Protection-free one-pot synthesis of 2'-deoxynucleoside 5'-triphosphates and DNA polymerization

By differentiating the functional groups on nucleosides, we have designed and developed a one-pot synthesis of deoxyribonucleoside 5'-triphosphates without any protection on the nucleosides. A facile synthesis is achieved by generating an in situ phosphitylating reagent that reacts selectively with the 5'-hydroxyl groups of the unprotected nucleosides. The synthesized triphosphates are of high quality and can be effectively incorporated into DNAs by DNA polymerase. This novel approach is straightforward and cost-effective for triphosphate synthesis.     

Quantitative Bestimmung von Desoxyribonucleosid-Triphosphaten in Ascitestumorzellen unter Verwendung von 32P

The acid soluble compounds of ascites tumor cells after incubation with ³²P-orthophosphate were separated by thin-layer chromatography. By using unlabelled deoxyribonucleoside triphosphates it was possible to localize the corresponding radioactive spots. From the radioactivity of the spots and the specific activity of the intracellular orthophosphate the amounts of the deoxyribonucleoside triphosphates could be calculated.     

Improved sample preparation method for high-performance liquid chromatography of deoxyribonucleoside triphosphates from cell culture extracts

The accurate determination of deoxyribonucleoside triphosphates in cells is difficult owing to the high concentrations of interfering ribonucleoside triphosphates. The latter can be degraded to their respective bases by periodate oxidation of cell extracts. However, the large amount of bases so produced can interfere with subsequent high-performance liquid chromatographic (HPLC) analysis. The use of a weak ion-exchange cartridge to partially purify and concentrate deoxyribonucleoside triphosphates in periodate-treated cell extracts, prior to HPLC, thus allowing accurate determination is described. The recovery of the deoxyribonucleoside triphosphates is greater than 95%, and greater than 90% of the interfering bases are removed.     

Quantitative Bestimmung von Desoxyribonucleosid-Triphosphaten in Ascitestumorzellen unter Verwendung von 32P

Zusammenfassung Von Ascitestumoren wurden nach Inkubation mit ³²P-Orthophosphat Extrakte der säurelöslichen Verbindungen hergestellt und dünnschichtchromatographisch getrennt. Aus dem ³²P-Gehalt auf den durch die Verwendung von Trägersubstanzen lokalisierbaren Positionen der Desoxyribonucleosid-Triphosphate und der spezifischen Aktivität des innercellulären Orthophosphats wurden die in den Zellen vorliegenden Gehalte an Desoxyribonucleosid-Triphosphaten ermittelt.

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Quantitative determination of deoxyribonucleoside triphosphates in ascites tumor cells by using ³²P

The acid soluble compounds of ascites tumor cells after incubation with ³²P-orthophosphate were separated by thin-layer chromatography. By using unlabelled deoxyribonucleoside triphosphates it was possible to localize the corresponding radioactive spots. From the radioactivity of the spots and the specific activity of the intracellular orthophosphate the amounts of the deoxyribonucleoside triphosphates could be calculated.

     

DNA mutation analysis based on capillary electrochromatography using colloidal poly(N-isopropylacrylamide) particles as pseudostationary phase

Poly(N-isopropylacrylamide) (PNIPAM) is an interesting class of temperature sensitive, water soluble polymer that has a lower critical solution temperature (LCST) of 32 °C. Above the LCST, PNIPAM gets phase-separated and precipitates out from water. The fascinating temperature-sensitive property of PNIPAM has led to a growing interest in diverse fields of applications. Recently, capillary electrochromatography (CEC) has gained attention due to the wide range of applications based on the use of open tubular capillaries. In this paper, the use of phase-separated PNIPAM as a pseudostationary phase for CEC is demonstrated for the detection of single nucleotide polymorphisms (SNPs). Owing to the dynamic coating, the phase-separated PNIPAM particles did not require any immobilization technique and could exist as a mobile stationary phase in the open tubular capillary. The heteroduplex analyses of mutation samples could be successfully performed based on the phase-separated PNIPAM particles in the constructed CEC system. The CEC system, based on PNIPAM particles capable of having a narrow size distribution, shows great potential as an alternative to conventional DNA mutation systems.     

Incorporation of a minimal nucleotide into DNA

Abasic sites are amongst the most frequent DNA lesions and result from spontaneous hydrolysis of the glycosidic bond or from the removal of damaged nucleobases. These depurination events can also occur on free deoxyribonucleoside triphosphates present in cells and lead to the formation of an abasic site triphosphate of which very little is known. Herein, we report the synthesis and biochemical characterization of the minimal triphosphate dФTP. Unexpectedly, dФTP is tolerated by various DNA polymerases and the incorporation efficiency obeys the A-rule. Single incorporation of dФMP units were also observed opposite abasic sites and the addition of prosthetic molecules mimicking base-pairs do not seem to favor the process.     

