Visualization of an AAF induced frameshift mutation: molecular views of base displacement in B-DNA from minimized potential energy calculations.

Energy minimized structures of base displacement in an AAF modified B-DNA dodecamer are presented. A rational search strategy, beginning with a global search of the conformation space of the modified deoxydinucleoside monophosphate, together with model building by computer graphics, has been employed. A number of different minimum energy conformations have been located which reveal base displaced structures. These show fluorene interstrand stacking, fluorene inter- and intrastrand stacking, and non-stacked fluorene situated in the denatured bulge. The local helix axis is bent to various extents in the different forms, and one or two base pairs are fully denatured. One structure of special interest offers a molecular view that suggests how AAF can induce the -2 deletion mutation observed in AAF modified E. coli.     

Carcinogen-base stacking and base-base stacking in dCpdG modified by (+) and (-) anti-BPDE

The low-energy conformations accessible to dCpdG modified at guanine N² via trans epoxide opening by (+) and (?) 7β,8α-dihydroxy-9α,10α-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene (anti-BPDE) have been delineated by minimized semiempirical potential-energy calculations with all torsion angles flexible. Nearly 4000 trials were made, representing a fairly thorough investigation of the conformation space of the adducts. Carcinogen–base stacked states and base–base stacked conformers were found in the low-energy regions of both enantiomers. Many ω′, ω, ψ domains accommodate the two types of conformations, with B-like backbones among the most preferred states in each case. The conformational differences between the two enantiomers on the dimer level reside in subtle distinctions in orientation of the carcinogen–base linkage.     

Low Temperature Absorption Spectra of Chlorophyll a in Polar and Nonpolar Solvents

Absorption spectra of chlorophyll a were measured in polar and non-polar solvents, as a function of temperature from 298 degrees to 77 degrees K. Both dilute and concentrated solutions were examined. In both types of solvents at room temperature, the absorption spectra of concentrated solutions differ from dilute ones in that the half width of the main red absorption band is greater, and all bands are shifted to longer wavelengths. These differences are largely due to the presence of dimers when the pigment concentration is high. In dilute ethanol solutions, where the chlorophyll is unassociated, cooling causes a red shift in all bands which is due to the increased polarity of the solvent at low temperature. On cooling at high concentrations in ethanol and EPA, a new band appears near 700 nm. This band is attributed to dimers present prior to cooling, but absorbing at shorter wavelengths at room temperature. In nonpolar solvents, a band near 700 nm appears at the solvent freezing point. In these solvents, the "700" nm absorption is attributed to dimers, and/or small polymers, partly formed by cooling. A change in aggregate geometry when the solvent becomes viscous or frozen can account for the appearance of this "700" nm absorption band at low temperature, in polar and nonpolar media.     

Spectral Studies of a Chlorophyll Pigment with Fluorescence Maximum at 698 mμ

A chlorophyll type pigment (F698) fluorescing maximally at 698 mμ at 77°K has been observed in preparations of chlorophyll. This fluorescence is quenched by small amounts of naturally occurring materials, including plastoquinone and the ubiquinones, and by nitrobenzene, probably by formation of a nonfluorescent complex. Fluorescence quenching does not occur in the presence of carotenes, xanthophylls, or reduced plastoquinone and ubiquinone. The fluorescence is sharply temperature dependent, with a steep rise in intensity occurring at 165°K. At 77°K the fluorescence yield is between 0.8 and 1.0. The red absorption maximum of the pigment is at 675 mμ at room temperature and at 688 mμ at 77°K. In vivo, a low temperature emission is also observed at 698 mμ, and this fluorescence is quenched by nitrobenzene. It is proposed that the pigment found in vitro is also the one responsible for emission at 698 mμ in vivo. A reaction of F698 with plastoquinone is suggested as the primary photochemical step in system II of photosynthesis.     

Influence of benzo[a]pyrene diol epoxide chirality on solution conformations of DNA covalent adducts: the (-)-trans-anti-[BP]G.C adduct structure and comparison with the (+)-trans-anti-[BP]G.C enantiomer.

Benzo[a]pyrene (BP) is an environmental genotoxin, which, following metabolic activation to 7,8-diol 9,10-epoxide (BPDE) derivatives, forms covalent adducts with cellular DNA. A major fraction of adducts are derived from the binding of N2 of guanine to the C10 position of BPDE. The mutagenic and carcinogenic potentials of these adducts are strongly dependent on the chirality at the four asymmetric benzylic carbon atoms. We report below on the combined NMR-energy minimization refinement characterization of the solution conformation of (-)-trans-anti-[BP]G positioned opposite C and flanked by G.C base pairs in the d(C1-C2-A3-T4-C5-[BP]G6-C7-T8-A9-C10-C11).d(G12-G13-T14++ +-A15-G16-C17- G18-A19-T20-G21-G22) duplex. Two-dimensional NMR techniques were applied to assign the exchangeable and non-exchangeable protons of the benzo[a]pyrenyl moiety and the nucleic acid in the modified duplex. These results establish Watson-Crick base pair alignment at the [BP]G6.C17 modification site, as well as the flanking C5.G18 and C7.G16 pairs within a regular right-handed helix. The solution structure of the (-)-trans-anti-[BP]G.C 11-mer duplex has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by lower and upper bounds deduced from NOE buildup curves as constraints in energy minimization computations. The BP ring spans both strands of the duplex in the minor groove and is directed toward the 3'-end of the modified strand in the refined structure. One face of the BP ring of [BP]G6 stacks over the C17 residue across from it on the partner strand while the other face is exposed to solvent.(ABSTRACT TRUNCATED AT 250 WORDS)     

Z-DNA conformation of N-2-acetylaminofluorene modified poly(dG-dC).poly(dG-dC) determined by reactivity with anti cytidine antibodies and minimized potential energy calculations.

