Small circular DNA complexes in eucaryotic cells

A small number of eucaryotic cells (100 to 1000 cells) were pressed by mica sheet; then the extruded contents were adsorbed on mica and processed for electron microscopy. In the absence of divalent cation, small polydisperse circular DNA molecules bound to proteins or membrane material were preferentially adsorbed. The small circular DNA complexes have been found in every eucaryotic cell, primary lymphoid tissue cells of bursa and thymus, primary cell lines of retina and liver, and established cultured cell lines of embryonal teratocarcinoma, F9 and PCC3, HeLa and 3T6. Size distribution of these DNA complexes varies, depending on the cell source. The circles less than 1 μm in contour length predominate in cultured cell lines and the larger ones in primary cell lines and cells in situ. Polydisperse covalently closed circular DNAs were recovered from thymus lymphocytes by the conventional dye-CsCl buoyant density method. Their size distribution was similar to that of the small circular DNA complexes detected by the mica-press-adsorption method. They are present in several tens to hundreds of copies per cell representing, at a maximum, 0.02% of the total cellular DNA. The possibility that small circular DNA complexes may result from gene rearrangement as well as from replicon “misfiring” (A. Varshavsky, 1981, Proc. Nat. Acad. Sci. USA 78, 3673–3677) are discussed.     

The circular polarization of fluorescence of the ionophore lasalocid A (X-537A) and some of its metal complexes

The conformation of the ionophore lasalocid A (X-537A) and its complexes with metal ions was probed by the circular polarization of their luminescence (CPL). The CPL of each complex in methanol was found to be different than when in n-hexane. Furthermore, the different metal ion complexes investigated had a different CPL spectrum in each solvent. These findings indicate wide variability in the conformation of the complexes depending on the metal ion and the solvent. From the spectral behaviour of the CPL it was concluded that at least some of the complexes exist in more than one form in solution. A comparison between the CPL and CD spectra indicates a change in the conformation of the ionophore in the vicinity of the salicylate chromophore upon electronic excitation.     

Structures of two N(1)-bound platinum(II)-6-oxopurine complexes. Comparisons with complexes derived from platinum (II) anti-tumor agents

The preparation and molecular structure of [(diethylenetriamine) (7,9-dimethylhypoxanthine) platinum(II)] (PF₆)₂·1.5H₂O and [(ethylenediamine) (7,9-dimethylhypoxanthine)₂platinum(II)] (PF₆)₂, are reported. These complexes represent the first structurally characterized N(1)-bound Pt(II) 6-oxopurine complexes. In each case, the Pt(II)N(1) bond length [2.051(6)A in the diethylenetriamine complex and 2.021(8)A in the ethylenediamine complex] indicates a strong metal-to-base binding. Both complexes contain interligand hydrogen bonds, with the ammine ligand acting as the donor and the O(6) atom of the base acting as the acceptor. These N(1)-bound complexes are compared with N(7)-bound 6-oxopurine and N(3)-bound cytosine complexes of Pt(II) anti-tumor agents.     

Conformational features of bradykinin. A circular dichroism study of some peptide fragments and structural analogues of bradykinin.

The vasoactive hormone bradykinin, its N-and C-terminal fragments and some structural analogues were studied by Circular Dichroism. Conformational features of the peptide can be detected by comparative analysis of the various CD spectra recorded as a function of aqueous pH, solvent and temperature. It is shown that the two biologically essential arginine residues (Arg1 and Arg9) are important for the specific folded bradykinin conformation. Differences between bradykinin, its fragments and analogues become clearly established in conformational terms, and are discussed in relation to the biological activity of these peptides.     

5-Thio-2-nitrobenzoate as a circular dichroism marker to detect the tense structure of bovine hemoglobin

A characteristic, strong CD absorption appeared at 312 nm, when a 5-thio-2-nitrobenzoate (TNB) group was anchored at Cys⁹³-S(βF9) of bovine hemoglobin (Hb) through-SS-linkage. The Hill coefficient, n = 2.7 of the TNB-modified Hb was practically identical with that of native Hb, demonstrating that the marker-anchoring was made successfully, without destroying the cooperativity function. The new 312-nm CD absorption disappears concurrently with the conversion from the tense to the relaxed quaternary structure of Hb, clearly indicating that TNB is an excellent CD marker to detect the tense structure of deoxy-Hb.     

