Counterion-Type Characteristic Effects on Intrinsic Bending Components of Calf Thymus DNA; Hydrodynamic Investigations

Abstract

This paper stresses structural differences in A · T clusters of the ammonium salt of calf thymus (et) DNA (ctNH₄DNA) and the respective sodium salt, ctNaDNA Sequence mediated intrinsic helix bends of ctNaDNA distributed along the molecule partially randomly and partially phased with the helix screw (accompanying paper), are enhanced in ctNH₄DNA. Additionally, the number of the most strongly bent segments (of A-tract character) is raised in ctNH₄NA by a counterion mediated shift of the equilibrium between at least two local DNA conformations. Nevertheless, the apparent DNA elongation, induced by the abolition of a single apparent solenoid-related DNA tertiary structure component which generates a special intrinsic DNA bend, is the same for NH₄DNA and NaDNA.

These conclusions follow from two independent sets of experimental results:

(1.) Titration viscometric measurements with ctNH₄DNA as a function of the cation concentration in comparison to ctNaDNA (KER et al. JBSD 9, 537 (1991)) and respective DNA conformational analyses.

(2.) Quantitative viscometric analysis of DNA conformational changes on netropsin (Nt) interaction of ctNHjDNA at different temperatures and comparison with the respective data for ctNaDNA (KER et al., NAR 9, 2335 (1981).     

Composites of peptide nucleic acids with titanium dioxide nanoparticles. II. Dissociation of DNA/PNA duplexes within TiO2 · polylysine · DNA/PNA nanocomposites and in solution. Effect of polylysine

When creating effective drugs, it is important not only to transport them into cells, but also allow them to be released from the “transporter” after the delivery. It was shown that the dissociation of peptide nucleic acids (PNA) from TiO₂ · PL · DNA/PNA nanocomposites occurred according to a typical thermal denaturation, and polylysine (PL) in the nanocomposite has almost no effect on the dissociation. These data suggest that the immobilization of PNA in the TiO₂ · PL · DNA/PNA nanocomposite is reversible and PNA can be easily released from TiO₂ carrier into solution. In contrast to that, the dissociation of DNA/DNA and DNA/PNA duplexes in physiological solution in the presence of PL was not observed. PL in solution dramatically influences the dependence of the optical density on temperature and time for DNA/DNA duplexes and to a lesser degree for DNA/PNA duplexes. It has been assumed that PL and DNA/DNA duplexes in physiological solutions form triple polycomplexes (DNA/DNA · PL) _m , which can aggregate and precipitate. PL in solution can also interact with DNA/PNA duplexes to form monocomplexes PL · (DNA/PNA) _n consisting of one PL chain and one or more (n) DNA/PNA duplexes. Although these monocomplexes do not precipitate, the dissociation of DNA/PNA duplexes from them is complicated.     

Insight into RNA–DNA primer length counting by human primosome

The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58_C) with the primer 5′-end, and (ii) flexible tethering of p58_C and the DNA polymerase alpha catalytic core domain (p180_core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58_C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.     

Endonuclease activities of MutLα and its homologs in DNA mismatch repair

MutLα is a key component of the DNA mismatch repair system in eukaryotes. The DNA mismatch repair system has several genetic stabilization functions. Of these functions, DNA mismatch repair is the major one. The loss of MutLα abolishes DNA mismatch repair, thereby predisposing humans to cancer. MutLα has an endonuclease activity that is required for DNA mismatch repair. The endonuclease activity of MutLα depends on the DQHA(X)₂E(X)₄E motif which is a part of the active site of the nuclease. This motif is also present in many bacterial MutL and eukaryotic MutLγ proteins, DNA mismatch repair system factors that are homologous to MutLα. Recent studies have shown that yeast MutLγ and several MutL proteins containing the DQHA(X)₂E(X)₄E motif possess endonuclease activities. Here, we review the endonuclease activities of MutLα and its homologs in the context of DNA mismatch repair.     

