Ultraviolet radiation response to the physical properties of the reconstituted nucleohistone

The effect of UV irradiation on the reconstituted nucleohistone have been studied with reference to its (nucleohistone) changes in physical properties, after irradiation at different UV doses. The rate of fall of specific viscosity ratio of the reconstituted nucleohistone as a function of UV dose decreased gradually with the increasing histone to DNA weight ratio (r). This effect, was not observed when the histones remained dissociated from DNA, in high ionic strength (1.5 M NaCl). Histone-DNA complex (r=0.97) irradiated up to a dose of 3.6×10⁴ J/m² had a stable melting temperature unlike free DNA where UV irradiation lowered the melting temperature and the heterogeneous melting profiles were observed. Rate of formaldehyde reaction, with DNA recovered from the irradiated complex, was slower than that with native DNA treated at the same dose. All this suggested that the effect of UV in the DNA of the nucleohistone was less, compared to that in free DNA.     

Helix-coil transition in nucleoprotein: renaturation of polylysine-DNA and polylysine-nucleohistone complexes

Thermal denaturation and renaturation of directly mixed and reconstituted polylysine–DNA, directly mixed polylysine–nucleohistone complexes, and NaCl-treated nucleohistones in 2.5 × 10^?4 M EDTA, pH 8.0 have been studied. At the same input ratio of polylysine to DNA, the percent of renaturation of free base pairs in a directly mixed polylysine–DNA complex is higher than that in a reconstituted complex. For a directly mixed complex, the renaturation of free base pairs is proportional to the fraction of DNA bound by polylysine or inversely proportional to the sizes of free DNA loops. A of large amount of renaturation of free base pairs has also been observed for 0.6 M and 1.6 M NaCl-treated nucleohistones. The binding of polylysine to nucleohistone enhances the renaturation of histone-bound base pairs. The percent of renaturation of polylysine–bound base pairs is high and is approximately independent of the extent of binding on DNA by polylysine. This is true in polylysine–DNA complexes prepared either by reconstitution or by directly mixing. It also applies for polylysine–nucleohistone complexes. The model where polylysine-bound base pairs collapse at T_m′ with two complementary strands still bound by polylysine is favored over the model where polylysine is dissociated from DNA during melting. The low renaturation of histone-bound base pairs in nucleo-histone indicates that either histones do not hold two complementary strands of DNA tightly or that histones are fully or partially dissociated from DNA when the nucleo-histone is fully denatured.     

Circular dichroism of histone-bound regions in chromatin.

Native, NaCl-treated, trypsin-treated, and polylysine-bound nucleohistones were studied in 2.5 × 10^?4 M EDTA, pH 8.0, using circular dichroism (CD) and thermal denaturation. Removal of histone I by 0.6 M NaCl has a much smaller effect on both Δε₂₂₀ and Δε₂₇₈ than the removal of other histones. This indicates that histone I has less helical content and less conformational effect on the DNA in nucleohistone. By extrapolating to 100% binding by histones other than I, the positive CD band near 275 nm is close to zero. Comparison is also made between the effects of binding by the more basic and the less basic halves of histones by trypsin-digestion and polylysine-binding experiments. Trypsin digestion of nucleohistone reduces melting band IV at 82°C much more than melting band III at 72°C. However, the CD changes of Δε₂₇₈ and Δε₂₂₀ induced by trypsin digestion are small, unless melting band III is also reduced by the use of a higher trypsin level. This implies that the less basic halves of histones, which stabilize DNA to 72°C (melting band III), have more helical structure and are more responsible for conformational change in DNA than are the more basic halves, which stabilize DNA to 82°C (melting band IV). Polylysine binding to nucleohistone diminishes melting band III but has no effect on melting band IV. This binding affects only slightly the Δε₂₂₀ of nucleohistone, indicating that polylysine interferes very little with the structure of the less basic halves of bound histones. The implications of these studies with respect to chromatin structure are discussed.     

Studies on the thermal denaturation of nucleohistones

The thermal denaturation profiles of nucleohistone from calf thymus, sea urchin sperm and sea cucumber male gonad, are studied and compared under a variety of conditions. These include melting in the presence of either one of the following agents: urea, methanol, divalent cations or excess histones. The influence of ionic strength, pH, formaldehyde treatment and partial denaturation is also studied. Particular attention is given to the factors which influence the bimodal appearance of the profiles. The melting curves of the three materials used are qualitatively similar under all conditions, although they show quantitative differences. The histone:DNA ratio appears to be the most important parameter to define the denaturation properties of a given nucleohistone preparation. It is shown that redistribution of histones may determine the melting profile, since during denaturation histones can migrate from locally denatured regions towards those regions which contain native DNA. It is also shown that there are regions of phosphate negative charges of DNA not protected by histone. These regions can be protected against denaturation either by additional histones or by certain divalent cations. The results are interpreted in terms of the various models possible for the distribution of histones on DNA in native nucleohistone. Their biological significance is also discussed.     