Intracellular location of small circular DNA complexes in mammalian cell lines

For determination of the cellular location of small polydisperse circular DNA complexes, rat myoblastic L6 cells, HeLa cells, and mouse L cells were enucleated and processed by the micapress-adsorption method for electron microscopy (H. Yamagishi, T. Kunisada, and T. Tsuda, 1982, Plasmid8, 299–306). Small circular DNA complexes from intact cells showed a heterogeneous size distribution of from 0.1 to more than 2 μm with a mean contour length of 0.6 to 0.8 μm, like that of covalently closed circular DNAs. Cells contained 400 to 1200 copies. The size distribution in the cytoplasts was narrow and the number-average length was 0.3 to 0.4 μm, whereas that in L6 karyoplasts was wide and the average length was 0.9 μm. The longer circular complexes appeared to be absent from the cytoplasts. The origin and biological functions of these complexes are discussed in relation to the cellular locations of the complexes.     

Interactions between polynucleotides and platinum (II) complexes

Reaction of either $\text{cis}$ or $\text{trans}$ Pt(NH₃)₂Cl₂ with poly(A) in dilute aqueous solution leads to quantitative precipitation of the polymer at Pt/nucleotide ratios above 0.5. It is proposed that at ratios less than this, intramolecular binding of one Pt to two bases is favored; at higher ratios, intermolecular cross-linking becomes important and precipitation results. The absence of isomer selectivity in precipitation implies that the biological specificity of the $\text{cis}$ form results from a process other than cross-linking of polynucleotide strands. Other observations suggest that the coordinated ammonia of nucleotide-platinum(II) ammine complexes may be unusually labile.     

Synthesis and characterization of tertiary phosphine Pd(0) complexes

The synthesis of PdL_n complexes (L = tertiary phosphine; n = 2,3,4) is reported. The coordination number results to be a function of the steric hindrance of the phosphine. Two-coordinate, 14-electron complexes, have been isolated with bulky phosphines (PPrⁱ₃, P (cyclohexyl)₃, PBu^t₂Ph). The behaviour in solution of the PdL_n complexes has been studied by ¹³C NMR spectroscopy.     

Optical properties of Cu(II) complexes with heparin and related glycosaminoglycans.

Absorption and circular dichroism measurements have been carried out to obtain information regarding the stability and the nature of complexes between Cu(II) and heparin, and between Cu(II) and related glycosaminoglycans. In the presence of Cu(II), all glycosaminoglycans, except keratan sulfate, show a characteristic absorption band near 237 nm, which we assign to charge-transfer bands involving ligands to metal ion. From the absorbance values, the formation constants of Cu(II)-heparin and Cu(II)-(itN)-desulfated heparin have been determined to be approximately 1 × 10⁴ and 2 × 10² mol^?1, respectively. The large difference in the stability constant values is attributed to the difference in the charge density of the polymers, and to involvement of more than one ligand in the case of heparin. The CD characteristics of the Cu(II)-heparin complex suggest that both carboxyl and sulfamino groups are involved as ligands. The appearance of extrinsic CD bands in heparin, heparan sulfate, dermatan sulfate, and N-desulfated heparin at pH > 5 is ascribed to asymmetry of chelate rings. Absence of CD change in chondroitin sulfate and N-desulfated heparin (pH < 5) in the presence of Cu(II) suggests that only the carboxyl group is involved in those complexes. The differences either in iduronic acid conformation (C-1 vs. 1-C) or in intersaccharide linkages between dermatan sulfate and heparin (or heparan sulfate) are revealed in the difference CD spectra between the complexes and the polymers. The change in the intrinsic Cotton effect on complex formation is accounted for as a change in spatial orientation of the ligand groups rather than as a major conformational change of the polymers.     