Unmethylated and methylated CpG dinucleotides distinctively regulate the physical properties of DNA

In eukaryotic cells, DNA has to bend significantly to pack inside the nucleus. Physical properties of DNA such as bending flexibility and curvature are expected to affect DNA packaging and partially determine the nucleosome positioning patterns inside a cell. DNA CpG methylation, the most common epigenetic modification found in DNA, is known to affect the physical properties of DNA. However, its detailed role in nucleosome formation is less well‐established. In this study, we evaluated the effect of defined CpG patterns (unmethylated and methylated) on DNA structure and their respective nucleosome‐forming ability. Our results suggest that the addition of CpG dinucleotides, either as a (CG)_n stretch or (CGX₈)_n repeats at 10 bp intervals, lead to reduced hydrodynamic radius and decreased nucleosome‐forming ability of DNA. This effect is more predominant for a DNA stretch ((CG)₅) located in the middle of a DNA fragment. Methylation of CpG sites, surprisingly, seems to reduce the difference in DNA structure and nucleosome‐forming ability among DNA constructs with different CpG patterns. Our results suggest that unmethylated and methylated CpG patterns can play very different roles in regulating the physical properties of DNA. CpG methylation seems to reduce the DNA conformational variations affiliated with defined CpG patterns. Our results can have significant bearings in understanding the nucleosome positioning pattern in living organisms modulated by DNA sequences and epigenetic features. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 517–524, 2014.     

Copper-dependent DNA damage induced by hydrazobenzene,an azobenzene metabolite

Hydrazobenzene is carcinogenic to rats and mice and azobenzene is carcinogenic to rats. Hydrazobenzene is a metabolic intermediate of azobenzene. To clarify the mechanism of carcinogenesis by azobenzene and hydrazobenzene, we investigated DNA damage induced by hydrazobenzene, using ³²P-5′-end-labeled DNA fragments obtained from the c-Ha-ras-1 proto-oncogene and the p53 tumor suppressor gene. Hydrazobenzene caused DNA damage in the presence of Cu(II). Piperidine treatment enhanced the DNA damage greatly, suggesting that hydrazobenzene caused base modification and liberation. However, azobenzene did not cause DNA damage even in the presence of Cu(II). Hydrazobenzene plus Cu(II) caused DNA damage frequently at thymine residues. Catalase and a Cu(I)-specific chelator inhibited Cu(II)-mediated DNA damage by hydrazobenzene. Typical ^·OH scavengers did not inhibit the DNA damage. The main active species is probably a metal oxygen complex, such as Cu(I)-OOH. Formation of 8-oxo-7, 8-dihydro-2′-deoxyguanosine was increased by hydrazobenzene in the presence of Cu(II). Oxygen consumption and UV-Visible spectroscopic measurements have shown that hydrazobenzene is autoxidized to azobenzene with H₂O₂ formation. It is considered that the metal-mediated DNA damage by hydrazobenzene through H₂O₂ generation may be relevant for the expression of carcinogenicity of azobenzene and hydrazobenzene.     

DNA SYNTHESIS IN NEURONAL, GLIAL AND LIVER NUCLEI ISOLATED FROM THE ADULT GUINEA PIG

Abstract— [³H]Deoxythymidine-5′-triphosphate incorporation into P₅₁ (51% neuronal nuclei: 49% glial nuclei), P₃ (3% neuronal nuclei: 97% glial nuclei) and liver nuclear preparations, isolated from the adult guinea pig, was determined in the presence of the other three complementary deoxyribonucleo-tides. The enzymic characteristics of the DNA synthesis reaction were studied and DNA polymerase contents were estimated in neuronal, glial and liver nuclei. (1) Cerebral and liver nuclei exhibited similar enzymic properties for DNA synthesis activities with a few discrepancies. (2) P₅₁ nuclei synthesized DNA 2.4-fold more actively than P₃ nuclei. Liver nuclei carried out the most active DNA synthesis. The proportion of chromatin DNA available as template and primer was estimated by comparison with native calf thymus DNA. The available proportions found, in terms of the total chromatin DNA. were 2.39% for P₅₁ nuclei, 1.38% for P₃ nuclei and 37.6% for liver nuclei. (3) Exogenous native and heat-denatured calf thymus DNA were utilized as template and primer by DNA polymerase in nuclei in different ways depending on the nuclear species. The enzyme was saturated with native DNA by elevating the concentration and the activity reached a plateau. Denatured DNA inhibited the activity at the higher concentrations. (4) From the enzyme activities at a saturation concentration of exogenous DNA, DNA polymerase contents were estimated: P₅₁ nuclei, 39.2 ± 2.6 (s.e.m. ) units (fmol of TMP incorporated/30 min at 31°C)/μg of nuclear DNA; P₃ nuclei. 24.5 ± 1.6; and liver nuclei, 72.5 ± 8.1; the specific activity obtained on a protein basis was 1.55 times higher with P₃ nuclei than with P₅₁ nuclei. (5) Denatured DNA inhibited the nuclear DNA polymerase activity dependent on native DNA. The efficiency of inhibition was in the order: P₃ > P₅₁ > liver nuclei.     

