Restriction endonuclease EcoO109 from Escherichia coli H709c with heptanucleotide recognition site 5'-PuG/GNCCPy

A new restriction endonuclease, EcoO109, has been isolated from Escherichia coli H709c by polyethyleneimine (PEI) precipitation, DEAE-cellulose chromatography and heparin agarose chromatography. The yield was high, more than 3000 units/g of wet cells. The EcoO109 endonuclease recognizes and cleaves a nucleotide sequence of (formula: see text), in the presence of 10 mM Mg2+. The enzyme will be useful for structural analysis and molecular cloning of DNA because of the stability, high yield and easy handling of the producer strain.     

Structure and dynamics of nucleosomal DNA

The last five years have seen exciting advances in our understanding of the structure of the nucleosome core particle, the basic repeating unit in all eukaryotic chromatin. A picture emerges in which nucleosomal DNA, while distorted and compacted fivefold by tight interactions with the histone octamer core, is at the same time highly dynamic and adaptable. Here, we summarize the salient features from recent structural studies of nucleosome core particles (both published and unpublished) that concern the structure and dynamics of nucleosomal DNA, and the nature of protein-DNA interactions. Current mechanisms for chromatin remodeling and nucleosome sliding are discussed in light of new structural evidence. Finally, techniques to study nucleosome stability and ultimately dynamics are introduced.     

Telomerase Activity Is Sensitive to Subtle Perturbations of the TLC1 Pseudoknot 3′ Stem and Tertiary Structure

Pseudoknot formation in the core region of the telomerase RNA has been demonstrated to be important for telomerase activity in vertebrates, ciliates, and yeast. Characterization of the Saccharomyces cerevisiae telomerase RNA (TLC1) pseudoknot identified tertiary structural interactions that are also important for telomerase activity, as previously observed for the Kluyveromyces lactis and human telomerase RNA pseudoknots. In addition, the contributions of backbone ribose 2′-OH groups in the pseudoknot to telomerase catalysis were investigated previously, using 2′-OH (ribose) to 2′-H (deoxyribose) or 2′-O-methyl substitutions in the stem 2 helix, and it was proposed that one or more 2′-OH groups from the stem 2 sequences at or near the triple helix participate in telomerase catalysis. Based on these studies and investigations of the structural and thermodynamic properties of the TLC1 RNA pseudoknot region, we have examined the structural and thermodynamic perturbations of the 2′-O-methyl and 2′-H substituted pseudoknots, using UV-monitored thermal denaturation, native gel electrophoresis, and circular dichroism spectroscopy. Our results demonstrate the presence of A-form helical geometry perturbations in the backbone sugar substituted pseudoknots, show a correlation between thermodynamic stability and telomerase activity, and are consistent with the identification of the U809 ribose 2′-OH as a potential contributor to telomerase activity.     

Novel aromatic sulfonyl naphthalene-based boronates as 20S proteasome inhibitors

A novel series of non-peptide proteasome inhibitors (PIs) that act on chymotrypsin-like (ChT-L) of the proteasome were developed. These PIs bearing 4-aromatic sulfonyl naphthalene-based scaffold and Leu-boronic moiety as covalent bonding group displayed far better activity than PI-8182 for inhibiting ChT-L in preliminary biological activity test. The results showed that 2a (IC₅₀?=?6.942?μM, MCF-7) and 2c (IC₅₀?=?6.905?μM, MCF-7) displayed higher anti-proliferative activities than Bortezomib (IC₅₀?=?18.37?μM, MCF-7) under our experimental conditions. Furthermore, in the microsomal stability assay, 2a demonstrated excellent metabolic stability profiles with 56% remaining after 40?min, as compared to Bortezomib of which approximately 30% was remaining. The compounds 2a, 2c emerged as promising lead compounds for the development of novel non-peptide boronate PIs.     

Acceleration of 5-Methylcytosine Deamination in Cyclobutane Dimers by G and Its Implications for UV-Induced C-to-T Mutation Hotspots

Sunlight-induced C→T mutation hotspots occur most frequently at methylated CpG sites in tumor suppressor genes and are thought to arise from translesion synthesis past deaminated cyclobutane pyrimidine dimers (CPDs). While it is known that methylation enhances CPD formation in sunlight, little is known about the effect of methylation and sequence context on the deamination of 5-methylcytosine (^mC) and its contribution to mutagenesis at these hotspots. Using an enzymatic method, we have determined the yields and deamination rates of C and ^mC in CPDs and find that the frequency of UVB-induced CPDs correlates with the oxidation potential of the flanking bases. We also found that the deamination of T^mC and ^mCT CPDs is about 25-fold faster when flanked by G's than by A's, C's or T's in duplex DNA and appears to involve catalysis by the O6 group of guanine. In contrast, the first deamination of either C or ^mC in AC^mCG with a flanking G was much slower (t_1/2 > 250 h) and rate limiting, while the second deamination was much faster. The observation that C^mCG dimers deaminate very slowly but at the same time correlate with C→T mutation hotspots suggests that their repair must be slow enough to allow sufficient time for deamination. There are, however, a greater number of single C→T mutations than CC→TT mutations at C^mCG sites even though the second deamination is very fast, which could reflect faster repair of doubly deaminated dimers.     

Q-band electron paramagnetic resonance study of nitrosylprotoheme dimethyl ester complexes with N-,O-, and S-donor ligand as model systems for nitrosylhemoproteins

Electron paramagnetic resonance (epr) spectra (at X- and Q band frequency) of nitrosyl(proto-porphyrin IX dimethyl ester) iron( II) complexes with a trans axial ligand of nitrogen-, oxygen-, and sulfur-donor ligand, in the trozen glass state at 77°K, have been investigated in order to understand the epr spectra of nitrosylhemoproteins. The Q-band spectra resolved the spectral features more clearly than the X-band spectra and distinctly exhibited two groups of absorptions, which were attributable to two molecular species. Significant relations were found between two g values (e.g., g_x-g_z, g_x-g_y) and between the g value and the degree of the hyperfine splitting in central absorption. The epr parameters were not very sensitive to the π-bonding ability of the axial ligand, but registered the steric interaction of the axial ligand with porphynnato core. These findings can be utilized in the characterization of an axial ligand trans to the nitrosyl group in nitrosylhemoproteins.     

A mouse DNA sequence that mediates integration and excision of polyoma virus DNA

In mouse cells transformed by a temperature-sensitive polyoma virus (Py) genome, the integrated viral genome recombines with adjacent chromosomal DNA to yield a small cyclic molecule (RmI) with defined viral and cellular components. We have cloned the cellular component (Ins), determined its sequence, and examined its distribution in normal mouse DNA. The sequence of Ins displays several homologies with that surrounding the replication origin (ori) of Py or SV40 DNA.     

An Unusual Pyridine Nucleotide Accumulating in Erythrocytes: Its Identity,and Positive Correlation with Degree of Renal Failure

We have investigated an unusual nucleotide that accumulates, with precursors, in the erythrocytes of patients in uraemia. This nucleotide is related chemically to the NAD breakdown product, N1‐methyl‐2‐pyridone‐5‐carboxamide (Me2Py), found in high concentrations in the plasma of uraemic patients. Both Me2Py and the nucleotide accumulate to high concentrations in the blood during uraemia: our investigations of samples from renal out‐patients have provided information on a plausible link between the two compounds.