DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Synthesis and characterization of carbohydrate-based phospholipids

Novel carbohydrate-based phospholipids containing two saturated C(12) (dilauroyl ribo-phosphocholine) (DLRPC), C(14) (dimyristoyl ribo-phosphocholine) (DMRPC), and C(20) (diarachadonyl ribo-phosphocholine) (DARPC) carboxylic acid chains were synthesized. The physical properties of the supramolecular structures formed by these compounds were compared to those formed by their direct glycerol analogues dilauroyl phosphocholine (DLPC), dimyristoyl phosphocholine (DMPC), and diarachadonyl phosphocholine (DAPC). Modulated differential scanning calorimetry (MDSC) and X-ray diffraction data indicated that with chain lengths < or =14 carbons, the carbohydrate backbone increased the thermal stability of the bilayer below the phase-transition temperature (T(m)) as compared to the glycerol-based lipids. With longer chains (C(20)), the bilayer structure was destabilized as compared to glycerol-based lipids. NMR studies of a DMRPC vesicle dispersion reveal split choline headgroup signals and distinct magnetization transfer effects arising from the "inner" and "outer" surfaces of the bilayer vesicle. Modulated differential scanning calorimetry also demonstrated that glycerol- and carbohydrate-based lipids mix, as evidenced by a single intermediate T(m). In addition, carbohydrate-based lipid/cholesterol mixtures exhibited a decrease in enthalpy with an increase in cholesterol concentration. Unlike glycerol phospholipids, carbohydrate lipids were resistant to enzymatic degradation by phospholipase A(2) (PLA(2)).     

Tuning the optical properties of fluorinated indolylfulgimides

Photochromic fluorinated indolylfulgides have been identified as potential candidates for a wide range of applications including optical switches, photoregulators of biological processes, and optical memory media. In humid environments or biological systems, hydrolytic stability is essential. In an effort to improve hydrolytic stability, a series of indolylfulgimides has been synthesized from a parent trifluoromethyl-substituted indolylfulgide. The nitrogen of the succinimide moiety is linked to either a dimethyl amino or one of seven substituted phenyl groups. The phenyl groups feature substituents with increasing electron-withdrawing ability. The spectral characteristics of each compound have been examined, revealing that the wavelength absorption maxima of each form increases with increasing electron-withdrawing ability of the substituted N-phenyl ring. The quantum yields of the photoreactions have been determined with the N-(phenyl)fulgimide showing a ring closure value of nearly 0.30 in toluene. In addition, the hydrolytic, thermal, and photochemical stabilities of each compound have been measured. The fulgimides exhibit at least a 200-fold enhancement of hydrolytic stability for the Z-form and over a 1000-fold enhancement for the C-form in comparison to the same form of the parent fulgide. The N-(2,3,5,6-tetrafluoro-4-trifluoromethylphenyl)fulgimide can undergo up to 3000 photochemical cycles (coloration followed by bleaching) before losing 20% of its initial absorbance at photostationary state.     

A mass spectrometric study of the pyrolysis of gibberellic acid

The behaviour of gibberellic acid (GA₃) under electron impact and chemical ionization conditions has been examined. The tendency of GA₃ to undergo pyrolysis by the loss of the elements of water and carbon dioxide has been identified. Two methods of sample introduction can be used to minimize the occurrence of this pyrolysis. Accurate mass measurement allows the composition of the pyrolysis product to be determined and metastable techniques confirm the structure of this product to be epi-allogibberic acid rather than its isomer allogibberic acid. This result corrects a misconception in the literature and illustrates the advantage of metastable methods compared with accurate mass measurements, for the determination of small structural differences within a molecule.     

THE MOLECULAR WEIGHT OF HAEMATOPORPHYRIN DERIVATIVE, ITS GEL COLUMN FRACTIONS and SOME OF ITS COMPONENTS IN AQUEOUS SOLUTION

Abstract— The average molecular weights of haematoporphyrin derivative (HPD), the fractions of HPD that can he obtained by gel chromatography and of purified haematoporphyrin and protoporphyrin in aqueous solution have been determined by ultracentrifugation. The results show that HPD contains polymeric material with the excluded fraction from the gel column (HPD aggregate) having an average molecular weight of greater than 20000. The two remaining gel column fractions of HPD have lower molecular weights and their similarity indicates that these fractions do not separate because of molecular weight differences. Purified haematoporphyrin has a comparatively low molecular weight in aqueous solution but the data is not capable of discriminating between monomer, dimer or slightly higher oligomer. In contrast, protoporphyrin sediments to the bottom of the centrifuge tube under the conditions of sedimentation equilibrium indicating that it has an average molecular weight considerably greater than that of HPD aggregate.     

