Structural feature of bent DNA recognized by HMGB1

High Mobility Group Box 1 (HMGB1) protein, a potential therapeutic target, binds bent DNAs structure-specifically. Here we report on a crucial structural feature of the bent DNA required for strong binding to HMGB1. NMR structures of two bent DNA oligomers, only one of which binds strongly to HMGB1, revealed that the presence of a pocket structure on the minor groove is crucial for strong binding through penetration of a phenylalanine residue.     

Collective conformations of DNA polymers assembled on surface density gradients

To study dense double-stranded DNA (dsDNA) polymer phases, we fabricated continuous density gradients of binding sites for assembly on a photochemical interface and measured both dsDNA occupancy and extension using evanescent fluorescence. Despite the abundance of available binding sites, the dsDNA density saturates after occupation of only a fraction of the available sites along the gradient. The spatial position at which the density saturates marks the onset of collective stretching of dsDNA, a direct manifestation of balancing entropic and excluded-volume interactions. The methodology presented here offers a new means to investigate dense dsDNA compartments.     

Stochastic ensembles of thermodynamic potentials

The provision of uncertainty estimates along with measurement results or values computed thereof is metrologically mandatory. This is in particular true for observational data related to climate change, and thermodynamic properties of geophysical substances derived thereof, such as of air, seawater or ice. The recent International Thermodynamic Equation of Seawater 2010 (TEOS-10) provides such properties in a comprehensive and highly accurate way, derived from empirical thermodynamic potentials released by the International Association for the Properties of Water and Steam (IAPWS). Currently, there are no generally recognised algorithms available for a systematic and comprehensive estimation of uncertainties for arbitrary properties derived from those potentials at arbitrary input values, based on the experimental uncertainties of the laboratory data that were used originally for the correlations during the construction process. In particular, standard formulas for the uncertainty propagation which do not account for mutual uncertainty correlations between different coefficients tend to systematically and significantly overestimate the uncertainties of derived quantities, which may lead to practically useless results. In this paper, stochastic ensembles of thermodynamic potentials, derived from randomly modified input data, are considered statistically to provide analytical formulas for the computation of the covariance matrix of the related regression coefficients, from which in turn uncertainty estimates for any derived property can be computed a posteriori. For illustration purposes, simple analytical application examples of the general formalism are briefly discussed in greater detail.     

Self-assembling ensembles of silicomolybdic acid-diamines

Modification of the surface of the conductive glass [conductive layer is indium-tin oxide (ITO)] by diamines (1,8-diaminooctane and piperazine) and organic polycations [poly(diallyldimethylammonium chloride) and poly(allylamine) hydrochloride] followed by the formation of electroactive composites with silicomolybdic acid H₄SiMo₁₂O₄₀ was carried out. The two-layer ITO/cationic/anionic coatings were shown to differ by the shape of cyclic voltammograms depending on the cationic component.     

Computer simulations of ligand–protein binding with ensembles of protein conformations: A Monte Carlo study of HIV‐1 protease binding energy landscapes

We present the results of molecular docking simulations with HIV‐1 protease for the sb203386 and skf107457 inhibitors by Monte Carlo simulated annealing. A simplified piecewise linear energy function, the standard AMBER force field, and the AMBER force field with solvation and a soft‐core smoothing component are employed in simulations with a single‐protein conformation to determine the relationship between docking simulations with a simple energy function and more realistic force fields. The temperature‐dependent binding free energy profiles of the inhibitors interacting with a single protein conformation provide a detailed picture of relative thermodynamic stability and a distribution of ligand binding modes in agreement with experimental crystallographic data. Using the simplified piecewise linear energy function, we also performed Monte Carlo docking simulations with an ensemble of protein conformations employing preferential biased sampling of low‐energy protein conformations, and the results are analyzed in connection with the free energy profiles. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 72: 73–84, 1999     

INDO study of bent radical anions

The INDO method has been used to calculate the ¹³C and β-proton coupling constants of some carboxyl anion radicals. It is concluded that the deviation from planarity in these radicals is approximately 6°. It is proposed that these radicals constitute models for the formation of tetrahedral intermediates in addition reactions of a nucleophile to a carbonyl group.     

Stimulated aggregation in ensembles of microcrystals

Aggregates of calcium carbonate microcrystals precipitated from a highly supersaturated aqueous solution were found to form in two stages. At the first stage, high-porosity disordered aggregates (floccules), and at the second, low-porosity ordered aggregates (agglomerates) formed. The application of an acoustic field with a frequency of 2.64 MHz and radiation power 3 W/cm² did not influence the kinetics of formation of microcrystals but accelerated aggregation by four orders of magnitude. This effect was explained by the sonostimulated desolvation of microcrystals colliding with the surface of aggregates and the corresponding decrease in the probability of the detachment from aggregates after collisions. The formation of microcrystals and aggregates in an acoustic field can be described by a Fokker-Planck-type equation. Taking this into account, a model of sonostimulated agglomeration revealing the direction of further investigations was formulated.     