Infectious DNA from coliphage T1

Summary DNA isolated from coliphage T1 is infective in spheroplasts of E. coli K12/1. The efficiency of the assay amounts to approximately 10^-4 plaque-forming units per DNA molecule of 32·10⁶ daltons. A linear relationship between DNA concentration and total phage yield or infective centers, respectively, holds for native DNA. For heat-treated DNA, however, the co-operation of 1.4 molecules is required for successful infection. Beyond a critical concentration of about 0.1g/ml a self-inhibiting effect of infectious T1-DNA is observed. Breakage by shearing and denaturation of the DNA-molecules destroy their infectious activity. Renaturation, however, restores infectivity to 60–90 per cent of the original activity. Heat treatment of T1-DNA in M/5 NCE buffer results in narrow-coiled, mismatched molecules with partially denatured regions. Though the efficiency of infection of such molecules is reduced by about 30 per cent, the critical concentration of T1-DNA shifts to higher values by a factor of ten, thus giving an increase in the total plaque yield of the system. The effect is explained by the transition of native into narrow-coiled molecular configuration.     

The dissociation of histone from deoxyribonucleohistone by γ-irradiation

1. Experiments were carried out to determine the extent of dissociation of histone from deoxyribonucleohistone as a result of irradiation with γ-rays from ⁶⁰Co. 2. The bulk of the nucleohistone was removed from the irradiated solutions either by sedimentation or by precipitation with dilute sodium chloride solution. The supernatants were then analysed for DNA and histone. 3. The ratios of histone to DNA in these supernatants were less than for the original nucleohistone. This indicated that histone was dissociated by the irradiation, and then aggregated either with itself or with other nucleohistone molecules, and so was removed with the bulk of the nucleohistone during sedimentation or precipitation.     

TherecA-dependent spontaneous degradation of proximal F merogenotes inEscherichia coli

Proximal F’ elements of KLF-1 type are relatively stable inEscherichia coli rec A recipients. In such merodiploids the transferability of F’-DNA and the plasmid determined fertility functions are expressed. When introduced into the wild typerecA ⁺ cells the F′-DNA is degraded and several classes of DNA molecules of molar mass about 66 Mg/mol and lower exist in the cell in 1–2 copies, per bacterial chromosome. As was detected by complementation analysis, the chromosomal genes determining the host specificity for DNA (hsd) originally located on the F’ element seem to be salvaged during the process of DNA degradation probably by recombination with the bacterial chromosome.     

Mg-induced transition to strongly cooperative binding of histone H1 to linear DNA

By addition of Mg²⁺ ions to histone H1-DNA complexes formed at 20mM NaCl a transition to strongly cooperative binding of histone H1 to DNA is induced. In the analytical ultracentrifuge, above a critical Mg²⁺ concentration of about 0.05 mM, the single component representing the original H1-DNA complex is replaced by two components: a higher order H1-DNA complex type characterized by a much higher sedimentation coefficient, and a slow-sedimenting component consisting of essentially H1-free DNA above 0.1 mM Mg^2-. The fast complex diappears upon removal of Mg²⁺, showing that the process is reversible, and also upon addition of urea. Electron microscopy shows the cooperatively formed H1-DNA complexes to appear predominatly as loosely twisted cable rings in unfixed specimens, and as strongly condensed circular structures of different diameter, but approximately uniform thickness (of about 12nm) after fixation with glutaraldehyde. Besides these higher order structures, only single fibres indistinguishable from control DNA may be seen; individual double fibres which, in the absence of Mg²⁺, represent the predominant H1-DNA complexe structure at about 0.4–0.8 w/w H1/DNA are no longer visible. The transition to strongly cooperative binding of H1 occurs at approximately the same Mg²⁺ concentration which is known to induce the folding of the 10 nm nucleosome chain into the 30nm solenoid structure of chromatin.     