Characterization of 1,25-dihydroxyvitamin D3-receptor complex interactions with DNA by a competitive assay

To identify and assess the specificity of the 1,25-dihydroxyvitamin D₃ chick intestinal cytoplasmic receptor's nucleotide binding site, a competitive DNA-cellulose binding assay was utilized. Unlike other steroid hormone receptors, the 1,25-dihydroxyvitamin D₃-receptor complex binds homologous DNA at 4 °C and does not appear to undergo thermal- or salt-induced activation. Data are presented which suggest that receptor binding discriminates between double-stranded DNA and RNA but is not specific with respect to DNA base sequences. However, DNA base sequence selectivity by 1,25-dihydroxyvitamin D₃-receptor complexes is observed using synthetic polydeoxyribonucleotides, particularly, poly(dA-dT) · poly(dA-dT) and poly(dA) · poly(dT). Preference for double-stranded over single-stranded DNA was also observed. Consistent with this finding, both actinomycin D and ethidium bromide caused a dose-dependent inhibition of receptor binding to DNA-cellulose. It is concluded that the 1,25-dihydroxyvitamin D₃-receptor complex has specificity for AT-rich segments of double-stranded DNA and that this interaction is not merely electrostatic, but also involves hydrophobic interaction with the major and/or minor grooves of the DNA helix.     

Experimental approaches to free radicals and ageing

Abstract

Probucol, a clinically used cholesterol lowering and antioxidant drug, was investigated for possible protection against lipid peroxidation and DNA damage induced by iron nitrilotriacetate (Fe-NTA) plus hydrogen peroxide (H₂O₂). Fe-NTA is a potent nephrotoxic agent and induces acute and subacute renal proximal tubular necrosis by catalyzing the decomposition of H₂O₂-derived production of hydroxyl radicals, which are known to cause lipid peroxidation and DNA damage. Fe-NTA is associated with a high incidence of renal adenocarcinoma in rodents. Lipid peroxidation and DNA damage are the principal manifestation of Fe-NTA induced toxicity, which could be mitigated by probucol. Incubation of renal microsomal membrane and/or calf thymus DNA with H₂O₂ (40 mM) in the presence of Fe-NTA (0.1 mM) induces renal microsomal lipid peroxidation and DNA damage to about 2.4-fold and 5.9-fold, respectively, as compared to control (P < 0.05). Induction of renal microsomal lipid peroxidation and DNA damage was inhibited by probucol in a concentration-dependent manner. In lipid peroxidation protection studies, probucol treatment showed a concentration-dependent inhibition (10–34% inhibition; P <0.05) of Fe-NTA plus H₂O₂-induced lipid peroxidation as measured by thiobarbituric acid reacting species' (TBARS) formation in renal microsomes. Similarly, in DNA damage protection studies, probucol treatment also showed a concentration-dependent strong inhibition (36–71% inhibition; P < 0.05) of DNA damage. From these studies, it was concluded that probucol inhibits peroxidation of microsomal membrane lipids and DNA damage induced by Fe-NTA plus H₂O₂. However, because the lipid peroxidation and DNA damage studied here are regarded as early markers of carcinogenesis, we suggest that probucol may be developed as a cancer chemopreventive agent against renal carcinogenesis and other adverse effects of Fe-NTA exposure in experimental animals, in addition to being a cholesterol-lowering drug, useful for the control of hypercholestrolemia.     

Studies on the Interaction of [SnMe2Cl2(bu2bpy)] Complex with ct-DNA Using Multispectroscopic,Atomic Force Microscopy (AFM) and Molecular Docking

The interaction of SnMe₂Cl₂(bu₂bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV–Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe₂Cl₂(bu₂bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859?nm were observed by using AFM for Sn(IV) Complex–DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO₂ group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe₂Cl₂(bu₂bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA–complex mixture confirmed the experimental results.     

