Differences In Conformational Behavior Research Articles

Data-mining the diaryl(thio)urea conformational landscape: Understanding the contrasting behavior of ureas and thioureas with quantum chemistry

The conformations adopted by urea and thiourea functional groups influence catalysis and binding. We combine data-mining with quantum chemical calculations to understand the differences in conformational behavior for these two important structural motifs. We developed a Python tool to automate the compilation of X-ray structural information and perform conformational clustering and visualization, based on SMILES input. While diarylureas have an overwhelming preference for the anti,anti-conformer, diarylthioureas adopt a mixture of anti,anti- and anti,syn-conformers. Computations show the anti,anti-thiourea conformer is destabilized by out-of-plane rotations which avoid a steric clash with the sulfur atom. These conformational preferences were studied computationally under a variety of conditions, and apart from in the gas-phase, a preference for anti,anti-ureas was found. Consistent with experiments, this preference increases in more polar environments. Quantitative predicted ratios are sensitive to the computational treatment of solvation effects, with COSMO-RS giving more realistic amounts of the anti,anti-conformer in THF and DMSO.

How Ionic Strength Affects the Conformational Behavior of Human and Rat Beta Amyloids – A Computational Study

Progressive cerebral deposition of amyloid beta occurs in Alzheimeŕs disease and during the aging of certain mammals (human, monkey, dog, bear, cow, cat) but not others (rat, mouse). It is possibly due to different amino acid sequences at positions 5, 10 and 13. To address this issue, we performed series of 100 ns long trajectories (each trajectory was run twice with different initial velocity distribution) on amyloid beta (1–42) with the human and rat amino acid sequence in three different environments: water with only counter ions, water with NaCl at a concentration of 0.15 M as a model of intracellular Na+ concentration at steady state, and water with NaCl at a concentration of 0.30 M as a model of intracellular Na+ concentration under stimulated conditions. We analyzed secondary structure stability, internal hydrogen bonds, and residual fluctuation. It was observed that the change in ionic strength affects the stability of internal hydrogen bonds. Increasing the ionic strength increases atomic fluctuation in the hydrophobic core of the human amyloid, and decreases the atomic fluctuation in the case of rat amyloid. The secondary structure analyses show a stable α-helix part between residues 10 and 20. However, C-terminus of investigated amyloids is much more flexible showing no stable secondary structure elements. Increasing ionic strength of the solvent leads to decreasing stability of the secondary structural elements. The difference in conformational behavior of the three amino acids at position 5, 10 and 13 for human and rat amyloids significantly changes the conformational behavior of the whole peptide.

Predicting the physicochemical profile of diastereoisomeric histidine‐containing dipeptides by property space analysis

This study aimed at measuring the lipophilicity and ionization constants of diastereoisomeric dipeptides, interpreting them in terms of conformational behavior, and developing statistical models to predict them. A series of 20 dipeptides of general structure NH(2)-L-X-(L or D)-His-OMe was designed and synthetized. Their experimental ionization constants (pK(1), pK(2) and pK(3)) and lipophilicity parameters (log P(N) and log D(7.4)) were measured by potentiometry. Molecular modeling in three media (vacuum, water, and chloroform) was used to explore and sample their conformational space, and for each stored conformer to calculate their radius of gyration, virtual log P (preferably written as log P(MLP), meaning obtained by the molecular lipophilicity potential (MLP) method) and polar surface area (PSA). Means and ranges were calculated for these properties, as was their sensitivity (i.e., the ratio between property range and number of rotatable bonds). Marked differences between diastereoisomers were seen in their experimental ionization constants and lipophilicity parameters. These differences are explained by molecular flexibility, configuration-dependent differences in intramolecular interactions, and accessibility of functional groups. Multiple linear equations correlated experimental lipophilicity parameters and ionization constants with PSA range and other calculated parameters. This study documents the differences in lipophilicity and ionization constants between diastereoisomeric dipeptides. Such configuration-dependent differences are shown to depend markedly on differences in conformational behavior and to be amenable to multiple linear regression.