Biochemical evidence of DNA transport from the silk gland to the fat body of the silkworm, Bombyx mori

β-DNA, a component of DNA found in the pupal fat body of the silkworm, Bombyx mori, has the same GC content but a smaller molecular weight than typical silkworm DNA (α-DNA). Its origin and time of synthesis were studied by MAK column chromatography of phenol extracts after labelling with radioactive precursors.The DNA components of the fat body changed greatly during the early pupal stage, the β-DNA showing a striking increase relative to α-DNA. Thymidine-6-³H and phosphoric acid-³²P injected into the animals 1 day before analysis caused labelling of α-DNA, but not of β-DNA of the fat body, indicating that β-DNA was not synthesized during the stage of its appearance in the fat body.On the other hand, injection of thymidine-6-³H into 2-day-old fifth instar larvae, when DNA of the silk gland was being actively synthesized, gave high incorporation of the isotope into β-DNA of the pupal fat body. The sudden appearance of highly labelled β-DNA in the fat body during the early pupal stage as well as the occurrence of β-DNA in both the silk gland and fat body suggested that DNA might move from the silk gland to the fat body.It is possible that the fat body stores DNA as a nutrient from the degenerating silk gland.     

Studies on interaction between histone V (f2c) and deoxyribonucleic acids.

Histone V (2fc) from chick erythroctes was used in the study of its interaction with DNA from various sources. Complexes between this histone and DNA were formed using the procedure of continuous NaCl gradient dialysis in urea. Two physical methods, namely thermal denaturation and circular dichroism (CD), were used as analytical tools. Thermal denaturation of nucleohistone V with chick or calf thymus DNA shows three melting bands: band I at 45-50 degrees corresponds to free base pairs; band II at 75-79 degrees, and band III at 90-93 degrees correspond to histone-bound base pairs. In histone-bound regions, there are 1.5 amino acid residues/nucleotide in nucleohistone V. In contrast, a value between 2.9 and 3.3 was determined for nucleohistone I (fl) (H. J. Li (1973), Biopolymers 12, 287). Similar melting properties have been observed for histone V complexed with bacterial DNA from Micrococcus luteus. Histone V binding to DNA induces a slight transition from a B-type CD spectrum to a C-type spectrum. Trypsin treatment of nucleohistone V reduces melting band III much more effectively than band II. Such a treatment also restores DNA to B conformation in the free state. Reduction of the melting bands of nucleohistone V by polylysine binding follows the order of I greater than II greater than III, accompanied by the increase of a new band at 100 degrees. When two bacterial DNAs of varied A + T (adenine + thymine) content simultaneously compete for the binding of histone V, the more (A " T)-rich DNA is selectively favored. Under experimental conditions described here, Clostridium perfringens DNA with 69% A + T is bound by histone V in preference to chicken DNA with 56% A + T although the latter has natural sequences for histone V binding.     

Circadian-Stage Dependent Acth1-17 Effect on DNA Synthesis in Murine Duodenum,Colon and Recum

The objective was to determine the effect of adrenocorticotropin (ACTH 1-17) on the incorporation of [³H]TdR into DNA (DNA synthesis) in the duodenum, colon and rectum of CD2F, mice standardised to 12hr of light alternating with 12hr of darkness. A question asked was whether the difference in times of administration along the 24 -hr time scale influenced any response found. The response was complex as ACTH 1-17 was capable of bringing about statistically significant increases in the incorporation of [³H]TdR into DNA at certain times, decreases at other times, or no response at still another time. A generalization that can be made from all these tissues is that ACTH 1-17 had a greater influence in bringing about a decrease in DNA synthesis when it was administered around the time of transition from dark to light. A similar finding was made earlier for the ACTH 1–17 effect upon the tongue, esophagus and stomach.

A 2- and 3-way analysis of variance supports our conclusion that the kind-of-treatment, time-of-treatment and the interval-to-kill (Sampling time) as well as their interactions are important factors when determining any response of ACTH 1-17 or placebo.     

Interaction between poly(L-lysine48, L-histidine52) and DNA.