Methods for the determination of deoxyribonucleic Acid homologies in streptomyces

Variations of the membrane filter technique for deoxyribonucleic acid (DNA) hybridizations were studied with respect to Streptomyces species. At the temperatures required for specific hybridization of DNA with the high melting temperature (T_m) characteristic of Streptomyces, large amounts (up to 97%) of filter-bound DNA became eluted, in all reaction mixtures studied, within 21 hr. In most solutions this leaching was increased by the presence of sheared denatured DNA. Incubation of DNA-loaded filters in a solution of 50% formamide containing 6× standard saline citrate, at 48 C for 40 hr, was judged to be the best set of conditions tested based on relatively good retention of immobilized DNA, very low hybridization with unrelated DNA of a similarly high T_m (from Sarcina lutea), and the formation of complexes similar in thermal stability to the native DNA. The expression of results as sheared DNA bound in relation to long-chain DNA retained is recommended when a high concentration of sheared DNA relative to immobilized DNA is used.     

Microcalorimetric Investigation of DNA,poly(dA)poly(dT) and poly[d(A-C)]poly[d(G-T)] Melting in the Presence of Water Soluble (Meso tetra (4 N oxyethylpyridyl) Porphyrin) and its Zn Complex

Abstract

Thermodynamic parameters of melting process (δH_m, T_m, δT_m) of calf thymus DNA, poly(dA)poly(dT) and poly(d(A-C))·poly(d(G-T)) were determined in the presence of various concentrations of TOEPyP(4) and its Zn complex. The investigated porphyrins caused serious stabilization of calf thymus DNA and poly poly(dA)poly(dT), but not poly(d(A-C))poly(d(G-T)). It was shown that TOEpyp(4) revealed GC specificity, it increased T_m of satellite fraction by 24°C, but ZnTOEpyp(4), on the contrary, predominately bound with AT-rich sites and increased DNA main stage T_m by 18°C, and T_m of poly(dA)poly(dT) increased by 40 °C, in comparison with the same polymers without porphyrin. ZnTOEpyp(4) binds with DNA and poly(dA)poly(dT) in two modes—strong and weak ones. In the range of r from 0.005 to 0.08 both modes were fulfilled, and in the range of r from 0.165 to 0.25 only one mode—strong binding—took place. The weak binding is characterized with shifting of T_m by some grades, and for the strong binding T_m shifts by ～ 30–40°C. Invariability of ΔH_m of DNA and poly(dA)poly(dT), and sharp increase of T_m in the range of r from 0.08 to 0.25 for thymus DNA and 0.01–0.2 for poly(dA)poly(dT) we interpret as entropic character of these complexes melting. It was suggested that this entropic character of melting is connected with forcing out of H₂O molecules from AT sites by ZnTOEpyp(4) and with formation of outside stacking at the sites of binding. Four-fold decrease of calf thymus DNA melting range width ΔT_m caused by increase of added ZnTO- Epyp(4) concentration is explained by rapprochement of AT and GC pairs thermal stability, and it is in agreement with a well-known dependence, according to which ΔT～T_GC-T_AT for DNA obtained from higher organisms (L. V. Berestetskaya, M. D. Frank-Kamenetskii, and Yu. S. Lazurkin. Biopolymers 13, 193–205 (1974)). Poly (d(A-C))poly(d(G-T)) in the presence of ZnTOEpyp(4) gives only one mode of weak binding. The conclusion is that binding of ZnTOEpyp(4) with DNA depends on its nucleotide sequence.     

