分子信标用于核酸连续复制过程的体外实时监测

利用分子信标核酸探针实时监测了核酸连续复制过程. 分子信标不仅作为模板参与复制反应, 而且同步将复制过程的信息转换为荧光信号, 实现复制过程的体外实时监测. 该方法不仅为DNA复制检测提供了一种实时研究手段, 而且为核酸复制动力学及与复制相关疾病的深入研究提供了一种新的思路.     

DNA replication in the third domain (of life)

DNA replication is the process underlying evolution and the propagation of living organisms. Since the discovery of DNA-dependent DNA polymerases more than 40 years ago, the mechanisms governing DNA replication have been extensively studied in bacteria and eukarya. During the last several years, these studies have been extended to the third domain of life, the archaea. Although archaea are prokaryotes, their replication machinery and the proteins participating in the initiation of DNA replication are more similar to those found in eukarya than bacteria. It appears, however, that replication in archaea is a simpler version of the eukaryotic one as fewer polypeptides participate in each phase of the replication process. The archaeal replication apparatus also has several unique features not found in eukaryotic organisms. Furthermore, like bacteria, members of this domain thrive under a broad range of environmental conditions including extreme temperature, high salt, pH, etc. Thus, the replication machinery had to adapt to these extreme conditions. This article summarizes our current understanding of the mechanisms governing DNA replication in archaea and highlights similarities and differences between archaeal replication and that of bacteria and eukarya.     

Inhibition of the In Vitro Replication of DNA by an Aptamer–Protein Complex in an Autonomous DNA Machine

DNA replication plays a central role in living organisms. Unregulated or uncontrollable DNA replication is well known to result in many pathological states, such as cancer, autoimmune diseases, and viral/bacterial infections. We report that an aptamer–protein complex could indirectly inhibit in vitro replication of DNA. An isothermal DNA machine based on the strand‐displacement amplification is employed to support our assumption. An antithrombin aptamer sequence is rationally encoded into the DNA replication template. Once thrombin binds to the template, the as‐formed aptamer–protein complexes can, in turn, become a barrier to the polymerase and inhibit the DNA replication activities in both static and dynamic modes. The inhibition is successfully confirmed by both fluorescence and gel‐electrophoresis experiments. Considering the availability of a broad library of aptamers and the existence of various DNA/protein interactions, our results imply the possibility for the rational regulation of DNA replication in vivo.     

Effector‐Triggered Self‐Replication in Coupled Subsystems

In living systems processes like genome duplication and cell division are carefully synchronized through subsystem coupling. If we are to create life de novo, similar control over essential processes such as self‐replication need to be developed. Here we report that coupling two dynamic combinatorial subsystems, featuring two separate building blocks, enables effector‐mediated control over self‐replication. The subsystem based on the first building block shows only self‐replication, whereas that based on the second one is solely responsive toward a specific external effector molecule. Mixing the subsystems arrests replication until the effector molecule is added, resulting in the formation of a host–effector complex and the liberation of the building block that subsequently engages in self‐replication. The onset, rate and extent of self‐replication is controlled by the amount of effector present.     

Next-generation sequencing-based analysis of the effect of N6-methyldeoxyadenosine modification on DNA replication in human cells

N⁶-methyldeoxyadenosine（6 mdA） modification is considered as a new epigenetic mark that may play important roles in various biological processes.However,it remains unclear about the effect of 6 mdA on DNA replication in human cells.Herein,we combined next-generation sequencing with shuttle vector technology to explore how 6 mdA affects the efficiency and accuracy of DNA replication in human cells.Our results showed that 6 mdA neither blocked DNA replication nor induced mutations in hu...     

The Effect of Dia2 Protein Deficiency on the Cell Cycle,Cell Size,and Recruitment of Ctf4 Protein in Saccharomyces cerevisiae

Cells have evolved elaborate mechanisms to regulate DNA replication machinery and cell cycles in response to DNA damage and replication stress in order to prevent genomic instability and cancer. The E3 ubiquitin ligase SCF^Dia2 in S. cerevisiae is involved in the DNA replication and DNA damage stress response, but its effect on cell growth is still unclear. Here, we demonstrate that the absence of Dia2 prolongs the cell cycle by extending both S- and G2/M-phases while, at the same time, activating the S-phase checkpoint. In these conditions, Ctf4—an essential DNA replication protein and substrate of Dia2—prolongs its binding to the chromatin during the extended S- and G2/M-phases. Notably, the prolonged cell cycle when Dia2 is absent is accompanied by a marked increase in cell size. We found that while both DNA replication inhibition and an absence of Dia2 exerts effects on cell cycle duration and cell size, Dia2 deficiency leads to a much more profound increase in cell size and a substantially lesser effect on cell cycle duration compared to DNA replication inhibition. Our results suggest that the increased cell size in dia2∆ involves a complex mechanism in which the prolonged cell cycle is one of the driving forces.     

