Comparative stability determination of oligonucleotide duplexes in gas and solution phase

The relative stability of RNA duplexes were determined in both solution and gas phase. Solution stability as determined by a spectrophotometric method indicated that the Watson-Crick duplexes were more stable than duplexes containing one GA mismatch or two tandem GA mismatches. Gas phase stability was determined using ESI-MS through variation of the collision energy in an ion trap. Stability curves similar to the melting curves obtained in solution were observed. The relative stability in gas phase differed, however, from that in solution. The duplexes with two tandem GA mismatches were found to be more stable than the Watson-Crick and single GA mismatch duplexes. The different trends observed in solution versus gas phase can be attributed to the primary means of interaction. In solution, stacking is expected to be the dominant interaction mode. In the gas phase, hydrogen bonding is expected to be the dominant interaction mode. Duplexes with tandem GA mismatches have the potential to undergo additional hydrogen bonding relative to the other duplexes which could account for their increased stability in the gas phase.     

Mass spectrometric and theoretical study of polyiodides: the connection between solid state, solution, and gas phases

Polyiodides have been transferred intact from acetonitrile solution to the gas phase and analyzed by mass spectrometry. A range of ions were observed, including [I(11)](-), [I(13)](-), and [I(15)](-), which have higher iodine/iodide ratios than any previously characterized ions. Theoretical calculations show that branched structures are strongly favored, a result which is in excellent agreement with with gas phase fragmentation studies (MS/MS) and also previous solid state studies. This study demonstrates the utility of mass spectrometry to provide structural information in the absence of other spectroscopic handles.     

A systematic study on the influences of linkage length on phase behaviours and charge carrier mobilities of discotic dimers

Two series of discotic dimers T3Dn and T5Dn based on hexapropoxytriphenylene (HAT3) and hexapentyloxytriphenylene(HAT5), respectively, with polymethylene linkage O(CH₂)_nO (n = 3–12) have been synthesised. Their mesomorphism was investigated by differential scanning calorimetry, polarising optical microscopy and X-ray diffraction. The results showed that side chains induced a phase transition from col_hp phase to col_h phase, namely dimers T3Dn (n = 6–12) based on HAT3 exhibiting a single col_hp phase, dimers T4Dn (n = 6, 7, 11, 12) based on HAT4 showing a highly ordered col_hp phase in low-temperature region and a col_h phase in high-temperature region, dimers T4Dn (n = 8–10) based on HAT4 displaying a single col_hp phase and dimers T5Dn (n = 6–11) based on HAT5 indicating a single col_h phase. Dimers T4Dn showed a phase competition between col_h phase and col_hp phase induced by linkages. Surprisingly, a unique phenomenon was found by us, that is, those compounds in which linkage lengths were twice those of side chains showed the largest enthalpies, the smallest intracolumnar spacings and the highest charge-carrier mobilities among their homologues, respectively, which implied that they formed the most highly ordered phase among their homologues.     

Preparation and characterization of poly(l-phenylalanine) chiral stationary phases with varying peptide length

Three new chiral stationary phases with different lengths of l-phenylalanine peptide were prepared by solid-phase synthesis with tert-butoxycarbonyl (Boc)-l-phenylalanine on silica. The effect of phenylalanine peptide length on enantioselectivity was studied. The best separation of R/S-warfarin was achieved by the chiral stationary phase with intermediate peptide length. These stationary phases were found to exist mainly in alpha-helical conformation by using FT-IR spectra. The end-capping reagents for the N-terminus of the peptide were also evaluated.     

The stability of intramolecular DNA quadruplexes with extended loops forming inter- and intra-loop duplexes

We have examined the formation of intramolecular quadruplex DNA structures in which the loops have been extended so as to generate short DNA duplexes. Fluorescence melting and DNase I cleavage studies show that duplexes can be formed within each loop, but that duplexes between the loops are not stable.     

Triphenyltin substituted benzoates: A spectroscopic study of structure in solution and solid phases

¹¹⁹Sn NMR and Mössbauer spectroscopic data have been recorded for 12 compounds of formula Ph₃SnO₂CC₆H₄X(X = H, Me-2, NH₂-2, NMe₂-2, Cl-2, Cl-3, Cl-4, OH-2, OH-4, SMe-4 or OMe-2) and Ph₃SnO₂CC₁₀H₇-1. On the basis of these measurements all the compounds are assigned a coordination number of four at tin in solution, and, with the exception of the Cl-2 and OH-2 derivatives, retain this structure in the solid. Both of these latter compounds exhibit enhanced Mössbauer quadrupole splittings (3.71 and 2.97 mm s⁻¹), which are attributed to carboxylate- and hydroxyl-bridged structures, respectively. The variable-temperature Mössbauer spectra of two compounds (X = OMe-2 or OH-2) are discussed.     