Phosphorothioate DNA as an antioxidant in bacteria

Diverse bacteria contain DNA with sulfur incorporated stereo-specifically into their DNA backbone at specific sequences (phosphorothioation). We found that in vitro oxidation of phosphorothioate (PT) DNA by hydrogen peroxide (H₂O₂) or peracetic acid has two possible outcomes: DNA backbone cleavage or sulfur removal resulting in restoration of normal DNA backbone. The physiological relevance of this redox reaction was investigated by challenging PT DNA hosting Salmonella enterica cells using H₂O₂. DNA phosphorothioation was found to correlate with increasing resistance to the growth inhibition by H₂O₂. Resistance to H₂O₂ was abolished when each of the three dnd genes, required for phosphorothioation, was inactivated. In vivo, PT DNA is more resistant to the double-strand break damage caused by H₂O₂ than PT-free DNA. Furthermore, sulfur on the modified DNA was consumed and the DNA was converted to PT-free state when the bacteria were incubated with H₂O₂. These findings are consistent with a hypothesis that phosphorothioation modification endows DNA with reducing chemical property, which protects the hosting bacteria against peroxide, explaining why this modification is maintained by diverse bacteria.     

Studying compaction-decompaction of DNA molecules induced by surfactants

The mechanism and detailed processes of DNA compaction and decompaction are essential for the life activities, as well as for the researches in the molecular biology, genetics and biomedicine. The compaction of two kinds of DNA molecules caused by Cetyltrimethyl Ammonium Bromide (CTAB) and their decompaction induced with sodium dodecyl sulfate (SDS) or excessive amount of CTAB have been investigated with multiple perspectives such as the UV-VIS spectrophotometry, dynamic light scattering, and zeta potential. The compaction phenomenon of DNA can easily be observed when the CTAB combines with the DNA, not just when the molar ratio Q_CTAB/Q_DNA is approximately equal to 1 as the conventional recognition, but also when Q_CTAB/Q_DNA <1,DNA can be compacted; Molecular state of DNA is only changed in the conformational structure, but not in the chemical structure. Finally, a model is suggested to help catch on the biophysical mechanism of DNA chain conformational change.     

Elucidation of the DNA-interacting properties and anticancer activity of a Ni(II)-coordinated mithramycin dimer complex

Mithramycin (Mith) forms a drug-metal complex with a 2:1 stoichiometry by chelation with a Ni(II) ion, which was determined using circular dichroism spectroscopy. Mith exhibits an increased affinity (~55 fold) for Ni(II) in the presence of DNA compared to the absence of DNA, suggesting that DNA acts as an effective template to facilitate chelation. Also, we characterized the DNA-acting properties of a Ni(II) derivative of Mith. Kinetic analysis using surface plasmon resonance and UV melting studies revealed that Ni^II(Mith)₂ binds to duplex DNA with a higher affinity compared to Mg^II(Mith)₂. The thermodynamic parameters revealed a higher free energy of formation for duplex DNA in the presence of Ni^II(Mith)₂ compared to duplex DNA in the presence of Mg^II(Mith)₂. The results of a DNA-break assay indicated that Ni^II(Mith)₂ is capable of promoting one-strand cleavage of plasmid DNA in the presence of hydrogen peroxide; the DNA cleavage rate of Ni^II(Mith)₂ was calculated to be 4.1 × 10^?4 s^?1. In cell-based experiments, Ni^II(Mith)₂ exhibited a more efficient reduction of c-myc and increased cytotoxicity compared to Mith alone because of its increased DNA-binding and cleavage activity. The evidence obtained in this study suggests that the biological effects of Ni^II(Mith)₂ require further investigation in the future.     

Novel zinc finger nuclease created by combining the Cys2His2- and His4-type zinc finger domains

To improve the DNA hydrolytic activity of the zinc finger nuclease, we have created a new artificial zinc finger nuclease (ZWH4) by connecting two distinct zinc finger domains possessing different types of Zn(II) binding sites (Cys₂His₂- and His₄-types). The overall fold of ZWH4 is similar to that of the wild-type Sp1 zinc finger (Sp1(zf123)) as revealed by circular dichroism spectroscopy. The gel mobility shift assay demonstrated that ZWH4 binds to the GC box DNA, although the DNA-binding affinity is lower than that of Sp1(zf123). Evidently, ZWH4 hydrolyzes the covalently closed circular plasmid DNA (form I) containing the GC box (pBSGC) to the linear duplex DNA (form III) in the presence of a higher concentration (50 times) of the protein than DNA for a 24-h reaction. Of special interest is the fact that the novel mixed zinc finger protein containing the Cys₂His₂- and His₄-type domains was first created. The present results provide the useful information for the redesign strategy of an artificial nuclease based on the zinc finger motif.