opposite signs and in all cases the sum of all non-additive part of intermolecular interactions do not exceed 2.6 kcal mol^-1. This stands for less than 5% of the overall binding energy of dinucleotide steps. Also replacements of guanine with 8-oxoguanine in d(GpG) systems introduces non-additivity of the same magnitude as for canonical dinucleotides. It is observed linear relationships between values of total binding energy obtained in the tetramer basis set and estimated energy exclusively in dimers basis sets with assumption of pairwise additivities. For all analyzed dinucleotides steps there are also linear correlations between amount of non-additive contributions and magnitude of pairs interactions. Based on differences in electrostatic contribution to the total binding energy of four nucleobases and polarity of dinucleotide steps three distinct classes of dinucleotide steps were identified.     

Self-association of bovine immunoglobulin G1.

The self-association properties of bovine serum immunoglobulin G1 and colostral immunoglobulin G1 (IgG1) in 0.32 M-NaCl/0.01 M-Tris/HCl, pH 8.0, were investigated by analysing sedimentation data according to a monomer-dimer association model. The self-association was characterized by an equilibrium constant of 5.3 X 10(4) +/- 3.5 X 10(4) M-1 for serum IgG1 and 1.6 X 10(3) +/- 0.69 X 10(3) M-1 for colostral IgG1. The removal of the Fc portion of IgG1 by pepsin digestion abolished its property of self-aggregation. At high total protein concentrations of serum IgG1, low concentrations of the ostensible trimer species were observed. However, no self-aggregation was evident when 0.14 M-NaCl/0.01 M-sodium phosphate. pH 6.0, was used as a solvent, thus confirming results published previously [Tewari & Mukkur (1975) Immunochemistry 12, 925--930].     

Nimodipine's interactions with other drugs: II. Diazepam

Adult Binghamton Heterogeneous (HET) stock mice were administered one of three doses of diazepam (0.1, 2.5, or 5.0 mg/kg) immediately followed by a second injection of either the slow calcium channel blocker, nimodipine (Bay e 9736), or its vehicle. Hypothermic responses and muscular incoordination were measured twenty and sixty minutes later as assessed by changes in rectal temperature and motoric activity on a rotating rod. Nimodipine (5 mg/kg) alone did not significantly affect body temperature or motor coordination. However, when administered in combination with the two highest doses of diazepam, nimodipine significantly potentiated the hypothermic response produced by these doses both twenty minutes and sixty minutes post-injection. Administration of high doses of diazepam (2.5 and 5.0 mg/kg) resulted in significant motor incoordination at both observation periods, but this effect was not potentiated by nimodipine.     

Stacking and hydrogen bond interactions between adenine and gallic acid

We have performed DFT and DFT-SAPT calculations on dimers of gallic acid, the model system for plant polyphenols, and the DNA base adenine. These dimers were selected for this study as they exhibit simultaneously hydrogen bonds and stacking interactions and it allows to quantify the relative values of these interactions. We calculate the relationships between the stability of the complexes, the charge transfer between monomers and the properties of the intermolecular bonds including hydrogen bonds and other bonds that do not involve hydrogen atoms. DFT-SAPT calculations were also performed to obtain the participation of the different types of energy and so the resulting physical effects. The results show that the presence of hydrogen bonds is the main stabilizing factor for dimers: the higher number and strength, the lower the dimer energy. The contribution of stacking to the stabilization is related to the strength and number of bonds between non-hydrogen atoms and quantified by the contribution of the dispersion terms to the interaction energy. Dimers I and II are mainly stabilized due to hydrogen bonds whereas dimer III is mainly stabilized by stacking interactions.     

Self-association of nucleotides

The self-association of nucleosides decreases within the series adenosine>guanosine>inosine>cytidine ≈uridine. The same trend is observed for the corresponding nucleotides, though less pronounced, as the charge effect governs series like adenosine ? AMP^2?>ADP^3??ATP^4?. Protonation of adenosine considerably reduces its self-stacking tendency: this is different with ATP^4?, where a maximum is reached for H₂(ATP)^2? caused by additional ionic interactions in the [H₂(ATP)]₂ ^4? dimer. Metal ion coordination may promote self-association, e.g., of ATP^4? via (mainly) charge neutralization (Mg²⁺) and the formation of intermolecular bridges in dimeric stacks (Zn²⁺, Cd²⁺). These results allow definition of conditions with negligible self-association and thus the determination of the stability and structure of monomeric nucleotide complexes in aqueous solution, e.g., quantification of macrochelate formation in M(ATP)^2? complexes. Some biological implications of the results are indicated.     

Self-association of mucin

Aggregation phenomena in aqueous solutions of purified human tracheobronchial mucin have been studied by rheological methods, steady-state fluorescence, quasielastic light scattering, and spin probe techniques. At temperatures below 30 degrees C and concentrations above 15 mg/mL and in the absence of chaotropic agents, mucin solutions are viscoelastic gels. A gel-sol transition is observed at temperatures above 30 degrees C that is manifested by the diminishing storage modulus and a loss tangent above unity throughout the studied frequency range of the oscillatory shear. No decline in the mucin molecular weight is observed by size-exclusion chromatography above 30 degrees C in the absence of redox agents or proteolytic enzymes. Aggregation of hydrophobic protein segments of the mucin chains at 37 degrees C is indicated by QELS experiments. The decreasing polarity of the microenvironment of pyrene solubilized into mucin solutions at temperatures above 30 degrees C, concomitant with the gel-sol transition, shows the hydrophobicity of the formed aggregates. ESR spectra of the fatty acid spin probe, 16-doxylstearic acid indicate that the aggregate-aqueous interface becomes more developed at elevated temperatures.