A new approach to stabilize complementary complexes formed by short oligonucleotides and their derivatives.

A proposed approach to stabilize complementary complexes is based on the stabilizing effect of oligonucleotide derivatives bearing polyaromatic residues on the adjacent short oligonucleotides if their recognition sites make a tandem on the target. This approach has been used to enhance efficiency and specificity of site-specific modification of nucleic acids.     

Size and structure of antigen-antibody complexes: thermodynamic parameters

The role of antigen-antibody (Ag-Ab) complexes in the immune response depends, in part, on the size of the complexes. Previously, we combined electron microscopy with classical and quasi-elastic light scattering to characterize the molecular weight distribution and the conformation of Ag-Ab complexes made from bovine serum albumin (BSA) and pairs of anti-BSA monoclonal antibodies at a single concentration and Ag:Ab molar ratio. In this report, the molecular weight distribution of Ag-Ab complexes was determined by classical light scattering at a single Ag:Ab ratio and over a range of concentrations, and binding of BSA to pairs of MAb was determined by radioimmunoassay at several Ag:Ab molar ratios. A thermodynamic model was developed for the equilibrium size distribution of Ag-Ab complexes formed between a pair of MAb, each with unique affinity and specificity, and an Ag containing a single epitope for each of the pair of MAb. The combined experimental data were used in conjunction with the model to determine the values of cyclization and polymerization constants. Successful determination of the parameters required data from both classical light scattering and electron microscopy. Cyclization constants were lower than those reported in other studies of Ag-Ab complexes; this may be attributable to our use of a protein Ag, as compared to a divalent hapten. In two out of three cases, cyclization constants increased with increasing number of Ab in the complex, in contrast to previous assumptions. The validity of the thermodynamic model was further shown by its ability, in combination with conformational and hydrodynamic model, to predict the hydrodynamic radius of the complexes over a wide range of experimental conditions.     

Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides

Results from optical melting studies of Watson–Crick complementary heteroduplexes formed between 2′-O-methyl RNA and RNA oligonucleotides are used to determine nearest neighbor thermodynamic parameters for predicting the stabilities of such duplexes. The results are consistent with the physical model assumed by the individual nearest neighbor-hydrogen bonding model, which contains terms for helix initiation, base pair stacking and base pair composition. The sequence dependence is similar to that for Watson–Crick complementary RNA/RNA duplexes, which suggests that the sequence dependence may also be similar to that for other backbones that favor A-form RNA conformations.     

Characterization of the discoidal complexes formed between apoA-I-CNBr fragments and phosphatidylcholine.

The structure, composition, and physico-chemical properties of lipid-protein complexes generated between dimyristoylphosphatidylcholine (DPMC) and the CNBr fragments of human apoA-I were studied. The fragments were separated by high performance liquid chromatography and purified on a reversed-phase column. The complexes with DMPC were isolated on a Superose column; their dimensions were obtained by gradient gel electrophoresis and by electron microscopy. The secondary structure of the protein in the complexes was studied both by circular dichroism and by attenuated total reflection infrared spectroscopy. The fragments 1 and 4 of apoA-I, containing, respectively, two and three amphipathic helices, recombined with the phospholipid to generate discoidal particles with sizes similar to that of apoA-I- and apoA-II-DMPC complexes. The infrared measurements indicated that in all complexes the apolipoprotein helical segments were oriented parallel to the phospholipid acyl chains and that the protein was located around the edges of the discs. Computer modelling of the complexes based on energy minimization techniques proposed a model for these particles in agreement with the dimensions measured experimentally. In conclusion, we propose that apoA-I and its longest CNBr fragments are able to generate discoidal particles with DMPC, with apolipoprotein helical segments oriented parallel to the acyl chains of the phospholipids.     

Spectrophotometric studies on complexes formed between tri-, di- and monobutyltin(IV) chlorides and 3-hydroxyflavone in different solvents

The complex formation of tri-, di- and monobutyltin(IV) chloride with 3-hydroxyflavone was studied spectrophotometrically in methanol, chloroform and toluene (the last two after extraction with buffer pH 9.0) by the molar ratio method. The composition of the chelates formed was found to be solvent and molar ratio (C_M/C_L) dependent. The complex formation constants were calculated.     