Velocity distributions of camphor particle ensembles

The spatial distribution of ensembles of camphor particles on a water surface can be classified into four phases with the following properties, for increasing density: (I) no clustering of particles and a minimum distance distribution similar to that of a 2D ideal gas; (II) reminiscent of a gas with clustering of particles; (III) net-like structure with occasional rearrangements; and (IV) motionless. While single particles have varying velocity distributions, the overall velocity distribution is Laplacian (the width decreasing with increasing camphor density) for all phases.     

Cluster analysis of molecular conformations

We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.     

Semi-empirical calculations of dihydropyran conformations

Semi-empirical calculations of dihydropyran conformations have been performed using a Karplus-type equation with the sum of chemical shifts as a correction parameter. A graphical method has been proposed to evaluate the conformational state of the molecules.     

Dynamic self-assembly in ensembles of camphor boats

Millimeter-sized gel particles loaded with camphor and floating at the interface between water and air generate convective flows around them. These flows give rise to repulsive interparticle interactions, and mediate dynamic self-assembly of nonequilibrium particle formations. When the numbers of particles, N, are small, particle motions are uncorrelated. When, however, N exceeds a threshold value, particles organize into ordered lattices. The nature of hydrodynamic forces underlying these effects and the dynamics of the self-assembling system are modeled numerically using Navier-Stokes equations as well as analytically using scaling arguments.     

Chain conformations of block copolymers

An analytical theory of block copolymer conformations is developed for systematically studying the effects of the chain length, chain architecture, and segment interactions. The main results obtained for AB diblock and ABA triblock chains are as follows: (i) In the absence of AA and BB interactions, both diblock and triblock chains collapse to a dense form if the AB interaction is attractive. In the collapsed coil form, the mean-square end-to-end distance 〈R²〉 is proportional to the square root of the number of segments n^1/2. (ii) The diblock chain has a dumbbell form if AA and BB interactions are attractive and AB interaction repulsive, but the triblock chain collapses. In the dumbbell form, 〈R²〉 is proportional to n.     

Unbiased sampling of lattice Hamilton path ensembles

Hamilton paths, or Hamiltonian paths, are walks on a lattice which visit each site exactly once. They have been proposed as models of globular proteins and of compact polymers. A previously published algorithm [Mansfield, Macromolecules 27, 5924 (1994)] for sampling Hamilton paths on simple square and simple cubic lattices is tested for bias and for efficiency. Because the algorithm is a Metropolis Monte Carlo technique obviously satisfying detailed balance, we need only demonstrate ergodicity to ensure unbiased sampling. Two different tests for ergodicity (exact enumeration on small lattices, nonexhaustive enumeration on larger lattices) demonstrate ergodicity unequivocally for small lattices and provide strong support for ergodicity on larger lattices. Two other sampling algorithms [Ramakrishnan et al., J. Chem. Phys. 103, 7592 (1995); Lua et al., Polymer 45, 717 (2004)] are both known to produce biases on both 2x2x2 and 3x3x3 lattices, but it is shown here that the current algorithm gives unbiased sampling on these same lattices. Successive Hamilton paths are strongly correlated, so that many iterations are required between statistically independent samples. Rules for estimating the number of iterations needed to dissipate these correlations are given. However, the iteration time is so fast that the efficiency is still very good except on extremely large lattices. For example, even on lattices of total size 10x10x10 we are able to generate tens of thousands of uncorrelated Hamilton paths per hour of CPU time.     

Probing the solvent accessibility and electron density of adenine: oxidation of 7-deazaadenine in bent DNA and purine doublets

The effect of DNA bending on nucleobase electron transfer was investigated by studying the oxidation of double-stranded sequences containing seven repeats of the known bent sequence d(GGCA(1)A(2)A(3)A(4)A(5)A(6)C) where 7-deazaadenine (zA) was substituted at the A(3) position. Native gel electrophoresis was used to show that the sequence remained bent upon substitution of zA, which provides for oxidation of the sequence by Ru(bpy)(3)(3+) (bpy = 2,2'-bipyridine). The Ru(III) oxidant was generated by photolysis of Ru(bpy)(3)(2+) in the presence of ferricyanide, and the oxidation was visualized by high-resolution gel electrophoresis of the radiolabeled DNA sequence following base treatment. Cleavage of the DNA strand at the guanine residues and at the zA residues was observed. Comparison of the oxidation of zA in bent DNA versus the normal B form showed that hybridization of the B form sequence to its Watson-Crick complement produced a reduction in cleavage by a factor of 5.19 +/- 0.46 while hybridization of the bent sequence only reduced cleavage by a factor of 1.58 +/- 0.23. This result implies that the zA in the double-stranded, bent sequence is much more solvent-exposed than in normal B-form DNA. When the zA occurred in a B-form 5'-zA-G doublet, the reactivity was 6.63 +/- 0.10 times higher for the zA compared to the G. This implies an even greater effect of a 3'-guanine on the oxidation potential of zA than in the well-known 5'-GG doublet.     