PHOTOSENSITIZATION OF HUMAN DIPLOID CELL CULTURES BY INTRACELLULAR FLAVINS AND PROTECTION BY ANTIOXIDANTS

Abstract— The damaging effects of near ultraviolet and visible light on WI-38 human diploid lung fibroblasts were investigated. WI-38 cells in culture were killed by light doses ranging from 2 to 10 × 10³ W/m² h. There was an inverse correlation between culture age, i.e. population doubling level and photosensitivity. However, this effect could not be related to capacity for DNA synthesis and cell division.
Flavins were clearly implicated as endogenous photosensitizers, and antioxidants such as d, l -α-tocopherol (vitamin E), BHT and ascorbic acid were found to afford the cells protection from light damage. Furthermore, products of lipid peroxidation could be detected in cell homogenates irradiated in the presence of ribofiavin.     

Aerolysin蛋白纳米孔道直接检测单个DNA碱基修饰

基于Aerolysin生物膜通道蛋白的纳米孔道电化学分析技术,因其高的电化学空间限域能力可实现超灵敏DNA单分子检测。本文利用单个Aerolysin纳米孔道在无需标记、无需扩增的条件下直接分辨3种具有单个碱基差异的单链DNA。实验结果显示,具有单个炔基侧链基团修饰的单个ss DNA在限域空间内与Aerol-ysin纳米孔道的相互作用时间较未修饰的ss DNA增长近7倍,电流阻断程度增大7%,且高斯峰半峰宽减小了44%,增强了Aerolysin纳米孔道对单个DNA分子的分辨能力。研究成果有望推动Aerolysin纳米孔在DNA直接测序及表观遗传修饰检测中的应用。     

An Optimized Ion-Pair HPLC Method for Simultaneous Analysis of Nucleoside Triphosphate Levels in Hepatoma Cell Line

An improved ion-pair HPLC method was developed for the simultaneous determination of ribonucleoside triphosphates and their corresponding deoxyribonucleoside triphosphates in HepG2 cell extracts. HPLC conditions, flow rate and column temperature were optimized and good linearity (r ²  > 0.9993) was obtained over the investigated concentration ranges. Reproducibility was evaluated by intra- and inter-day assays and RSD values were below 5.39%. Recoveries ranged from 98.2 ± 3.49% to 103.1 ± 1.75%, respectively. Finally, the method was successfully applied to the analysis of eight compounds present in HepG2 cell extracts.     

Preliminary study of mechanism of action of SN38 derivatives. Physicochemical data,evidence of interaction and alkylation of DNA octamer d(GCGATCGC)2

The synthesis of water‐soluble SN38 derivatives is presented, and their stability in solutions used during drug development studies has been investigated. A preliminary study of mechanism of action of 9‐aminomethyl SN38 is presented. Using NMR techniques, the interaction of the oligomer d(GCGATCGC)₂ is studied, showing that the terminal GC base pairs are the main site of interaction. Using pulsed field gradient spin echo and mass spectroscopy, evidence of a spontaneous alkylation reaction of the DNA oligomer with SN38 derivatives is presented. A proposed mechanism of reaction is suggested. Copyright © 2016 John Wiley & Sons, Ltd.     

A combination chemical and enzymatic approach for the preparation of azole carboxamide nucleoside triphosphate

Alternative substrates for DNA and RNA polymerases offer an important set of biochemical tools. Many of the standard methods for nucleoside triphosphate synthesis fail in the cases of nonpurine and nonpyrimidine nucleosides. An efficient preparation of the 5'-O-tosylates for both the deoxy- and ribonucleosides enabled preparation of the diphosphate esters by displacement with tris(tetra-n-butylammonium) pyrophosphate. Enzymatic synthesis of the azole carboxamide deoxyribonucleoside triphosphate was based on ATP as the phosphate donor, nucleoside diphosphate kinase as the catalyst, coupled with phosphoenol pyruvate (PEP) and pyruvate kinase as an ATP regeneration system. Ribonucleoside triphosphate synthesis required PEP as the phosphate donor and pyruvate kinase as the catalyst. An optimized purification procedure based upon boronate affinity gel was developed to yield highly purified nucleoside triphosphates. The strategy outlined here provides a new and efficient method for preparation of nucleoside 5'-triphosphate and is likely applicable to a broad variety of base and sugar modified nucleoside analogues.     

