Structural Basis for The Recognition of Deaminated Nucleobases by An Archaeal DNA Polymerase

With increasing temperature, nucleobases in DNA become increasingly damaged by hydrolysis of exocyclic amines. The most prominent damage includes the conversion of cytosine to uracil and adenine to hypoxanthine. These damages are mutagenic and put the integrity of the genome at risk if not repaired appropriately. Several archaea live at elevated temperatures and thus, are exposed to a higher risk of deamination. Earlier studies have shown that DNA polymerases of archaea have the property of sensing deaminated nucleobases in the DNA template and thereby stalling the DNA synthesis during DNA replication providing another layer of DNA damage recognition and repair. However, the structural basis of uracil and hypoxanthine sensing by archaeal B-family DNA polymerases is sparse. Here we report on three new crystal structures of the archaeal B-family DNA polymerase from Thermococcus kodakarensis (KOD) DNA polymerase in complex with primer and template strands that have extended single stranded DNA template 5’-overhangs. These overhangs contain either the canonical nucleobases as well as uracil or hypoxanthine, respectively, and provide unprecedented structural insights into their recognition by archaeal B-family DNA polymerases.     

尿嘧啶和它的分子识别膜之间相互作用机理的理论研究

运用密度泛函方法研究尿嘧啶分子识别膜的作用机理,提出了分子识别膜的4种可能的分子间相互作用方式,对基于分子间氢键相互作用构建的复合物结构进行了优化,求得了相应的结合能;同时,对这4种可能存在的复合物的振动模式实施了理论计算预测,并与实验数据相对比,最终推断出该分子识别膜内的主要作用方式。     

Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation

DNA repair proteins participate in extensive protein−protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent “RPA−Spy−UNG2” complex could identify and excise uracil bases in duplex areas next to ssDNA−dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA−Spy−UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA−dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.     

Double Variational Binding—(SMILES) Conformational Analysis by Docking Mechanisms for Anti-HIV Pyrimidine Ligands

Variational quantitative binding–conformational analysis for a series of anti-HIV pyrimidine-based ligands is advanced at the individual molecular level. This was achieved by employing ligand-receptor docking algorithms for each molecule in the 1,3-disubstituted uracil derivative series that was studied. Such computational algorithms were employed for analyzing both genuine molecular cases and their simplified molecular input line entry system (SMILES) transformations, which were created via the controlled breaking of chemical bonds, so as to generate the longest SMILES molecular chain (LoSMoC) and Branching SMILES (BraS) conformations. The study identified the most active anti-HIV molecules, and analyzed their special and relevant bonding fragments (chemical alerts), and the recorded energetic and geometric docking results (i.e., binding and affinity energies, and the surface area and volume of bonding, respectively). Clear computational evidence was also produced concerning the ligand-receptor pocket binding efficacies of the LoSMoc and BraS conformation types, thus confirming their earlier presence (as suggested by variational quantitative structure-activity relationship, variational-QSAR) as active intermediates for the molecule-to-cell transduction process.     

Epitaxial nucleation,modulated structure of molecular aggregation,and enhanced thermal degradation temperature of poly(ethylene adipate): Effects of the naturally occurring uracil as a nucleator

We fabricated a novel bio-composite using the poly(ethylene adipate) (PEA) and naturally occurring uracil (URA), in which the URA with the full biocompatibility and degradability acted as a nucleator (NA). A distinct enhancement was found in the crystallizability, melt-crystallization temperature (T_c), and crystallization rate of the PEA upon incorporation of the URA, an indicative of a good NA of the URA. The underlying nucleation mechanism of the PEA is the epitaxial nucleation, attributed to the extremely good matching between the crystal lattice of the PEA and URA. The H-bond interaction exists between the carbonyl/ester segment of the PEA crystalline phase and URA. With loading of the URA, both the carbonyl and ester fell behind the CH₂ in the segmental reorganization in the crystallization process of the PEA. The PEA/1%URA showed an enhancement in the T_d in the TG measurement (i.e. increased stability in thermal degradation), mainly attributed to the flame retardance effect of the URA.     