Energy landscapes of dynamic ensembles of rolling triplet repeat bulge loops: implications for DNA expansion associated with disease states

DNA repeat domains can form ensembles of canonical and noncanonical states, including stable and metastable DNA secondary structures. Such sequence-induced structural diversity creates complex conformational landscapes for DNA processing pathways, including those triplet expansion events that accompany replication, recombination, and/or repair. Here we demonstrate further levels of conformational complexity within repeat domains. Specifically, we show that bulge loop structures within an extended repeat domain can form dynamic ensembles containing a distribution of loop positions, thereby yielding families of positional loop isomers, which we designate as "rollamers". Our fluorescence, absorbance, and calorimetric data are consistent with loop migration/translocation between sites within the repeat domain ("rollamerization"). We demonstrate that such "rollameric" migration of bulge loops within repeat sequences can invade and disrupt previously formed base-paired domains via an isoenthalpic, entropy-driven process. We further demonstrate that destabilizing abasic lesions alter the loop distributions so as to favor "rollamers" with the lesion positioned at the duplex/loop junction, sites where the flexibility of the abasic "universal hinge" relaxes unfavorable interactions and/or facilitates topological accommodation. Another strategic siting of an abasic site induces directed loop migration toward denaturing domains, a phenomenon that merges destabilizing domains. In the aggregate, our data reveal that dynamic ensembles within repeat domains profoundly impact the overall energetics of such DNA constructs as well as the distribution of states by which they denature/renature. These static and dynamic influences within triplet repeat domains expand the conformational space available for selection and targeting by the DNA processing machinery. We propose that such dynamic ensembles and their associated impact on DNA properties influence pathways that lead to DNA expansion.     

DNA fragment conformations. I—methods for the assignment of DNA fragment proton resonances. 1H NMR spectra of dApTpGpT and dApCpApTpGpT

A general method for the assignment of DNA fragment proton resonances, especially for the sugar protons, has been presented and used to interpret the 400 MHz proton spectra of dApTpGpT and dApCpApTpGpT in neutral aqueous solution. Only fine splittings of about 3 Hz are observed in the H-2″ resonances, and the total splitting is larger for the H-2′ (≈29 Hz) than for the H-2″ (22–23 Hz) multiplets. The purine and pyrimidine resonances can be distinguished on the basis of the H-2″ and H-2″ chemical shifts. The resonances of the H-2′ and H-2″ protons (above and below the sugar plane, respectively) of dA and dG exhibit chemical shifts of 2.65—2.80 ppm, while those of dC and dT residues are located at higher fields between 1.95 and 2.40 ppm. At high temperature (≥60°C), δH-2′>YδH-2″ for the purine family, while δH-2′ « δH-2″ in the case of the pyrimidine family. Except for the terminal residue, the H-3′ resonances of dA and dG are located at lower fields compared with those of the dC and dT residues. The same is true for the H-4′ resonances. In general δA_1′>δG_1′ and in the case of self complementary duplexes the H-1′ and H-2′ chemical shift variations versus temperature are found to be larger for the dC than for the dT residues.     

Synthesis and structures of novel luminescent bent acenedithiophenes

1,4-dithienyl-2,5-divinylbenzenes are readily available compounds that undergo oxidative photocyclization to afford bent anthradithiophenes (BADTs). The new parent and didodecyl-functionalized derivatives have been structurally characterized, and their absorption and emission spectra are reported.     

Macromolecular conformations at the water-air interface: Interactions between alpha and beta conformations of polypeptides

Bidimensional miscibility between alpha and beta conformations of polypeptides was investigated at the water-air interface in the 15°–30°C temperature range. The polypeptides were poly--methyl-L-glutamate (PGMG), poly--benzyl-L-glutamate (PGBG) and poly--benzyl-L-aspartate (PBBA). The polypeptide conformations, alpha or beta, were checked by IR spectroscopy using the MIR technique.The spreading isotherms for mixed monolayers alpha-PGMG/alpha-PGBG and beta-PGMG/beta-PBBA showed bidimensional miscibility both for alpha-alpha and beta-beta mixtures.For the alpha-alpha system, attractive interactions among the polypeptide alphahelices were found (G_mix<0) and the driving factor appeared to be the entropic one (packing). Compressibility moduli and surface potential measurements showed a fluidification effect of alpha-PGBG on mixed monolayers. In the case of beta-beta mixed monolayers, ideal behaviour was observed and no fluidification effect detected.Scanning electron micrographs made on collapsed monolayers showed hexagonal structures for alpha-alpha mixtures and no well-defined or characterized features for the beta-beta system.