Electronic spectra for nitrosyl(protoporphyrin IX dimethyl ester)iron(II) and its complexes with nitrogenous bases as model systems for nitrosylhemoproteins

Soret and visible absorption spectra for nitrosyl(protoporphyrin IX dimethyl ester)iron(II) (Fe(PPIXDME)(NO] and its complexes with nitrogenous bases (imidazoles, pyridines, aliphatic amines, and cyclic secondary amines) as model systems for nitrosylhemoproteins have been measured in various solvents. As the solvent polarity increases, the Soret and visible absorption bands for the five-coordinate Fe(PPIXDME) (NO) were shifted to shorter wavelengths. Accompanying the coordination of a nitrogenous base to the vacant axial position of Fe(PPIXDME)(NO), the Soret band becomes sharp and the band maximum is shifted to longer wavelengths. The band positions for the six-coordinate Fe(PPIXDME)(NO)(Base) complex are not sensitive to the pi-bonding ability of the axial ligand trans to NO group. The electronic spectra of five-coordinate Fe(PPIXDME)(NO) and six-coordinate Fe(PPIXDME)(NO)(Base) complexes are interpreted in relation to the structural information. The comparison of the spectra for model systems with those for nitrosylhemoproteins is discussed.     

Effect of bovine growth hormone on rat liver plasma membranes as studied by circular dichroism and fluorescence using the extrinsic probe 7,12-dimethylbenzanthracene

Conformational changes produced by in vitro bovine growth hormone addition to plasma membranes of hypophysectomized rat liver proteins and lipids have been studied by circular dichroism as well as intrinsic and extrinsic fluorescence. 7,12-Dimethylbenzanthracene has been used as a fluorescent probe of changes in membrane structure. The exposure of membranes to bovine growth hormone produced a change in membrane negative ellipticity. Dimethylbenzanthracene at concentrations similar to those employed in fluorescence studies had no effect on the membrane circular dichroism spectrum. Its presence did, however, prevent a response to growth hormone. There was a decrease in peak fluorescence intensity and a peak shift when bovine growth hormone (0.5 · 10^?12 M) was added to liver membranes. The addition of dimethylbenzanthracene (1.6 · 10^?6 M) to membranes resulted in a decrease in the intensity of the protein fluorescence peak at 335 nm and the appearance of two peaks at 430 and 407 nm, assignable to the probe. The addition of bovine growth hormone (0.5 · 10^?12 M) produced a decrease in fluorescence at 335 nm and also in the peaks at 407 and 430 nm. These data are consistent with the conclusion that bovine growth hormone produces a conformational change in rat liver plasma membrane proteins and lipids.     

Nuclear magnetic resonance spectroscopy of cobalt (II) porphyrin-quinone complexes

Weak intermolecular complexes of cobalt(II) and nickel(II) mesoporphyrin dimethyl ester with 1,4-naphthoquinone, vitamin K-3, vitamin K-1 and ubiquinone 30 have been detected by ¹H-NMR spectroscopy in chloroform solutions. The relative orientation of the components of complexes is discussed.     

Interaction of poly(L-lysine) and copolymers of lysine with immobilized DNA.

Sonicated DNA has been covalently attached to Sepharose 4B by a carbodiimide method [Rickwood, P. (1972) Biochim. Biophys. Acta269, 47–50] which minimizes modification of the DNA and matrix. Columns of this material have been used to study the interaction between cationic polypeptides and DNA. When poly(l-lysine) is bound to such columns at low ionic strength and then eluted with a linear salt gradient the polypeptide elutes over a broad range of salt concentration, presumably reflecting different strengths of interaction with various sites on the DNA. The broadness of the elution profile cannot be attributed to heterogeneity in the poly(l-lysine) sample but rather to the $\text{AT}\text{GC}$ content of various DNA sites. Studies with other polypeptides, poly(l-Lys⁷⁹, l-Leu²¹) and poly-(l-Lys-l-Ala-Gly), as well as studies at different temperatures, have helped to clarify the possible roles of conformational mobility, polypeptide hydrophobicity, and the presence of contiguous lysines in determining the strength of interaction of polypeptides and proteins with DNA sites.     