GENERAL PURPOSE LAMPS INDUCE POLYOMA DNA REPLICATION IN H3 CELLS

Abstract— We have previously demonstrated the ability of UVC (254 nm) radiation to induce asynchronous polyoma replication in rat fibroblast cells (H3 line) that contain an integrated copy of polyoma virus. In the present study we show that general purpose lamps can induce polyoma replication in these cells as well. The amount of UV radiation emitted by three different light sources was determined and the effects of each source on the replication of polyoma DNA was assessed. Our findings indicate that a 100 W incandescent lamp had a minimal effect on replication, whereas a 90 s exposure to a halogen lamp or a 160 W mercury vapor lamp induced replication 1.5-fold and 2-fold, respectively, in comparison with nontreated controls. We have previously shown that asynchronous polyoma replication in H3 cells involves UV-inducible cellular protein factors. Our present results indicate that these factors are also activated by exposure to commonly used lamps that emit comparable doses of UV radiation.     

Replication and surface properties of micro injection molded PLA/MWCNT nanocomposites

Multi-walled carbon nanotube (MWCNT) reinforced polylactide (PLA) nanocomposites were injected molded into a mold with micro needle patterns. In order to alleviate the hesitation effect caused by an increased melt viscositgy of PLA/CNT nanocomposites, the effects of the injection speed and holding pressure on the replication property were investigated. The effects of MWCNTs on the crystallization, thermal behavior, replication properties, replication and surface properties of micro injection molded PLA/CNT nanocomposites were investigated. An analysis of crystallinity and thermal behavior indicated that the MWCNTs promoted the unique α’ to α crystal transition of PLA, leading to an enhancement of surface modulus and hardness, as measured using a nanoindentation technique. The specific interaction between PLA and MWCNTs was characterized using an equilibrium melting point depression technique. Furthermore, the MWCNTs increased the activation energy for thermal degradation of PLA due to the physical barrier effect. The improved replication quality of the microfeatures in the PLA/MWCNT nanocomposites has been achieved by elevating injection speed and holding pressure, which enhances the polymer filling ability within the micro cavity. A replication ratio greater than 96% for the micro injection molded PLA/CNT nanocomposites were achieved at holding pressure of 100 MPa and injection speed of 120 mm/s. This study shows that processing conditions significantly influence the replication and surface properties of micro injection molded PLA/CNT nanocomposites.     

Replication NAND gate with light as input and output

Logic operations can highlight information transfer within complex molecular networks. We describe here the design of a peptide-based replication system that can be detected by following its fluorescence quenching. This process is used to negate the signal of light-activated replication, and thus to prepare the first replication NAND gate.     

Repair replication in Chinese hamster cells after damage from ultraviolet light

Abstract— After irradiation with u.v. light, Chinese hamster cells perform repair replication of their DNA. Small numbers of nucleosides are inserted into DNA, such that when BrUdR is used there is no detectable change in density. Repair replication begins immediately after irradiation, but it decelerates steadily and at least half is complete within 4 hr. Repair replication saturates above 200 ergs/mm² at a level which represents 0.055 per cent replacement of all thymine sites in 4 hr. Repair replication in mammalian cells, in contrast to that in microorganisms, does not appear to replace pyrimidine dimers excised from DNA in acid soluble form, and neither repair nor semiconservative replication discriminates between BrUdR and TdR.     

Peroxisome proliferator-activated receptor alpha antagonism inhibits hepatitis C virus replication

Hepatitis C virus (HCV) is a global health problem and a leading cause of liver disease. Here, we demonstrate that the replication of HCV replicon RNA in Huh-7 cells is inhibited by a peroxisome proliferator-activated receptor (PPAR) antagonist, 2-chloro-5-nitro-N-(pyridyl)benzamide (BA). Downregulation of PPARgamma with RNA interference approaches had no effect on HCV replication in Huh-7 cells, whereas PPARalpha downregulation inhibited HCV replication. Fluorescence and coherent anti-Stokes Raman scattering (CARS) microscopy demonstrate a clear buildup of lipids upon treatment with BA. These observations are consistent with the misregulation of lipid metabolism, phospholipid secretion, cholesterol catabolism, and triglyceride clearance events associated with the inhibition of PPARalpha. The inhibition of HCV replication by BA may result from disrupting lipidation of host proteins associated with the HCV replication complex or, more generally, by disrupting the membranous web where HCV replicates.     

Accelerated Self‐Replication under Non‐Equilibrium,Periodic Energy Delivery

Self‐replication is a remarkable phenomenon in nature that has fascinated scientists for decades. In a self‐replicating system, the original units are attracted to a template, which induce their binding. In equilibrium, the energy required to disassemble the newly assembled copy from the mother template is supplied by thermal energy. The possibility of optimizing self‐replication was explored by controlling the frequency at which energy is supplied to the system. A model system inspired by a class of light‐switchable colloids was considered where light is used to control the interactions. Conditions under which self‐replication can be significantly more effective under non‐equilibrium, cyclic energy delivery than under equilibrium constant energy conditions were identified. Optimal self‐replication does not require constant energy expenditure. Instead, the proper timing at which energy is delivered to the system is an essential controllable parameter to induce high replication rates.     