Poly(Lys⁴⁸, His⁵²), a random copolypeptide of L -lysine (48%) and L -histidine (52%), was used as a model protein for investigating the effects of protonation on the imidazole group of histidines on protein binding to DNA. The complexes formed between poly(Lys⁴⁸, His⁵²) and DNA were examined using absorbance, circular dichroism (CD), and thermal denaturation. Although increasing pH reduces the charges on histidine side chains in the model protein, the protein still binds the DNA with approximately one positive charge per negative charge in protein-bound regions. Nevertheless, CD and melting properties of poly(Lys⁴⁸, His⁵²)-DNA complexes still depend upon the solution pH which determines the protonation state of imidazole group of histidine side chains. At pH 7.0, the complexes show two characteristic melting bands with a t_m (46–51°C) for free base pairs and a t′_m (94°C) for protein-bound base pairs. The t′_m of the complexes is reduced to 90°C at pH 9.2, although at this pH there is still one lysine per phosphate in protein-bound regions. Presumably, the presence of deprotonated histidine residues destabilizes the native structure of protein-bound DNA. The binding of this model protein to DNA causes a red shift of the crossover point and both a red shift and a reduction of the positive CD band of DNA near 275 nm. This phenomenon is similar to that caused by polylysine binding. These effects, however, are greatly diminished when histidine side chains in the model protein are deprotonated. The structure of already formed poly(Lys⁴⁸, His⁵²)·DNA complexes can be perturbed by changing the solution pH. However, the results suggest a readjustment of the complex to accommodate charge interactions rather than a full dissociation of the complex followed by reassociation between the model protein and DNA.     

In vitro synthesis of oat globulin

Thermal denaturation of cytochrome P450 is shown to be a complex process which occurs in two steps. The first (about 50°C) takes place in several stages which can be attributed to denaturation of different regions in the cytochrome P450 with different stability. The second transition (about 90°C) is fully reversible and similar to those described for other hemoproteins.     

Structural and conformational changes of β-lactoglobulin B: an infrared spectroscopic study of the effect of pH and temperature

Infrared spectra of 2.5 mM solutions of β-lactoglobulin B were recorded as a function of pH (from pH 2 to pH 13) and as a function of temperature (from −100°C to +90°C). An analysis of the pH- and temperature-induced changes in the secondary structures was performed based on changes in the conformation-sensitive amide I bands of β-lactoglobulin. Whereas the total of β-structure remains constant (56–59%) between pH22 and pH 10, the proportions of the various β-components do change. In particular, the dimerization of the monomeric protein, induced by raising the pH from 20 to 3, leads to an increase in the intensity of the 1636 cm⁻¹ band (associated with antiparallel β-sheet), at the expense of the 1626 cm⁻¹ band (associated with exposed β-strands). Both the thermal and alkaline denaturation of β-lactoglobulin occur in two distinct stages. Although the spectra (i.e., the structures) after complete thermal or alkaline denaturation are clearly different, the spectrum of the protein after the first stage of thermal denaturation (at about 60°C) is the same as that after the first stage of alkaline denaturation (at pH 11), suggesting a common denaturation intermediate, which probably represents a crossover point in a complex potential hypersurface.     

Identification of Critical Residues for the Tight Binding of Both Correct and Incorrect Nucleotides to Human DNA Polymerase λ

DNA polymerase λ (Pol λ) is a novel X-family DNA polymerase that shares 34% sequence identity with DNA polymerase β. Pre-steady-state kinetic studies have shown that the Pol λ-DNA complex binds both correct and incorrect nucleotides 130-fold tighter, on average, than the DNA polymerase β-DNA complex, although the base substitution fidelity of both polymerases is 10^− 4 to 10^− 5. To better understand Pol λ's tight nucleotide binding affinity, we created single-substitution and double-substitution mutants of Pol λ to disrupt the interactions between active-site residues and an incoming nucleotide or a template base. Single-turnover kinetic assays showed that Pol λ binds to an incoming nucleotide via cooperative interactions with active-site residues (R386, R420, K422, Y505, F506, A510, and R514). Disrupting protein interactions with an incoming correct or incorrect nucleotide impacted binding to each of the common structural moieties in the following order: triphosphate ? base > ribose. In addition, the loss of Watson-Crick hydrogen bonding between the nucleotide and the template base led to a moderate increase in K_d. The fidelity of Pol λ was maintained predominantly by a single residue, R517, which has minor groove interactions with the DNA template.     

Studies on poly(L-lysine50, L-tyrosine50)-DNA interaction

Interaction between poly(Lys⁵⁰, Tyr⁵⁰) and DNA has been studied by absorption, circular dichroism (CD), and fluorescence spectroscopy and thermal denaturation in 0.001M Tris, pH 6.8. The binding of this copolypeptide to DNA results in an absorbance enhancement and fluorescence quenching on tyrosine. There is also an increase in the tyrosine CD at 230 nm. The CD of DNA above 250 nm is slightly shifted to the longer wavelength which is qualitatively similar to, but quantitatively much smaller than, that induced by polylysine binding. At physiological pH the poly(Lys⁵⁰, Tyr⁵⁰)–DNA complex is soluble until there is one lysine and one tyrosine per nucleotide in the complex. The same ratio of amino acid residues to nucleotide has also been observed in copolypeptide-bound regions of the complex. The addition of more poly(Lys⁵⁰, Tyr⁵⁰) to DNA yields a constant melting temperature, T_m′, for bound base pairs at 90°C which is close to that of polylysine-bound DNA under the same condition. The melting temperature, T_m, of free base pairs at about 60°C on the other hand, is increased by 10°C as more copolypeptide is bound to DNA. As the temperature is raised, both absorption and CD spectra of the complexes with high coverage are changed, suggesting structural alteration, perhaps deprotonation, on bound tyrosine. The results in this report also suggest that intercalation of tyrosine in DNA is unlikely to be the mode of binding.     