The thermodynamic contribution of the 5-methyl group of thymine in the two- and three-stranded complexes formed by poly(dU) and poly(dT) with poly(dA)

To assess the thermodynamic contribution of the 5-methyl group of thymine, we have studied the two-stranded helical complexes poly(dA).poly(dU) and poly(dA).poly(dT) and the three-stranded complexes--poly(dA).2poly(dU), poly(dA).poly(dT).poly(dU) and poly(dA).2poly(dT)--by differential scanning calorimetry, and uv optical melting experiments. The thermodynamic quantities associated with the 3 --> 2, 2 --> 1, and 3 --> 1 melting transitions are found to vary with salt concentration and temperature in a more complex manner than commonly believed. The transition temperatures, T(m), are generally not linear in the logarithm of concentration or activity of NaCl. The change in enthalpy and in entropy upon melting varies with salt concentration and temperature, and a change in heat capacity accompanies each transition. The poly(dA).2poly(dU) triple helix is markedly different from poly(dA).2poly(dT) in both its CD spectrum and thermodynamic behavior, while the poly(dA).poly(dT).poly(dU) triple helix resembles poly(dA).2poly(dT) in these properties. In comparing poly(dA).2poly(dT) with either the poly(dA).poly(dT).poly(dU) or the poly(dA).2poly(dU) triplexes, the substitution of thymine for uracil in the third strand results in an enhancement of stability against the 3 --> 2 dissociation of deltadeltaG degrees = -135 +/- 85 cal (mol A)(-1) at 37 degrees C. This represents a doubling of the absolute stability toward dissociation compared to the triplexes with poly(dU) as the third strand. The poly (dA).poly (dT) duplex is more stable than poly(dA).poly(dU) by deltadeltaG degrees = -350 +/- 60 cal (mol base pair)(-1) at 37 degrees C. Poly(dA).poly(dT) has 50% greater stability than poly(dA).poly(dU) as a result of the dT for dU substitution in the duplex.     

Mismatches in DNA double strands: thermodynamic parameters and their correlation to repair efficiencies.

The helix-coil transitions of the 16 octadecameric DNA duplexes dCGTCGTTTXACAACGTCG X dCGACGTTGTX1AAACGACG with A, T, G, and C for X and X1 were measured by UV-absorption. This sequence was taken from former studies of in vivo determination of efficiencies of mismatch repair (Kramer, Kramer, and Fritz (1984) Cell 38, 879-887). The thermodynamic parameters for double strand and mismatch formation have been obtained by evaluating the partition function of a stack model which allowed for loop formation. As a result the mismatches could be classified into wobble base pairs (T/G, G/G, C/A, A/A, A/G), open base pairs, i.e. permanent loops (T/T, C/T, T/C, C/C), and intermediate or weak base pairs (G/T, A/C, G/A). There is no correlation between Tm and the biological repair efficiency of X/X1. The structure classes, however, as described above show a close correlation: Open base pairs show the lowest repair efficiencies, whereas mismatches with high repair efficiency always belong to the structural class of wobble base pairs. Because of the palindromic nearest neighbors of the variation site X/X1, the influence of next-nearest neighbor interactions could be detected and be estimated to about 1 kJ/mol for one stack.     

How the 'forceps' of Lithophaga aristata (Bivalvia: Mytiloidea) are formed

The calcareous substratum borer, Lithopaga aristata Dillwyn, 1817, secretes posterior incrustations that take the form of interlocking 'forceps'. These are secreted, initially, as asymmetrical ridges by similarly asymmetrical dorsal and ventral glands in the left and right middle folds of the posterior mantle lobes. In the adult, the secretions are more uniformly spread over the posterior shell margins, concealing the juvenile ridges.
Opening and closing of the valves smooths the outer surfaces of the 'forceps' against the burrow wall, which also comes to be lined with calcium carbonate that is reciprocally smoothed, so that they occlude the borehole more effectively. Extension and retraction of the siphons probably smooths the inner surfaces of the 'forceps' which are sharpened by abrasion, one against the other, during valve opening and closing. The pair of inequilateral spikes so produced, project from the burrow aperture, occluding it, but probably, more importantly, distancing aperturally attacking predators from the true posterior shell margin. Interlocking of the 'forceps' and their sharpness may further deter would-be predators.     