A New Pyrimidine Schiff Base with Selective Activities against Enterococcus faecalis and Gastric Adenocarcinoma

Enterococcus faecalis is known as a significant nosocomial pathogen due to its natural resistance to many antibacterial drugs. Moreover, it was found that E. faecalis infection causes inflammation, production of reactive oxygen species, and DNA damage to human gastric cancer cells, which can induce cancer. In this study, we synthesized and tested the biological activity of a new Schiff base, 5-[(4-ethoxyphenyl)imino]methyl-N-(4-fluorophenyl)-6-methyl-2-phenylpyrimidin-4-amine (3), and compared its properties with an analogous amine (2). In the biological investigation, 3 was found to have antibacterial activity against E. faecalis 29212 and far better anticancer properties, especially against gastric adenocarcinoma (human Caucasian gastric adenocarcinoma), than 2. In addition, both derivatives were non-toxic to normal cells. It is worth mentioning that 3 could potentially inhibit cancer cell growth by inducing cell apoptosis. The results suggest that the presence of the –C=N– bond in the molecule of 3 increases its activity, indicating that 5-iminomethylpyrimidine could be a potent core for further drug discovery research.     

Investigation of MTH1 activity via mismatch-based DNA chain elongation

Accumulation and misincorporation of oxidative damaged 8-oxo-7,8-dihydroguanine triphosphates (8-oxo-dGTP) in genomic DNA may cause serious cellular function disorders. MutT Homolog 1 (MTH1), a protein enzyme that can help to prevent 8-oxo-dGTP misincorporation, plays critical roles in oxidative stress neutralization, oncogene-associated tumor malignancy, and anticancer therapies. So, in this work, a simple and function-oriented method is developed for the assay of MTH1 activity. Specifically, a mismatch-based (“8-oxoG: A” mismatch) DNA chain elongation strategy (MB-DCE) is firstly proposed to reveal the misincorporation efficiency of 8-oxo-dGTP. Then, further coupled with the inherent activity of MTH1 to prevent 8-oxo-dGTP misincorporation, a relationship can be established to reveal the activity of MTH1 through MB-DCE. As the method is designed directly towards the cellular function of MTH1, activity of MTH1 in different breast cancer cell lines has been detected, implying the potential application of this assay method for biomedical research and clinical diagnose in the future.     

A New Kid on the Block: Sacituzumab Govitecan for the Treatment of Breast Cancer and Other Solid Tumors

Human trophoblast cell-surface antigen-2 (Trop-2) is a membrane glycoprotein involved in cell proliferation and motility, frequently overexpressed in epithelial tumors. Thus, it represents an attractive target for anticancer therapies. Sacituzumab govitecan (SG) is a third-generation antibody-drug conjugate, consisting of an anti-Trop-2 monoclonal antibody (hRS7), a hydrolyzable linker, and a cytotoxin (SN38), which inhibits topoisomerase 1. Specific pharmacological features, such as the high antibody to payload ratio, the ultra-toxic nature of SN38, and the capacity to kill surrounding tumor cells (the bystander effect), make SG a very promising drug for cancer treatment. Indeed, unprecedented results have been observed with SG in patients with heavily pretreated advanced triple-negative breast cancer and urothelial carcinomas, and the drug has already received approval for these indications. These results are coupled with a manageable toxicity profile, with neutropenia and diarrhea as the most frequent adverse events, mainly of grades 1–2. While several trials are exploring SG activity in different tumor types and settings, potential biomarkers of response are under investigation. Among these, Trop-2 overexpression and the presence of BRCA1/2 mutations seem to be the most promising. We review the available literature concerning SG, with a focus on its toxicity spectrum and possible biomarkers of its response.     

Potato Peels Mediated Synthesis of Cu(II)-nanoparticles from Tyrosinase Reacted with bis-(N-aminoethylethanolamine) (Tyr-Cu(II)-AEEA NPs) and Their Cytotoxicity against Michigan Cancer Foundation-7 Breast Cancer Cell Line

The synthesis of nanoparticles is most important in the context of cancer therapy, particularly copper nanoparticles, which are widely used. In this work, copper(II)-tyrosinase was isolated from potato peel powder. Copper nanoparticles (Tyr-Cu(II)-AEEA NPs) were synthesized via the reaction of tyrosinase with N-aminoethylethanolamine to produce Cu(II)-NPs and these were characterized by means of FT-IR, UV-Spectroscopy, XRD, SEM, TEM and a particle size analyzer. These Tyr-Cu(II)-AEEA NPs were tested as anticancer agents against MCF-7 breast cancer cells. Fluorescence microscopy and DNA fragmentation were also performed, which revealed the inhibiting potentials of Cu(II)-AEEA NPs and consequent cell death; Tyr-Cu(II)-AEEA NPs show potential cytotoxicity activity and this nano material could be contemplated as an anticancer medicament in future investigations.     

