金属配合物-寡聚核苷酸定位断裂剂研究进展

核酸切割试剂与寡聚核苷酸(ODN)偶联制得的人工核酸酶能在特定位点断裂DNA或RNA,为人工核酸酶的分子设计提供了一种新方法.本文综述了金属配合物-ODN识别切割试剂的偶联方式及其与靶分子的作用机制,并指出了今后的研究方向.     

Synthesis of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified oligonucleotides: hybridization affinity, resistance to nuclease, and protein binding characteristics

Synthesis of a series of 2′-O-[2-[(N,N-dialkylamino)oxy]ethyl]-modified 5-methyluridine nucleoside phosphoramidites and solid supports are described. Using these monomers, modified oligonucleotides containing phosphodiester linkages were synthesized in high yields. These modified oligonucleotides showed enhanced binding affinity to the complementary RNA (and not to DNA) and excellent nuclease stability with t_1/2>24 h. The human serum albumin binding properties of modified oligonucleotides have been evaluated to assess their transport and toxicity properties.     

Immobilization of single-strand specific nuclease (S1 nuclease) fromAspergillus oryzae

S1 nuclease fromAspergillus oryzae (EC 3.1.30.1) was coupled to gelatin-alginate composite matrix using the residual free aldehyde groups on the surface of glutaraldehyde crosslinked matrix. The immobilized enzyme retained approximately 10% activity of the soluble enzyme. When partially purified enzyme was bound to the matrix, the immobilized preparation did not show any detectable enzyme activity. However, the activity could be restored when the coupling was carried out in the presence of a coprotein or substrate. The optimum pH of the immobilized S1 nuclease shifted to 3.8 from 4.3 for the soluble enzyme. Also, optimum temperature increased to 65°C after immobilization. Bound S1 nuclease showed increased pH and temperature stabilities. Immobilization brought about a twofold decrease in the Michaelis-Menton constant (K _m).     

Dinuclear Cu(II) complexes based on p‐xylylene‐bridged bis(1,4,7‐triazacyclononane) ligands: Synthesis,characterization, DNA cleavage abilities and evaluation of superoxide dismutase‐ and catalase‐like activities

Three new dinuclear Cu(II) complexes with the formulas [Cu₂(pxdmbtacn)Cl₄] ( 1 ), [Cu₂(pxdmbtacn)Cl_0.7(NO₃)_1.3(OH)₂(H₂O)_1.3]?6H₂O ( 2 ) and [Cu₂(pxdiprbtacn)Cl₄] ( 3 ) together with one previously reported complex, [Cu₂(pxbtacn)Cl₄] ( 4 ), were obtained from Cu(II) salts with three p‐xylylene‐bridged bis‐tacn ligands bearing pendant alkyl substituents or without pendant group. Complex 2 was structurally characterized as a centrosymmetric dinuclear molecule with each metal center being coordinated to some labile ligands in addition to one tacn ring. Based on the results of mass spectrometry and UV–visible spectroscopy, complexes 1 and 3 are capable of existing in aqueous solution as dinuclear species but 4 can partially form a dimer of the original dinuclear motif. Complexes 1 , 3 and 4 can all effectively cleave supercoiled DNA oxidatively in the presence of hydrogen peroxide. The superoxide dismutase (SOD) activities of 1 and 3 measured under physiological conditions are comparable to that of the native CuZnSOD enzyme but the enzymatic activity of 4 is about three‐ to fourfold lower. Furthermore, complexes 1 , 3 and 4 demonstrate moderate scavenging effect on hydrogen peroxide and their catalase activities are in the decreasing order of 3 > 1 > 4 .     

Bioinformatics analysis of a non-specific nuclease from Yersinia enterocolitica subsp. palearctica

In this paper, the physical and chemical characteristics, biological structure and function of a non-specific nuclease from Yersinia enterocolitica subsp. palearctica (Y. NSN) found in our group were studied using multiple bioinformatics approaches. The results showed that Y. NSN had 283 amino acids, a weight of 30,692.5 ku and a certain hydrophilic property. Y. NSN had a signal peptide, no transmembrane domains and disulphide bonds. Cleavage site in Y. NSN was between pos. 23 and 24. The prediction result of the secondary structure showed Y. NSN was a coil structure-based protein. The ratio of α-helix, β-folded and random coil were 18.73%, 16.96% and 64.31%, respectively. Active sites were pos. 124, 125, 127, 157, 165 and 169. Mg²⁺ binding site was pos. 157. Substrate binding sites were pos. 124, 125 and 169. The analysis of multisequencing alignment and phylogenetic tree indicated that Y. NSN shared high similarity with the nuclease from Y. enterocolitica subsp. enterocolitica 8081. The enzyme activity results showed that Y. NSN was a nuclease with good thermostability.     