Insights into conformational changes of procarboxypeptidase A and B from simulations: a plausible explanation for different intrinsic activity

Different forms of carboxypeptidase proenzymes (zymogens) are observed experimentally to show different behavior: procarboxypeptidase A (proCPA, forms proCPA1 and proCPA2) exhibit some activity against small substrates, but proCPB does not. In this work, these three zymogen forms (subtypes A1, A2 and B) are investigated by means of 15-ns molecular dynamics simulations and principal component analysis to shed light on their dynamic/conformational behaviors that may be relevant to those experimental observations. The simulations revealed that proCPA (both A1 and A2) shows different conformational behavior from proCPB: the former undergoes a major conformational change (opening and closing), and the latter exhibits only a minor conformational change (remaining closed throughout the simulation). Differences center on the interface between the globular moiety of the pro-segment and the catalytic domain. Analysis of the trajectories demonstrates the importance of hydrogen bonds and salt-bridges in stabilizing the zymogen structures and shows different hydrogen-bond patterns between proCPA and proCPB: the former shows fewer strong H-bonds formed between the globular domain and the catalytic domain. The observed difference in conformational behavior between proCPA and proCPB may explain why small substrates and inhibitors can access the active sites of proCPA1 and proCPA2 but not of proCPB.

Synthesis and an Evaluation of Molecular Conformation and Crystal Packing in Two Substituted 4-Phenylquinolines

The title compounds, namely Methyl 2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (II) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)° in (I), and 79.02 (8)° in (II) respectively. It is the weak C–H···O=C H-bond and C–H···π interactions which dictate packing of molecules in (I). In (II), it is C–H···N and C–H···π, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, π···π aromatic stacking interactions involving the quinoline fragment is present in all the molecules. The title compounds, namely methyl-2-methyl-4 -phenylquinoline-3-carboxylate (I), C18H15NO2, and (2E)-3-(3,4-dimethoxyphenyl)-1-(2-methyl-4 -phenylquinolin-3-yl)prop-2-en-1-one (II), C27H23NO3, comprising of the phenyl ring, exhibit differences in conformational behaviour with respect to the plane of the quinoline fragment. (I) contains the methyl ester moiety whereas (III) contains the chalcone fragment, consisting of a double bond and phenyl group containing dimethoxy groups as substituents. The dihedral angles between the phenyl group and the quinoline ring is 82.77 (7)° in (I), and 79.02 (8)° in (II) respectively. It is the weak C–H···O=C H-bond and C–H···π interactions which dictate packing of molecules in (I). In (II), it is C–H···N and C–H···π, involving the dimethoxy ring, which controls packing of molecules in the crystal lattice. In addition, π···π aromatic stacking interactions involving the quinoline fragment is present in all the molecules.

Corroles Cannot Ruffle

X-ray structures of Co(III)[(CF(3))(3)Cor](PPh(3)) [(CF(3))(3)Cor = meso-tris(trifluoromethyl)corrolato] and Cu[(CF(3))(4)Por] [(CF(3))(4)Por = meso-tetrakis(trifluoromethyl)porphyrinato] revealed planar and highly ruffled macrocycle conformations, respectively, in line with analogous observations for a handful of other meso-perfluoroalkylated porphyrins and corroles reported in the literature. To gain insights into the difference in conformational behavior, we evaluated DFT (BP86-D/TZP) ruffling potentials for a variety of corrole complexes, as well as their porphyrin analogues. The calculations led us to conclude that corrole derivatives, in essence, cannot ruffle.

Effect of Fluorination on Molecular Conformation in the Solid State: Tuning the Conformation of Cocrystal Formers

We present a detailed analysis of the effect of fluorination on the conformation of perfluorosuccinic acid in the solid state, using database analysis, crystal structure determination, and computational analysis of molecular conformations. Our results indicate that perfluorosuccinic acid exhibits strikingly different conformational preferences to its hydrocarbon analogue despite similarity in molecular size. This difference in conformational behavior also extends to the pair of adipic and perfluoroadipic acids. A search of the Cambridge Structure Database indicates that our analysis is valid for neutral molecules, salts, cocrystals, and metal−organic materials, suggesting fluorination as a general means to modify the shape of a molecular building block without changing its size. The difference in molecular shape between hydrocarbon and perfluorocarbon molecules is expected to lead to significant differences in solid-state structures of the resulting materials. We illustrate this by comparing the structures of new multicomponent crystals involving the model pharmaceutical ingredient caffeine and perfluorosuccinic or perfluoroadipic acid with the structures of analogous crystals based on the hydrocarbon diacids. Unlike hydrocarbon-based succinic and adipic acids which provide structurally similar hydrogen-bonded cocrystals and inclusion hosts with caffeine, perfluorosuccinic acid provides a salt and perfluoroadipic acid yields a cocrystal. Combined crystal structure analysis, solid-state and solution NMR analysis, single molecule conformational analysis, and calculations of acid dissociation energies indicate that the different solid-state behaviors of perfluoro- and hydrocarbon acids toward caffeine should be interpreted as a result of their distinct conformational properties rather than differences in pKa values.