The conformation of poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), and calf thymus DNA modified with N-acetoxy-N-2-acetylaminofluorene (N-acetoxy-AAF) was examined by extent of reaction with anti cytidine antibodies. In contrast to modified poly(dG).poly(dC0 and DNA, modified poly(dG-dC).poly (dG-dC) failed to react with the antibodies indicating that the base pairing in this polymer is intact. This in consistent with induction of the Z-DNA conformation in AAF modified poly(dG-dC).poly(dG-dC). Using minimized potential energy calculations on the dCpdG-AAF dimer as a model for the modified polymer, it is shown that the proposed Z-DNA conformation is energetically stable. A model is proposed for an AAF modified tetramer, dGpdCpdGpdC, in which the AAF is external to the Z-DNA duplex.     

The A and B conformations of DNA and RNA subunits. Potential energy calculations for dGpdC

In order to obtain a molecular picture of the A and B forms of a DNA subunit, potential energy calculations have been made for dGpdC with C(3′)-endo and C(2′)-endo [or C(3′)-exo] sugar puckerings. These are compared with results for GpC. The global minima for dGpdC and GpC are almost identical. They are like A-form duplex DNA and RNA, respectively, with bases anti, the ω′, ω angle pair near 300°, 280°, and sugar pucker C(3′)-endo. For dGpdC, a B-form helical conformer, with sugar pucker C(2′)-endo and ω′ = 257°, ω = 298°, is found only 0.4 kcal/mol above the global minimum. A second low-energy conformation (2.3 kcal/mol) has ω′ = 263°, ω = 158° and ψ near 180°. This has dihedral angles like the original Watson–Crick model of the double helix. In contrast, for GpC, the C(2′)-endo B form is 6.9 kcal/mol above the global minimum. These theoretical results are consistent with experimental studies on DNA and RNA fibers. DNA fibers exist in both A and B forms, while RNA fibers generally assume only the A form. A low-energy conformation unlike the A or B forms was found for both dGpdC and GpC when the sugars were C(3′)-endo. This conformation—ω′,ω near 20°,80°—was not observed for C(2′)-endo dGpdC. Energy surface maps in the ω′,ω plane showed that C(2′)-endo dGpdC has one low-energy valley. It is in the B-form helical region (ω′ ～ 260°, ω ～ 300). When the sugar pucker is C(3′)-endo, dGpdC has two low-energy regions: the A-form helical region and the region with the minimum at ω′ = 16°, ω = 85°.     

Structure of guanylyl-3',5'-cytidine monophosphate. II. Description of the molecular and crystal structure of the calcium derivative in space group P2(1).

The structural features of calcium guanosine-3′,5′-cytidine monophosphate (GpC) have been elucidated by X-ray diffraction analysis. The molecule was crystallized in space group P2₁ with cell constants of a = 21.224 Å, b = 34.207 Å, c = 9.327 Å, and β = 90.527°, Z = 8. The hydration of the crystal is 21% by weight with 72 water molecules in the unit cell. The four GpC molecules in the asymmetric unit occur as two Watson-Crick hydrogen-bonded dimers related by a pseudo-C face centering. Each dimer consists of two independent GpC molecules whose bases are hydrogen bonded to each other in the traditional Watson-Crick fashion. Each dimer possesses a pseudo twofold axis broken by a calcium ion and associated solvent. The four molecules are conformationally similar to helical RNA, but are not identical to it or to each other. Instead, values of conformational angles reflect the intrinsic flexibility of the molecule within the range of basic helical conformations. All eight bases are anti, sugars are all C3′-endo, and the C4′-C5′ bond rotations are gauche-gauche. The R factor is 12.6% for 2918 observed reflections at 1.2-Å resolution.     

A Conformational Analysis of the (+) Anti BPDE Adduct to the Guanine Amino Group of dCpdG

Abstract

The (+) anti isomer of benz[a]pyrene diol epoxide (BPDE), 7β, 8a-dihydroxy-9α,10α-epoxy- 7,8,9,10-tetrahydrobenz[a]pyrene has been identified as the probable tumorigenic lesion in mammalian systems. It forms a predominant adduct with DNA at N² of guanine. In order to elucidate its conformation in atomic resolution detail, minimized conformational potential energy calculations were performed for the adduct with dCpdG. A global conformation search involving about 1000 trials was made. The lowest energy conformation had stacking between the hydrocarbon and the adjacent cytidine, in agreement with CD studies on modified GpU and UpG. This conformer differed from the B form most notably in the guanine glycosidic torsion, which is high anti. The next lowest energy form had torsion angles like the B form, with guanine-cytidine stacking. These two conformers differ in energy by only 2.1 kcal./mole, suggesting that their relative stability could easily be reversed in larger polymers, or under specific environmental conditions. Other conformations, with base-hydrocarbon or base-base stacking are also found, at somewhat higher energies. The Z form is at 7.8 kcal./mole. Thus, this adduct stabilizes the B form, in contrast with the N²linked AAF adduct, which stabilizes the Z conformation.