Graphene Oxide Protected Nucleic Acid Probes for Bioanalysis and Biomedicine

Recently, the binding ability of DNA on GO and resulting nuclease resistance have attracted increasing attention, leading to new applications both in vivo and in vitro. In vivo, nucleic acids absorbed on GO can be effectively protected from enzymatic degradation and biological interference in complicated samples, making it useful for targeted delivery, gene regulation, intracellular detection and imaging with high uptake efficiencies, high intracellular stability, and very low toxicity. In vitro, the adsorption of ssDNA on GO surface and desorption of dsDNA or well‐folded ssDNA from GO surface result in the protection and deprotection of DNA from nucleic digestion, respectively, which has led to target‐triggered cyclic enzymatic amplification methods (CEAM) for amplified detection of analytes with sensitivity 2–3 orders of magnitude higher than that of 1:1 binding strategies. This Concept article explores some of the latest developments in this field.     

Ultrafast solvation dynamics at internal sites of staphylococcal nuclease investigated by site-directed mutagenesis

Internal solvation of protein was studied by site-directed mutagenesis,with which an intrinsically fluorescent probe,tryptophan,is inserted into the desired position inside a protein molecule for ultrafast spectroscopic study.Here we review this unique method for protein dynamics research.We first introduce the frontiers of protein solvation,site-directed mutagenesis,protein stability and characteristics,and the spectroscopic methods.Then we present time-resolved spectroscopic dynamics of solvation dynamics inside cavities of active sites.The studies are carried out on a globular protein,staphylococcal nuclease.The solvation at sites inside the protein molecule’s cavities clearly reveals characteristics of the local environment.These solvation behaviors are directly correlated to enzyme activity.     

金黄色葡萄球菌调控基因agr及sae对其耐热核酸酶分泌的影响

金黄色葡萄球菌(Staphylococcus aureus,SA)是一种重要的人畜共患病病原,它能产生一种由nuc基因编码的胞外耐热核酸酶。耐热核酸酶是金黄色葡萄球菌的毒力因子之一,agr及sae位点是编码金黄色葡萄球菌的主要毒力调节因子,研究发现sae调节位点在影响耐热核酸酶的表达上占主导地位。分析金黄色葡萄球菌各毒力因子和金黄色葡萄球菌现有疫苗,为解决金黄色葡萄球菌的耐药性,寻找更好的防治方法,有必要进行探索性实验寻找一种因素或药物,用来阻抑sae调控因子对耐热核酸酶的分泌过程进行调节,从而为金黄色葡萄球菌的防治研究提供一种新材料。     

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies

Background: The translation or stability of the mRNAs from ferritin, m-aconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of higher-solution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms.Results: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern.Conclusions: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes, The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.     

Copper complexes as chemical nucleases

Redox active mononuclear and binuclear copper(II) complexes have been prepared and structurally characterized. The complexes have planar N-donor heterocyclic bases like 1,10-phenanthroline (phen), dipyridoquinoxaline (dpq) and dipyridophenazine (dppz) ligands that are suitable for intercalation to B-DNA. Complexes studied for nuclease activity have the formulations [Cu(dpq)₂(H₂O)] (ClO₄)₂.H₂O (1), [CuL(H₂O)₂(μ-ox)](ClO₄)₂ (L = bpy,2; phen,3; dpq,4; and dppz,5) and [Cu(L)(salgly)] (L = bpy,6; phen,7; dpq,8; and dppz,9), where salgly is a tridentate Schiff base obtained from the condensation of glycine and salicylaldehyde. The dpq complexes are efficient DNA binding and cleavage active species. The dppz complexes show good binding ability but poor nuclease activity. The cleavage activity of thebis-dpq complex is significantly higher than thebis-phen complex of copper(II). The nuclease activity is found to be dependent on the intercalating nature of the complex and on the redox potential of the copper(II)/copper(I) couple. The ancillary ligand plays a significant role in binding and cleavage activity.