The uracil permease of Schizosaccharomyces pombe: A representative of a family of 10 transmembrane helix transporter proteins of yeasts

The uracil permease gene of Schizosaccharomyces pombe was cloned and sequenced. The deduced protein sequence shares strong similarities with five open reading frames from Saccharomyces cerevisiae, namely the uracil permease encoded by the FUR4 gene, the allantoin permease encoded by DAL4, a putative uridine permease (YBL042C) and two unknown ORFs YOR071c and YLR237w. A topological model retaining ten transmembrane helices, based on predictions and on experimental data established for the uracil permease of S. cerevisiae by Galan and coworkers (1996), is discussed for the four closest proteins of this family of transporters. The sequence of the uracil permease gene of S. pombe has been deposited in the EMBL data bank under Accession Number X98696. © 1998 John Wiley & Sons, Ltd.     

Nucleation Effects of Nucleobases on the Crystallization Kinetics of Poly(L‐lactide)

The effects of nucleobases, especially uracil, on the nonisothermal and isothermal crystallization, melting behavior, spherulite morphology, and crystalline structure of bio‐based and biodegradable PLLA are studied. The melt‐ and cold‐crystallization rates of PLLA increase with increasing uracil loading. The melting behavior of nonisothermally melt‐ and cold‐crystallized PLLAs depends on the uracil content. The isothermal crystallization kinetics is analyzed based on an Avrami model. The incorporation of uracil changes the t_1/2/T_c profile of PLLA due to the more distinct heterogeneous nucleation effects at small supercooling. The crystalline structure of PLLA is not affected by uracil presence. The nucleation density increases and the spherulite size decreases by uracil incorporation.

     

微波辅助下5-碘尿嘧啶衍生物的快速合成

在微波辐射下,I2在稀硝酸水溶液中快速在尿嘧啶5位发生碘化反应,以较高产率得到了9个5-碘嘧啶衍生物(75%~90%)。产物结构经1HNMR和13CNMR确证。     

6-三氟甲基脲嘧啶衍生物的合成与除草生物活性

合成了9个6-三氟甲基脲嘧啶类化合物,用1H NMR、MS、IR等对其结构进行了表征;初步除草生物活性实验结果表明:大多化合物对双子叶杂草苘麻、刺苋和藜以及单子叶杂草马唐、稗和狗尾表现出显著的除草活性,其中3-(2,4-二氯苯基)-6-三氟甲基脲嘧啶在375 g a.i./ha初筛剂量下,对双子叶杂草苘麻、刺苋和藜都具有100%的除草活性。     

The kinetics and primary products of uracil chlorination

The reaction between free available chlorine (FAC) and the pyrinidine base uracil, was studied over a pH range of 5–9 and at a range of FAC to uracil ratios between 0.5 and 5 mol mol⁻¹. Rate constants for the reaction were obtained and the primary uracil chlorination products identified.The reaction was found to adhere very well to mixed second order kinetics at FAC to uracil molar ratios 1.0. At a ratio of 5 mol mol⁻¹, the reaction demonstrated a reasonable empirical fit to the same kinetic model. The rate constant was markedly pH dependent increasing from approx. 0.3 M⁻¹ s⁻¹ at pH = 5 to 5 M⁻¹ s⁻¹ above pH = 7 at low molar ratios while the respective values at high molar ratios were approx. 7 and 90 M⁻¹ s⁻¹.At low FAC uracil ratios the chlorination reaction yielded exclusively 5-chlorouracil while at the higher ratios, a dichlorouracil was isolated in a pure form and characterized spectrometrically. This material was the only organic chloramine detected in any of the systems. While evidence was obtained for breakdown of the uracil ring, little evidence for formation of secondary chloramines was found. The characteristic odor of nitrogen trichloride was noted at the higher FAC/uracil ratios. FAC consumption increased from 1 mol of FAC per mol of uracil consumed at the low molar ratios to 3 mol mol⁻¹ at initial ratios of ≈ 5 mol FAC per mol uracil.