A density-functional study on the stability of anatase-type phases in the system Mg-Ta-O-N

Magnesium-doped tantalum oxynitrides, which were prepared by ammonolysis of amorphous mixed oxides, have been investigated using quantum-theoretical methods. For small magnesium amounts (5 cat%), density-functional total-energy calculations indicate an anatase-type structure consisting of stretched, corner-sharing TaO₃N₃ octahedra with a tetrahedrally distorted equatorial plane. The calculated structural parameters are in excellent agreement with those obtained using X-ray powder diffraction and synchrotron radiation. Additionally, the quantum-chemical results show a clear preference for an ordered anionic distribution (space group I4₁md, no. 109) of the host lattice, which is locally disturbed around Mg²⁺. For thermodynamical reasons, the excess oxygen anions, which replace nitrogen on account of the lower charge of the dopant cation, segregate next to magnesium, thus forming local MgO “domains”. For higher magnesium contents (?10%), minor phases of rutile-type structure have to be expected, which is in good agreement with experimental data.     

Visualization of complexes of Hoechst 33258 and DNA duplexes in solution by atomic force microscopy

Tertiary structure changes in DNA duplexes, induced by Hoechst 33258 binding, have been examined by the use of atomic force microscopy. Besides minor groove binding, which is an established mode of binding for this drug, Hoechst 33258 has now been found to show another binding mode, which causes an unwinding of the duplex. When the drug concentration is as high as 0.5 microg/ml, the Hoechst 33258 molecule seems to function as a clamp for two DNA chains and forms a condensate. The condensate was found to have a toroidal shape. By surveying more than 100 microscopic images of such condensates formed in I microg/ml drug solution, a mechanism of toroidal condensate formation has been proposed.     

Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA.

DNA bases in the three-base-pair (3bp) region of duplexes with the two major lesions of cisplatin (cis-PtCl(2)(NH(3))(2)) with DNA, namely d(XGG) and d(XAG) ( = N7-platinated base), differ in their relative positions by as much as approximately 3.5 A in structures in the literature. Such large differences impede drug design and assessments of the effects of protein binding on DNA structure. One recent and several past structures based on NMR-restrained molecular dynamics (RMD) differ significantly from the reported X-ray structure of an HMG-bound XGG 16-mer DNA duplex (Ohndorf, U.-M.; Rould, M. A.; He, Q.; Pabo, C. O.; Lippard, S. J. Nature 1999, 399, 708). This 16-mer structure has several significant novel and unique features (e.g., a bp step with large positive shift and slide). Hypothesizing that novel structural features in the XGG or XAG region of duplexes elude discovery by NMR methods (especially because of the flexible nature of the 3bp region), we studied an oligomer with only G.C bp's in the XGGY site by NMR methods for the first time. This 9-mer gave a 5'-G N1H signal with a normal shift and intensity and showed clear NOE cross-peaks to C NHb and NHe. We assigned for the first time (13)C NMR signals of a duplex with a GG lesion. These data, by adding NMR-based criteria to those inherent in NOESY and COSY data, have more specifically defined the structural features that should be present in an acceptable model. In particular, our data indicated that the sugar of the X residue has an N pucker and that the GG cross-link should have a structure similar to the original X-ray structure of cis-Pt(NH(3))(2)(d(pGpG)) (Sherman S. E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368). With these restrictions added to NOE restraints, an acceptable model was obtained only when we started our modeling with the 16-mer structural features. The new X-ray/NMR-based model accounted for the NOESY data better than NOE-based models, was very similar in structure to the 16-mer, and differed from solely NOE-based models. We conclude that all XGG and XAG (X = C or T) duplexes undoubtedly have structures similar to those of the 16-mer and our model. Thus, protein binding does not change greatly the structure of the 3bp region. The structure of this region can now be used in understanding structure-activity relationships needed in the design of new carrier ligands for improving Pt anticancer drug activity.     

Spin-orbit Ab initio investigation of the photodissociation of dibromomethane in the gas and solution phases

A clear and reliable theoretical investigation on dibromomethane (CH(2)Br(2)) photodissociation is desired. The calculation must consider: (i) relativistic effects; (ii) the potential energy curves (PECs) of spin-orbit coupling states; (iii) geometry optimization by the method with both static and dynamic electron correlations; (iv) solvent effects on the photodissociation in the solution. All these have been considered in this study by state-of-the-art quantum chemical calculations. The experimentally observed photodissociation in the gas phase with products of spin-orbit-coupled states, Br((2)P(3/2)) and Br*((2)P(1/2)), was assigned by multi-state second order multiconfigurational perturbation theory in conjunction with spin-orbit interaction through complete active space state interaction (MS-CASPT2/CASSI-SO) PECs. The mechanisms of the experimentally observed photodissociation and photoisomerization in solvent were elucidated by the MS-CASPT2/CASSI-SO method combined with polarized continuum model of the solvent.     