Accelerated Self‐Replication under Non‐Equilibrium,Periodic Energy Delivery

Self‐replication is a remarkable phenomenon in nature that has fascinated scientists for decades. In a self‐replicating system, the original units are attracted to a template, which induce their binding. In equilibrium, the energy required to disassemble the newly assembled copy from the mother template is supplied by thermal energy. The possibility of optimizing self‐replication was explored by controlling the frequency at which energy is supplied to the system. A model system inspired by a class of light‐switchable colloids was considered where light is used to control the interactions. Conditions under which self‐replication can be significantly more effective under non‐equilibrium, cyclic energy delivery than under equilibrium constant energy conditions were identified. Optimal self‐replication does not require constant energy expenditure. Instead, the proper timing at which energy is delivered to the system is an essential controllable parameter to induce high replication rates.     

Modulation of Fatty Acid Synthase Enzyme Activity and Expression during Hepatitis C Virus Replication

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Highlights? Enzymatic activity of FASN was investigated by ABPP methods during HCV replication ? During HCV replication the activity and expression of FASN increases ? Cellular triglyceride levels rise with increased FASN enzyme activity in Huh7 cells ? Active FASN does not colocalize with HCV replication complexes during HCV replication     

The DNA polymerase activity of Pol ε holoenzyme is required for rapid and efficient chromosomal DNA replication in Xenopus egg extracts

Background  

DNA polymerase ε (Pol ε) is involved in DNA replication, repair, and cell-cycle checkpoint control in eukaryotic cells. Although the roles of replicative Pol α and Pol δ in chromosomal DNA replication are relatively well understood and well documented, the precise role of Pol ε in chromosomal DNA replication is not well understood.     

Construction of a Live‐Attenuated HIV‐1 Vaccine through Genetic Code Expansion

A safe and effective vaccine against human immunodeficiency virus type 1 (HIV‐1) is urgently needed to combat the worldwide AIDS pandemic, but still remains elusive. The fact that uncontrolled replication of an attenuated vaccine can lead to regaining of its virulence creates safety concerns precluding many vaccines from clinical application. We introduce a novel approach to control HIV‐1 replication, which entails the manipulation of essential HIV‐1 protein biosynthesis through unnatural amino acid (UAA*)‐mediated suppression of genome‐encoded blank codon. We successfully demonstrate that HIV‐1 replication can be precisely turned on and off in vitro.     

ENHANCED REPLICATION OF DAMAGED SV40 DNA IN CARCINOGEN-TREATED MONKEY CELLS

Abstract Treatment of mammalian cells with certain chemical or physical carcinogens prior to infection with ultraviolet-irradiated virus results in enhanced survival or reactivation of the damaged virus. To investigate the molecular basis of this enhanced reactivation (ER), we have examined Simian virus 40 DNA replication in carcinogen-treated cells. We find that treatment of monkey kidney cells with N-acetoxy-2-acetylamino-fluorene or UV radiation 24 h prior to infection with ultraviolet-irradiated Simian virus 40 leads to enhancement of viral DNA replication measured at 36 h after infection by [³H]thymidine incorporation or hybridization. The enhancement of DNA replication is observed when cells are treated from 1 to 60 h before infection or 1 to 16 h after infection. The fact that enhancement is observed also when cells are treated after infection rules out the possibility that enhancement occurs at the level of adsorption or penetration of the virus. Measurements of the time course of viral DNA replication indicate that pretreatment of cells does not alter the time of onset of viral DNA replication. We conclude from these studies that ER of Simian virus 40 occurs at the level of viral DNA replication.     

Optimization of unnatural base pair packing for polymerase recognition

As part of an effort to expand the genetic alphabet, we have been examining the ability of predominately hydrophobic nucleobase analogues to pair in duplex DNA and during polymerase-mediated replication. We previously reported the synthesis and thermal stability of unnatural base pairs formed between nucleotides bearing simple methyl-substituted phenyl ring nucleobase analogues. Several of these pairs are virtually as stable and selective as natural base pairs in the same sequence context. Here, we report the characterization of polymerase-mediated replication of the same unnatural base pairs. We find that every facet of replication, including correct and incorrect base pair synthesis, as well as continued primer extension beyond the unnatural base pair, is sensitive to the specific methyl substitution pattern of the nucleobase analogue. The results demonstrate that neither hydrogen bonding nor large aromatic surface area is required for polymerase recognition, and that interstrand interactions between small aromatic rings may be optimized for replication. Combined with our previous results, these studies suggest that appropriately derivatized phenyl nucleobase analogues represent a promising approach toward developing a third base pair and expanding the genetic alphabet.