Effects of backbone substitutions on the conformational behavior of Shigella flexneri O-antigens: implications for vaccine strategy

The O-antigen (O-Ag), the polysaccharide part of the lipopolysaccharide, is the major target of the serotype-specific protective humoral response elicited upon host infection by Shigella flexneri, the main causal agent of the endemic form of bacillary dysentery. The O-Ag repeat units (RUs) of 12 S. flexneri serotypes share the tetrasaccharide backbone →2)-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-α-l-Rhap-(1→3)-β-d-GlcpNAc-(1→, with site-selective glucosylation(s) and/or O-acetylation defining the serotypes. To investigate the conformational basis of serotype specificity, we sampled conformational behaviors during 60ns of molecular dynamic simulations for oligosaccharides representing three RUs of each one of the O-Ags corresponding to serotypes 1a, 1b, 2a, 2b, 3a, 3b, 4a, 4b, 5a, 5b, X and Y, respectively. The calculated trajectories were checked by nuclear magnetic resonance (NMR) for 1a, 2a, 3a and 5a O-Ags. The simulations predict that in all O-Ags, but 1a and 1b, serotype-specific substitutions of the backbone do not induce any new backbone conformations compared with the linear type O-Ag Y, although they restrain locally the accessible conformational space. Moreover, the influence of any given substituent on the backbone is independent of the eventual presence of other substituents. Finally, only slight differences in conformational behavior between terminal and inner RUs were observed. These results suggest that the reported serotype-specificity of the protective immune response is not due to recognition of distinct backbone conformations, but to binding of the serotype-defining substituents in the O-Ag context. The gained knowledge is discussed in terms of impact on the development of a broad-serotype coverage vaccine.

The marked difference in conformational behavior of the two diastereomers of 7-substituted-1,1-dichloro-7b-((Z)-8-chloro-6,7-dihydro-5H-benzo[7]annulen-9-yl)-1a,2,3,7b-tetrahydro-1H-cyclopropa[a]naphthalene, single crystal X-ray, 1H NMR and AM1 studies

The 7-substituted of 1 and 2 were synthesized and conformational analysis carried out. While 7-substituted of 2 show two conformers in solution, 7-substituted of 1 show only one form in solution. AM1 semi-empirical molecular orbital calculations show that the conformation of cycloheptadiene ring in 1 and 2 is a twist boat form. In this conformation, the C-7 substituents can be oriented in pseudo equatorial (exo) and pseudo axial (endo) positions. The 3 J calculation with Haasnoot equation on optimized structure of 2 reproduces the observed 3 J coupling constants in exo and endo forms. Ring inversion of cycloheptadiene moiety in substituted 2 interconvert the e′–a′ (exo–endo) positions. The 3 J calculation on optimized structure of 1 shows that 7-substitution is in pseudo equatorial (exo) direction, as found in the crystal structure of 1a by single crystal X-ray crystallography. The barrier to ring inversion in 2a is determined by dynamic 1H NMR spectroscopy to be Δ G ≠ (335K) = 68.0 ± 0.5 kJ/mol.

Dithioether ligands containing a 2,6-disubstituted pyridine linker with two thioether-heterocycle arms

The structure of 2,6-bis(2-pyridyltsulfanylmethyl)pyridine (pytmp), (I), C(17)H(15)N(3)S(2), presents a twisted conformation, with the three planar moieties almost perpendicular to each other. The structures of two related derivatives, namely 2,6-bis(6-methyl-2-pyridylsulfanylmethyl)pyridine (mpytmp), (II), C(19)H(19)N(3)S(2), and 2,6-bis(4-methyl-2-pyrimidylsulfanylmethyl)pyridine (mprtmp) n-pentane hemisolvate, (III), C(17)H(17)N(5)S(2).0.5C(5)H(12), present extended planar fragments with just one quasi-perpendicular arylsulfanylmethyl side arm, such that the molecules are folded in an L-shaped conformation. All three conformations appear different from those adopted by similar compounds, demonstrating the great flexibility of such species, although such differences in conformational behaviour might drive specific coordination modes.