Polysaccharide-polynucleotide complexes VIII. Cation-induced complex formation between polyuridylic acid and schizophyllan

Raman spectroscopy has recently been applied ex vivo and in vivo to address various biomedical issues such as the early detection of cancers, monitoring of the effect of various agents on the skin, determination of atherosclerotic plaque composition, and rapid identification of pathogenic microorganisms. This leap in the number of applications and the number of groups active in this field has been facilitated by several technological advancements in lasers, CCD detectors, and fiber-optic probes. However, most of the studies are still at the proof of concept stage. We present a discussion on the status of the field today, as well as the problems and issues that still need to be resolved to bring this technology to hospital settings (i.e., the medical laboratory, surgical suites, or clinics). Taken from the viewpoint of clinicians and medical analysts, the potential of Raman spectroscopic techniques as new tools for biomedical applications is discussed and a path is proposed for the clinical implementation of these techniques.     

Sexual dimorphism: why the sexes are (and are not) different

Sex differences often call sexual selection to mind; however, a new damselfly study cautions on being too hasty, and implicates viability selection in the evolution of male and female colouration.     

Hybridization between Ischnura graellsii (Vander Linder) and 2. elegans (Rambur) (Odonata: Coenagrionidae): are they different species?

Two closely related damselflies, Ischnura graellsii and I. elegans , were analysed for morphological differences and reproductive isolation in the north coast of Galicia (NW Spain). We compared animals from sympatric and allopatric localities, including I. elegans from Belgium and I. graellsii from southern Spain as pure allopatric populations. A set of morphometric characters were studied by means of multivariate discriminant analysis to determine if these two species can be unambiguously distinguished. Discriminant analysis revealed that I. graellsii and I. elegans are well differentiated on the first two axis (86% and 11%, respectively). I. graellsii individuals are distinguished from I. elegans by their smaller size and, specifically, by their narrower and shorter wings and shorter tibiae. In addition, I. elegans has a narrower space between the branches of each cercus, and greater distance between the branches of each paraproct. Sympatric individuals are morphologically intermediate, suggesting hybridization. When the species were put together in the laboratory, they showed partial temporal separation in mating behaviour, but males of I. elegans readily mated with females of I. graellsii , and hybrid individuals were obtained. The opposite heterospecific cross was almost impossible, apparently because of mechanical problems with the tandem linkage. Laboratory-reared hybrids (from male I. elegans × female I. graellsii ) are morphologically intermediate, mainly resembling the maternal phenotype. Although hybridization between both taxa is common, we suggest maintaining the specific status for both phenotypes because they show incipient reproductive isolation, as it is reported in the literature. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 76 , 225–235.     

Structure and thermodynamic properties of the complexes between phospholipase A2 and lipid micelles.

The interaction between porcine pancreatic phospholipase A2 and a homogeneous population of micelles of the subtrate analogue n-hexadecylphosphorylcholine containing 155 lipid monomers was studied by light scattering, equilibrium gel filtration, and isothermal calorimetry. From the detergent/protein molar ratio and the equivalent "molecular weight" of the resulting complex it is concluded that insertion of the enzyme into the detergent micelle results in a protein--detergent complex containing two phospholipase A2 molecules and 80 lipid monomers at 25 degrees C. The affinity constants and complex composition have been determined at different temperatures, allowing calculation of the thermodynamic parameters of the binding process. It is concluded that the interaction of phospholipase A2 with micellar lipids is predominantly hydrophobic.     

Simultaneous determination of thermodynamic and kinetic parameters of aminopolycarbonate complexes of cobalt(II) and nickel(II) based on isothermal titration calorimetry data

The influence of the different side chain residues on the thermodynamic and kinetic parameters for complexation reactions of the Co²⁺ and Ni²⁺ ions has been investigated by using the isothermal titration calorimetry (ITC) technique supported by potentiometric titration data. The study was concerned with the 2 common tripodal aminocarboxylate ligands, namely, nitrilotriacetic acid and N‐(2‐hydroxyethyl) iminodiacetic acid. Calorimetric measurements (ITC) were run in the 2‐(N‐morpholino)ethanesulfonic acid hydrate (2‐(N‐morpholino) ethanesulfonic acid), piperazine‐N ,N ′‐bis(2‐ethanesulfonic acid), and dimethylarsenic acid buffers (0.1 mol L⁻¹, pH 6) at 298.15 K. The quantification of the metal‐buffer interactions and their incorporation into the ITC data analysis enabled to obtain the pH‐independent and buffer‐independent thermodynamic parameters (K , ΔG , ΔH , and ΔS ) for the reactions under study. Furthermore, the kinITC method was applied to obtain kinetic information on complexation reactions from the ITC data. Correlations, based on kinetic and thermodynamic data, between the kinetics of formation of Co²⁺ and Ni²⁺ complexes and their thermodynamic stabilities are discussed.     