Magnetic circular dichroism of non-heme iron proteins

The magnetic circular dichroism (MCD) at 45 kgauss has been determined for a group of non-heme iron proteins. Both transferrin and conalbumin exhibit a single, positive ellipticity band at 330 nm ([θ]_M = 560). Oxy- and methemerythrin, spinach and clostridial ferredoxins and rubredoxin all display distinctive multibanded spectra which may reflect such factors as coordination of the metal, its ligands, metal bridging by other atoms, and varying degrees of metalmetal coupling. The MCD spectra of both ferredoxins and rubredoxin undergo dramatic change upon oxidoreduction providing a potential means for relating the electronic structure of the iron to protein function. In contrast to the plant ferredoxins, the magnetic field does not significantly affect the CD spectra of adrenodoxin and putidaredoxin.     

Circular dichroism and the conformational properties of soybean beta-amylase

The conformational properties of soybean β-amylase were investigated by the circular dichroism probe and measurement of enzyme activity. The enzyme exhibited a positive circular dichroism band at 192 nm, a negative band at 222 nm, and a shoulder near 210 nm. Analysis of the spectrum in the far ultraviolet zone indicated the presence of approximately 30% of α helix and 5–10% of β-pleated sheet, the rest of the polypeptide main chain possessing aperiodic structure. In the near ultraviolet reagion, the enzyme protein showed at least six positive peaks at 259, 265, 273, 281, 292, and 297 nm. The positive bands at 292 and 297 nm remained unaltered on acetylation of the enzyme by N-acetylimidazole and were assigned to tryptophanyl chromophores. These bands were affected in intensity in the presence of maltose or cycloheptaamylose, which indicates that some tryptophan residues are situated at the binding sites. The native conformation of soybean β-amylase was found to be sensitive to pH variation (below pH 5 and above pH 10), sodium dodecyl sulfate, guanidine hydrochloride, and heating to 50–55 °C. Complete disorganization of the secondary structure was attained by 6 m guanidine hydrochloride. Sodium dodecyl sulfate was effective in disturbing the tertiary structure of the enzyme but did not affect significantly the secondary structure. Enzymatic inactivation was paralleled by the decrease of circular dichroism bands in the near ultraviolet region as produced by the denaturants. It is concluded that the uniquely folded structure of the enzyme contains some less rigid domains and a rigid core stabilized by hydrophobic interactions, electrostatic interactions, and hydrogen bonds.     

Thermodynamics of base interaction in (A)n and (A.U)n

Using precision scanning microcalorimetry we studied (A)_n and (A·U)_n melting in highly diluted solutions (0.3 to 5.0 mm) with different Na⁺ activity. This permitted us to determine directly the thermodynamic functions of stacking interaction in (A)_n and base-pairing in (A·U)_n. For (A-A) stacking at (A)_n melting temperature we obtained ΔH^(A)n_m = 12.6 kJ mol^?1; ΔS^(A)n_m = 41 J K^?1 mol^?1. For A·U base-pairing at a standard temperature of 298 K and 0.1 m-Na⁺ we have: ΔH^(A·U) = 34 kJ mol^?1; ΔS^(A·U) = 102 J K^?1 mol^?1ΔG^(A·U) = ?3.5 kJ mol^?1.     

Isolation of yeast histone genes H2A and H2B

Analysis of cloned sequences for yeast histone genes H2A and H2B reveals that there are only two copies of this pair of genes within the haploid yeast genome. Within each copy, the genes for H2A and H2B are separated by approximately 700 bp of spacer DNA. The two copies are separated from one another in the yeast genome by a minimum distance of 35-60 kb. Sequence homology between the two copies is restricted to the genes for H2A and H2B; the spacer DNA between the genes is nonhomologous. In both copies, the genes for H2A and H2B are divergently transcribed. In addition, both plasmids code for other nonhistone proteins. Sequences coding for histones H3 and H4 have not been detected in the immediate vicinity of the genes for H2A and H2B.