Cryoprotection with L‐ and meso‐Trehalose: Stereochemical Implications

Two unnatural stereoisomers of alpha,alpha-trehalose (L- and meso-trehalose) were synthesized and evaluated as cryoprotectants in order to determine the functional consequences of relative or absolute stereochemistry on their physicochemical properties. Adherent yeast cell cultures were frozen in 10% solutions of D-, L-, and meso-trehalose for periods of 7-28 days, then evaluated by a MTT viability assay. D- and L-trehalose were equally effective in maintaining high rates of cell survival, thus demonstrating the absence of chiral discrimination at the carbohydrate-lipid interface, whereas meso-trehalose was inferior in cryoprotection efficacy. Differential scanning calorimetry revealed a difference in the glass transition temperatures (Tg) of D- and meso-trehalose of nearly 75 degrees C. This can be attributed to differences in conformational behavior, as portrayed by torsional energy maps for rotation about the glycosidic bonds of D- and meso-trehalose. We conclude that the biostabilizing properties of alpha,alpha-trehalose depend on relative stereochemical factors, but are independent of absolute stereochemical configuration.

Range and Sensitivity as Descriptors of Molecular Property Spaces in Dynamic QSAR Analyses

In this paper, we report the first study aimed at correlating pharmacological properties with molecular parameters derived from the physicochemical property space of bioactive molecules. A dataset of 36 ligands of the alpha(1a)-, alpha(1b)-, and alpha(1d)-adrenoceptors as published by Bremner et al. (Bioorg. Med. Chem. 2000, 8, 201-214) was used. One thousand conformers were generated for each ligand by Monte Carlo conformational analysis, and four 3D-dependent physicochemical properties were computed for each conformer of each ligand, namely virtual lipophilicity (log P), dipole moment, polar surface area (PSA), and solvent-accessible surface area (SAS). Thus, a space of four physicochemical properties was obtained for each ligand. These spaces were assessed by two descriptors, namely their range and their sensitivity (i.e., the variation amplitude of a given physicochemical property for a given variation in molecular geometric properties). Little or no correlation was found to exist between the physicochemical properties and their range or sensitivity, indicating that the latter descriptors do not encode the same molecular information as the former properties. As expected, neither the range nor the sensitivity of any of the four physicochemical properties correlated with receptor affinities. In contrast, range and sensitivity showed promising correlations with deltapK(a-b) (i.e., the alpha(1a)/alpha(1b) selectivity) for the complete dataset. The correlations were lower for deltapK(a-d) (i.e., the alpha(1a)/alpha(1d) selectivity), whereas there was no correlation at all with deltapK(b-d). These results are consistent with the results of Bremner et al., which indicate that the alpha(1a)-AR ligands bind in an extended geometry, whereas the alpha(1b)-AR and alpha(1d)-AR ligands assume more folded conformations. Since the property space descriptors presented here take structural variability into account, their correlation with deltapK(a-b) and deltapK(a-d) indicates that these selectivities are indeed driven by differences in conformational behavior and hence in property spaces.

Calorimetric and computational study of 1,3,5-trithiane.

To understand the differences in conformational behavior and reactivity of oxygen- and sulfur-containing 1,3,5-heterocyclohexanes, the enthalpies of formation and sublimation of 1,3,5-trithiane, 1, have been measured. The numerical value of the enthalpy of formation for this compound in the solid state is -8.6 +/- 2.6 kJ mol(-1), while the corresponding value in the gaseous state is 84.6 +/- 2.6 kJ mol(-1). The value for the enthalpy of sublimation is 93.2 +/- 0.2 kJ mol(-1). Standard ab initio molecular orbital calculations at the G2(MP2), G2, and G3 levels were performed, and the calculated enthalpies of formation are compared with the experimental data. These experimental and theoretical studies support the relevance of through-space lone pair-lone pair electronic repulsion in the sulfur heterocycle.