Lipid-F1 nucleohistone interactions

Summary High concentrations of phospholipids determine destabilization of F1 histone-DNA complex at the weight ratios, histone: DNA, 0.8:1 and 1:1, but low concentrations cause only negligible destabilization. Cholesterol at high weight ratios has little effect on nucleohistone stability. Only linolenic acid of the fatty acids used reproduces similar changes in the thermal stability of F1 histone-DNA complex as phospholipids.The type of interaction of phospholipids with the F1 histone-DNA complex is analyzed, and the involvement of phospholipids in DNA replicationin vivo is discussed.     

Photoreaction of psoralen and other furocoumarins with nucleic acids

The 360-nm photoinitiated reactions of certain furo[3,2-g]coumarins with DNA have been examined using ethidium fluorescence assays. Psoralent at 1.85 × 10^?4M gives 3.3 × 10^?5, 1.8 × 10^?5, and 4.5 × 10^?6 interstrand cross-links/nucleotide with DNAs of (A + T) content 70, 60, and 50%, respectively. The relative rates of cross-linking of λ-DNA are 4-methylpsoralen > psoralen > angelicin ? 4-phenylpsoralen. Angelicin (isopsoralen) gives a small (12–14%) but reproducible amount of DNA interstrand cross-links. Addition of netropsin, an antibiotic that binds preferentially to (A + T)-rich regions, to Clostridium perfringens DNA reduces the extent of cross-linking by psoralen from 66 to 10% in 50 min. In contrast, pretreatment of DNA with olivomycin or chromomycin A₃ [which bind to (G + C)-rich regions] has little effect on psoralen cross-linking. Relative rates of monoadduction of furocoumarins to PM2-CCC-DNA detected by thermal depyrimidation and alkaline strand scission is angelicin > 4-methyl-4′,5′-dihydropsoralen > 4′,5′-dihydropsoralen > 3,4-dihydropsoralen (no monoadduction), indicating angelicin is suitable for photolabeling of chromatin. Binding of netropsin to the PM2-DNA prevents cross-linking by angelicin but permits and enhances monoadduction. In contrast neither olivomycin nor chromomycin affects the reaction of angelicin with DNA. In the frozen solution, where the photoinduced cross-linking of DNA by psoralen may be suppressed, psoralen forms monoadducts about twice as readily as angelicin. Subsequent 360-nm irradiation of the psoralen monoadducts at ambient temperatures (and in separate experiments after dialysis to remove unreacted psoralen) completes the cross-links.     

In situ localization and characterization of different classes of chromosomal DNA: acridine orange and quinacrine mustard fluorescence

In situ denaturation of metaphase chromosomes with alkali results in a shift from green to yellow, orange, brown and red fluorescence with acridine orange, indicating increasing denaturation of chromosomal DNA. The kinetics and characteristics of denaturation are described. Mouse and Microtus agrestis chromosomes denature uniformly but human cells show sequential denaturation. With increasing concentrations of alkali, the secondary constrictions in chromosomes 1, 9 and 16 are the first, and the distal half of the Y chromosome the last, to become denatured. — Reassociation of chromosomal DNA occurs within seconds after the start of incubation in salt solution. Areas containing repetitious DNA, e.g. mouse centromeres, fluoresce much more strongly than other regions with acridine orange after prolonged reassociation. Since human and Microtus centromeric regions behave similarly, it is proposed that they, too, contain repetitious DNA. — Reassociation treatment leads to enhancement of bright quinacrine mustard fluorescence in regions already bright before treatment. Furthermore, regions containing repetitious DNA, e.g. the secondary constrictions in human chromosomes 1, 9 and 16, whose fluorescence is dull before treatment, turn bright after reassociation. — The methods of fluorescence analysis of mammalian chromosomes with acridine orange and quinacrine mustard permit the localization and study of different classes of chromosomal DNA.