Crystal structure of the complementary quadruplex formed by d(GCATGCT) at atomic resolution

Here we report the crystal structure of the DNA heptanucleotide sequence d(GCATGCT) determined to a resolution of 1.1 Å. The sequence folds into a complementary loop structure generating several unusual base pairings and is stabilised through cobalt hexammine and highly defined water sites. The single stranded loop is bound together through the G(N2)–C(O2) intra-strand H-bonds for the available G/C residues, which form further Watson–Crick pairings to a complementary sequence, through 2-fold symmetry, generating a pair of non-planar quadruplexes at the heart of the structure. Further, four adenine residues stack in pairs at one end, H-bonding through their N7–N6 positions, and are additionally stabilised through two highly conserved water positions at the structural terminus. This conformation is achieved through the rotation of the central thymine base at the pinnacle of the loop structure, where it stacks with an adjacent thymine residue within the lattice. The crystal packing yields two halved biological units, each related across a 2-fold symmetry axis spanning a cobalt hexammine residue between them, which stabilises the quadruplex structure through H-bonds to the phosphate oxygens and localised hydration.     

Complexes formed by (pyrimidine)n . (purine)n DNAs on lowering the pH are three-stranded.

(Pyrimidine)n . (purine)n DNAs of repeating sequences form a distinctive complex on lowering the pH below 6. Previously this complex was thought to be tetra-stranded. The present work is inconsistent with this view, and four lines of evidence show that the complex consists of a triplex together with a poly d(purine) possessing secondary structure. Formula: (see text). (a) S1 nuclease digestion leads to degradation of 50% of the poly d(purine) content of the pH 5-induced complex. (b) Buoyant density studies demonstrate that there is no interaction between the triplex and added free poly d(purine) and also that the complex formed from duplex DNA contained poly d(purine) which is free to form a triplex on addition of an appropriate poly d(pyrimidine) in the correct stoichiometry. (c) The hyperchromic shifts of the triplex and poly d(purine), upon melting, are mutually independent. (d) The circular dichroism spectrum of the complex is simply the weighted average of a triplex together with a free poly d(purine). The triplexes have tm's approximately 20 degrees higher than the corresponding duplexes under comparable conditions and they are extremely resistant to various deoxyribonucleases; properties which may prove useful for their isolation from natural sources.     

The nature of the complexes formed between the Int protein and DNA

The λ Int protein interacts with DNA to form highly condensed complexes of a non-specific nature. Complexes formed with DNA carrying the bacterial attachment site or lacking any attachment site are dissociated by incubation with heparin or single-stranded DNA. Complexes formed with DNA carrying the phage attachment site are converted to simple complexes by these treatments, and the bound Int molecules are localized at the phage attachment site. Int is present in these complexes as an oligomer.     

Kinetic and crystallographic analysis of complexes formed between elastase and peptides from beta-casein.

Human beta-casomorphin-7 (NH2-Tyr-Pro-Phe-Val-Glu-Pro-Ile-CO2H) is a naturally occurring peptide inhibitor of elastase that has been shown to form an acyl-enzyme complex stable enough for X-ray crystallographic analysis at pH 5. To investigate the importance of the N-terminal residues of the beta-casomorphin-7 peptide for the inhibition of elastase, kinetic and crystallographic analyses were undertaken to identify the minimum number of residues required for effective formation of a stable complex between truncated beta-casomorphin-7 peptides and porcine pancreatic elastase (PPE). The results clearly demonstrate that significant inhibition of PPE can be effected by simple tri-, tetra-and pentapeptides terminating in a carboxylic acid. These results also suggest that in vivo regulation of protease activity could be mediated via short peptides as well as by proteins. Crystallographic analysis of the complex formed between N-acetyl-Val-Glu-Pro-Ile-CO2H and PPE at pH 5 (to 1.67 A resolution) revealed an active site water molecule in an analogous position to that observed in the PPE/beta-casomorphin-7 structure supportive of its assignment as the 'hydrolytic water' in the deacylation step of serine protease catalysis.