Photoinduced intramolecular charge separation in donor/acceptor-substituted bicyclohexylidene and bicyclohexyl

The photophysical properties of a bicyclohexylidene (1DA) and a bicyclohexyl (2DA) substituted with an anilino electron donor and a dicyanoethylene electron acceptor have been studied. Quenching of local donor emission is observed for these compounds as well as quenching of the "pseudo-local" acceptor emission. Transient absorption spectra show dialkylanilino-type radical-cation and dicyanoethylene-type radical-anion absorptions. These results show that intramolecular charge separation takes place in 1DA and 2DA. This was corroborated by time-resolved microwave conductivity measurements from which large excited-state dipole moments were found for both 1DA and 2DA. Time-resolved fluorescence spectroscopy revealed that in the charge-separated state in cyclohexane for 2DA, molecular folding takes place on a nanosecond timescale. For 1DA in cyclohexane, either charge separation takes place in a (fully) folded conformation or very rapid (subnanosecond timescale) folding takes place subsequent to charge separation. In addition to this difference in conformational behavior, the presence of the exocyclic double bond between the cyclohexyl-type rings results in efficient quenching of the anilino donor triplet state and acceleration of the charge recombination rate by a factor of 20.

Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.

Structure of Water, Proteins, and Lipids in Intact Human Skin, Hair, and Nail

Raman spectroscopy is a nondestructive analytical method for determining the structure and conformation of molecular compounds. It does not require sample preparation or pretreatment. Recently, near-infrared Fourier transform Raman spectroscopy has emerged as being specially suited for investigations of biologic material. In this study, we obtained near-infrared Fourier transform Raman spectra of intact human skin, hair, nail, and stratum corneum. We disclosed major spectral differences in conformational behavior of lipids and proteins between normal skin, hair, and nail. The amide I and III band location indicated that the majority of proteins in all samples have the same secondary alpha-helix structure. Positions of (S-S) stretching bands of proteins revealed a higher stability of the disulfide bonds in the hair and the nail. Analysis of vibrations of protein -CH groups showed that in the hair and the nail the proteins are apparently highly folded, interacting with the surroundings only to a small degree. The position of lipid specific peaks in spectra of hair, nail, and stratum corneum suggested a highly ordered, lamellar crystalline lipid structure. A greater lipid fluidity was found in whole skin. Assessment of the structure of water clusters revealed that mainly bound water is present in the human skin, stratum corneum, and nail. In conclusion, structural changes of water, proteins, and lipids in intact skin and skin appendages may be analyzed by Raman spectroscopy. This technique may be used in the future in a noninvasive analysis of structural changes in molecular compounds in the skin, hair, and nail associated with different dermatologic diseases.

Tautomeric and conformational equilibria in dinitrosomethane

The keto-enolic equilibrium has been investigated for dinitrosomethane. Ab initio tautomeric and conformational analyses are presented for the 11 plausible forms of this molecular system. Full geometry optimizations for all enolic and ketonic forms have been performed at the HF level with the 3–21G and 6–31G ∗∗ basis sets. All of the eight enolic forms are more stable than the three ketonic species. The most stable conformer of the enolic tautomer has been predicted to be the most extended one. The difference in conformational behavior with respect to the isoelectronic malonaldehyde is discussed.

Constrained C-terminal hexapeptide neurotensin analogues containing a 3-oxoindolizidine skeleton