Constrained near-minimax approximation by weighted expansion and interpolation using Chebyshev polynomials of the second,third, and fourth kinds

Well known results on near-minimax approximation using Chebyshev polynomials of the first kind are here extended to Chebyshev polynomials of the second, third, and fourth kinds. Specifically, polynomial approximations of degreen weighted by (1–x ²)^1/2, (1+x)^1/2 or (1–x)^1/2 are obtained as partial sums of weighted expansions in Chebyshev polynomials of the second, third, or fourth kinds, respectively, to a functionf continuous on [–1, 1] and constrained to vanish, respectively, at ±1, –1 or +1. In each case a formula for the norm of the resulting projection is determined and shown to be asymptotic to 4^–2logn +A +o(1), and this provides in each case and explicit bound on the relative closeness of a minimax approximation. The constantA that occurs for the second kind polynomial is markedly smaller, by about 0.27, than that for the third and fourth kind, while the latterA is identical to that for the first kind, where the projection norm is the classical Lebesgue constant _n . The results on the third and fourth kind polynomials are shown to relate very closely to previous work of P.V. Galkin and of L. Brutman.Analogous approximations are also obtained by interpolation at zeros of second, third, or fourth kind polynomials of degreen+1, and the norms of resulting projections are obtained explicitly. These are all observed to be asymptotic to 2^–1logn +B +o(1), and so near-minimax approximations are again obtained. The norms for first, third, and fourth kind projections appear to be converging to each other. However, for the second kind projection, we prove that the constantB is smaller by a quantity asymptotic to 2^–1log2, based on a conjecture about the point of attainment of the supremum defining the projection norm, and we demonstrate that the projection itself is remarkably close to a minimal (weighted) interpolation projection.All four kinds of Chebyshev polynomials possess a weighted minimax property, and, in consequence, all the eight approximations discussed here coincide with minimax approximations when the functionf is a suitably weighted polynomial of degreen+1.     

Nonabelian orbifolds and the boson-fermion correspondence

For a positive integerl divisible by 8 there is a (bosonic) holomorphic vertex operator algebra (VOA) associated to the spin lattice _l . For a broad class of finite groupsG of automorphisms of we prove the existence and uniqueness of irreducibleg-twisted -modules and establish the modular-invariance of the partition functionsZ(g, h, ) for commuting elements inG. In particular, for any finite group there are infinitely many holomorphic VOAs admittingG for which these properties hold. The proof is facilitated by a boson-fermion correspondence which gives a VOA isomorphism between and a certain fermionic construction, and which extends work of Frenkel and others.Supported by NSA grant MDA904-92-H-3099.Supported by NSF grant DMS-9122030.     

High-Valent Manganese in Polyoxotungstates. 3. Dimanganese Complexes of gamma-Keggin Anions

Dimanganese-substituted gamma-Keggin heteropoly tungstates have been synthesized by reaction of the lacunary species gamma-[(SiO(4))W(10)O(32)](8)(-) with appropriate mixtures of Mn(II) and MnO(4)(-). The crystal structure of [(CH(3))(3)(C(6)H(5))N](4)[(SiO(4))W(10)Mn(III)(2)O(36)H(6)].2CH(3)CN.H(2)O (anion 1) was determined by X-ray diffraction. Crystallographic data: space group P&onemacr;, a = 12.951(3) ?, b = 14.429(3) ?, c = 20.347(4) ?, alpha = 81.95(3) degrees, beta = 88.92(3) degrees, gamma = 67.48(3) degrees, V = 3475.2(13) ?(3), and Z = 2. The final R value is 7.29% for 15861 reflections with I > 2sigma(I). The anion has the anticipated gamma-Keggin structure with virtual C(2)(v)() symmetry. The two Mn cations occupy adjacent, edge-shared octahedra with bridging hydroxo and terminal aqua ligands. Anion 1 can be oxidized and reduced to the corresponding Mn(III)Mn(IV) (2) and Mn(II)(2) (3) species respectively. The magnetic susceptibility of 1 between 2 and 300 K indicates that the Mn(III) cations are antiferromagnetically coupled, with J = -17.0 cm(-)(1) and g = 1.965. No simple magnetic behavior was observed for 2 or 3.     

The Landau-Lifshitz equation,elliptic curves and the ward transform

The Landau-Lifshitz (LL) equation is studied from a point of view that is close to that of Segal and Wilson's work on KdV. The LL hierarchy is defined and shown to exist using a dressing transformation that involves parameters ₁, ₂, ₃ that live on an elliptic curve . The crucial role of the groupK ₂ × ₂ of translations by the half-periods of and its non-trivial central extension is brought out and an analogue of Birkhoff factorisation for -equivariant loops in is given. This factorisation theorem is given two treatments, one in terms of the geometry of an infinite-dimensional Grassmannian, and the other in terms of the algebraic geometry of bundles over . Further, a Ward-like transform between a class of holomorphic vector bundles on the total spaceZ of a line-bundle over and solutions of LL is constructed. An appendix is devoted to a careful definition of the Grassmannian of the Frechet spaceC (S ¹).