Heterocyclic diamidine interactions at AT base pairs in the DNA minor groove: effects of heterocycle differences, DNA AT sequence and length

Given the increasing significance of diamidines as DNA-targeted therapeutics and biotechnology reagents, it is important to establish the variations in thermodynamic quantities that characterize the interactions of closely related compounds to different sequence AT binding sites. In this study, an array of methods including biosensor-surface plasmon resonance (SPR), isothermal titration microcalorimetry (ITC), circular dichroism (CD), thermal melting (Tm) and molecular modeling have been used to characterize the binding of dicationic diamidines related to DB75 (amidine-phenyl-furan-phenyl-amidine) with alternating and nonalternating AT sequences. Conversion of the central furan of DB75 to other similar groups, such as thiophene or selenophene, can yield compounds with increased affinity and sequence binding selectivity for the minor groove. Calorimetric measurements revealed that the thermodynamic parameters (Delta G, Delta H, Delta S) that drive diamidine binding to alternating and nonalternating oligomers can be quite different and depend on both DNA sequence and length. Small changes in a compound can have major effects on DNA interactions. By choosing an appropriate central group it is possible to "tune" the shape of the molecule to match DNA for enhanced affinity and sequence recognition.     

Theoretical study of the relative stability of rotational conformers of alpha and beta-D-glucopyranose in gas phase and aqueous solution

The alpha-beta anomer energy difference and the stability of 10 rotamers of counterclockwise D-glucopyranose were studied in vacuo and in aqueous solution at the B3LYP/6-31+G(d,p) level. To obtain the solute charge distribution and the solvent structure around it, we used the averaged solvent electrostatic potential from molecular dynamics method, ASEP/MD, which alternates molecular dynamics and quantum mechanics calculations in an iterative procedure. The main characteristics of the anomeric equilibrium, both in vacuo and in solution, are well reproduced. The relative stability of the different anomers is related to the availability of the free pairs of electrons in the anomeric oxygen to interact with the water molecules. The influence of solvation in the conformer equilibrium is also analyzed.     

A DSC study of the liquid crystalline phases of salmon sperm DNA

Thermodynamic stabilities of the liquid crystalline (LC) and gel (G) phases of salmon sperm DNA were investigated by differential scanning calorimetry (DSC). The enthalpic and the entropic components of the thermal denaturation free energy are briefly discussed. In order to evaluate the thermodynamic data for the denaturation of the gel (G) phase of DNA and compare it with those for the LC DNA phase, a hypothesis for the thermal denaturation mechanism of G DNA is proposed. A comparison between these two sets of data has shown that DNA in the LC phase is thermally and thermodynamically more stable than in the G phase over the temperature range which was investigated.     

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions     

Radiochemical study of interaction of the nucleogenic diethylgermylium cations with benzene in the gas and condensed phases

Interaction of free diethylgermylium ions with benzene in the gas and condensed phases was studied by the radiochemical method. A possible mechanism of the ion-molecular reactions was suggested. At the interaction of these ions with benzene the products of germylation of the latter were not detected. More advantageous are the processes of degermylation leading to the formation of tritium-labeled benzene. A possibility of rearrangement of the nucleogenic diethylgermylium cation into other isomeric forms was revealed, these forms were calculated by B3LYP method with the 6–31G* and cc-pVTZ basis sets.     

Quantitative determination of lysozyme-ligand binding in the solution and gas phases by electrospray ionisation mass spectrometry

Affinity constants for the binding of a range of substrate and non-substrate oligosaccharides to hen egg white lysozyme were determined by direct observation of the protein.ligand complexes using electrospray ionisation mass spectrometry (ESI-MS) with a chip-based nano-ESI source. The values obtained for a series of beta-1,4-N-acetylglucosamine oligomers (NAGn) were found to be in good agreement with those determined by fluorescence measurement. Oligomers of alpha-1,4-glucose (Glcn), which are believed to bind to lysozyme non-specifically, exhibited a 10(6)- to 10(8)-fold lower affinity for the enzyme. Lysozyme.NAGn complexes displayed an increase in Ka from n=2 to n=4, but then reached a plateau. In contrast non-specific lysozyme.Glcn complexes showed no such trend. Determination of gas-phase complex stability was achieved by quantitative collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD) measurements. The collision energy (Ec50) or laser power (IRMPD50) required to dissociate precursor ions to 50% of their original intensity was determined for lysozyme.NAGn and Glcn complexes using the [M+8H]8+ charge state. An excellent correlation between trends in Ka and gas-phase stability was seen for NAGn oligomers bound to lysozyme, whereas no such relationship was observed with the non-specific, weaker lysozyme.Glcn complexes. These results illustrate that ESI-MS can be used to quantify the interactions between lysozyme and oligosaccharides in both the solution and gas phase and that measurement of gas-phase complex stability by CID or IRMPD can provide information about specific solution binding events.