In order to enforce different spatial orientations in the C-terminal hexapeptide of neurotensin (NT8−13) and to gain information about the importance of the 10–11 peptide bond for binding to NT receptors, the Pro10-Tyr11 fragment has been replaced with (2R,8S,8aR)-, (2S,8S,8aR)-, (2S,8S,8aS)-, (2S,8R,8aS)- and (2R,8R,8aS)-8-amino-2-benzyl-3-oxoindolizidine-2-carboxylic acid. Molecular dynamics calculations and energy minimization studies have shown that, contrarily to the Pro-Tyr moiety, none of these indolizidines display a tendency to adopt type I and III β-turns, but those having (8S,8aR) or (8R,8aS) stereochemistry essentially adopt extended conformations and the (8S,8aS) stereoisomer prefers a nonstandard folding. The four diastereomeric NT8−13 analogues incorporating (8S,8aR) or (8R,8aS) indolizidines displayed binding affinities for the brain NT receptor similar to that of [Ala11]-NT8−13 and only five- to ninefold lower than that of the corresponding analogue, [Phe11]NT8−13. Although this slight decrease could be attributed to differences in conformational behavior between these constrained NT8−13 analogues and [Phe11]NT8−13 or NT8−13, it is not clear whether the β-turn around Pro10-AA11 (AA=Phe, Tyr) is conserved upon receptor binding. An excessive restriction in the motions of the aromatic side chain, imposed by the highly steric constraint of the indolizidine moiety, emerges as an alternative explanation. The findings reported here demonstrate the possibility of replacing the Pro10-Tyr11 dipeptide in NT8−13 with a non-peptide residue without affecting considerably the affinity for brain NT receptors.

Solution conformations of GM3 gangliosides containing different sialic acid residues as revealed by NOE-based distance mapping, molecular mechanics, and molecular dynamics calculations.

The conformation of the GM3 ganglioside, Neu5Ac alpha 2-3Gal beta 1-4Glc beta 1-1 Cer, and its analogs containing the Neu5Gc or Neu4Ac5Gc residues (Gc = glycolyl, CH2OHCO) was investigated in Me2SO-d6 solution with the aid of a distance-mapping procedure based on rotating-frame NOE contacts, with hydroxyl protons being used as long-range sensors defining the distance constraints. A pronounced flexibility found for both the Neu-Gal and Gal-Glc linkages was confirmed by 1000-ps molecular dynamics simulations. Similar results, although based on a smaller number of NOE constraints, were obtained for GM3 gangliosides anchored in mixed D2O/dodecylphosphocholine-d38 micelles and for the Neu5Ac-, Neu5Gc-, and Neu5,9Ac2-sialyllactoses dissolved in D2O. No noteworthy differences in conformational behavior of the glycan chains of the three gangliosides or sialyllactoses were observed in either of the media.

Influence of uracil on the conformational behaviour of RNA oligonucleotides in solution

NMR studies were carried out on some alternating pyrimidine-purine sequences: the single-stranded tetramers CACA and UGUG and the self-complementary octamer CACAUGUG. Assignments, based upon COSY, homonuclear Hartmann-Hahn, and NOESY experiments, are given for the resonances of all base protons and of several sugar protons. Chemical shift vs temperature profiles were used to obtain thermodynamic parameters for the single-stranded stack in equilibrium with random coil and the duplex in equilibrium with random coil equilibria. The populations of N-type conformer of the ribose rings were estimated from the observed J1'2'. Comparisons with another alternating pyrimidine-purine sequence Um2(6)AUm2(6)A and with the deoxyribose counterparts d(CACA), d(TGTG) and d(CACATGTG) are given. Previous 1H-NMR investigations of Um2(6)AUm2(6)A revealed that the population of bulge-out structure diminishes compared to m2(6)AUm2(6)A due to the U(1)-m2(6)A(2) stacking interaction. In CACA a strong stacking proclivity (Tm = 310 K) together with a clear preference for N-type ribose is observed. However, the stacking interactions in UGUG are relatively less stable (Tm = 288 K) and a bias towards S-type sugar is present. Besides a small amount of stack, a significant contribution of bulge out structure is proposed for UGUG. We conclude that the nature of the pyrimidine base mainly determines the formation of bulge-out structures. The poor stacking properties of uracil now appear to be mainly responsible for this phenomenon. Comparison with the deoxyribose counterparts shows a reasonable agreement between the Tm values of CACA and d(CACA), whereas the Tm of UGUG (288 K) is much lower than the Tm of d(TGTG) (315 K). It is suggested that the absence of bulge-out structures in DNA purine-pyrimidine-purine sequences is related to the relatively strong stacking proclivity of dT residues compared to that of U residues. The Tm values (average 341 K) for the duplex in equilibrium with random coil transition obtained for each residue of CACAUGUG appear very similar. All ribose rings, except the G(8), adopt a pure N conformer in the duplex. This is taken to mean that the differences in conformational behaviour of the constituent tetramers disappear upon duplex formation.