7‐Aryl‐7‐deazaadenine 2′‐Deoxyribonucleoside Triphosphates (dNTPs): Better Substrates for DNA Polymerases than dATP in Competitive Incorporations

A series of 7‐substituted 7‐deazaadenine and 5‐substituted cytosine 2′‐deoxyribonucleoside triphosphates (dNTPs) were tested for their competitive incorporations (in the presence of dATP and dCTP) into DNA by several DNA polymerases by using analysis based on cleavage by restriction endonucleases. 7‐Aryl‐7‐deazaadenine dNTPs were more efficient substrates than dATP because of their higher affinity for the active site of the enzyme, as proved by kinetic measurements and calculations.     

Fluorous base-pairing effects in a DNA polymerase active site

We describe selective "fluorous" effects in the active site of a DNA polymerase, by using nucleotide analogues whose pairing edges are perfluorinated. The 5'-triphosphate deoxynucleotide derivatives of DNA base analogues 2,3,4,5-tetrafluorobenzene ((F)B) and 4,5,6,7-tetrafluoroindole ((F)I), as well as hydrocarbon controls benzene (B) and indole (I), were synthesized and studied as substrates for the DNA Polymerase I Klenow fragment (KF exo-). Modified nucleotides were present in the DNA template or were supplied as nucleoside triphosphates in studies of the steady-state kinetics of single nucleotide insertion. When supplied opposite the non-natural bases in the template strand, the hydrophobic nucleoside triphosphates were incorporated by up to two orders of magnitude more efficiently than the natural deoxynucleoside triphosphates. The purine-like fluorinated indole nucleotide ((F)I) was the most efficiently inserted of the four hydrophobic analogues, with the most effective incorporation occurring opposite the pyrimidine-like tetrafluorobenzene ((F)B). In all cases, the polyfluorinated base pairs were more efficiently processed than the analogous hydrocarbon pairs. A preliminary test of polymerase extension beyond these pairs showed that only the (F)B base is appreciably extended; the inefficient extension is consistent with recently published data regarding other nonpolar base pairs. These results suggest the importance of hydrophobicity, stacking, and steric interactions in the polymerase-mediated replication of DNA base pairs that lack hydrogen bonds. These findings further suggest that the enhanced hydrophobicity of polyfluoroaromatic bases could be employed in the design of new, selective base pairs that are orthogonal to the natural Watson-Crick pairs used in replication.     

Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase

Coupling nucleic acid processing enzymes to nanoscale pores allows controlled movement of individual DNA or RNA strands that is reported as an ionic current/time series. Hundreds of individual enzyme complexes can be examined in single-file order at high bandwidth and spatial resolution. The bacteriophage phi29 DNA polymerase (phi29 DNAP) is an attractive candidate for this technology, due to its remarkable processivity and high affinity for DNA substrates. Here we show that phi29 DNAP-DNA complexes are stable when captured in an electric field across the α-hemolysin nanopore. DNA substrates were activated for replication at the nanopore orifice by exploiting the 3'-5' exonuclease activity of wild-type phi29 DNAP to excise a 3'-H terminal residue, yielding a primer strand 3'-OH. In the presence of deoxynucleoside triphosphates, DNA synthesis was initiated, allowing real-time detection of numerous sequential nucleotide additions that was limited only by DNA template length. Translocation of phi29 DNAP along DNA substrates was observed in real time at ?ngstrom-scale precision as the template strand was drawn through the nanopore lumen during replication.     

Development of a Genus-Universal Nucleotide Signature for the Identification and Supervision of Ephedra-Containing Products

Ephedra plants generally contain ephedrine alkaloids, which are the critical precursor compounds of methamphetamine (METH). METH could cause serious physical and mental damage, and therefore Ephedra materials are strictly in supervision internationally. However, unlawful utilization of Ephedra herbs and its products still exist. Thus, it is imperative to establish a universal method for monitoring Ephedra ingredients in complex mixtures and processed products. In this study, 224 ITS2 sequences representing 59 taxa within Ephedra were collected, and a 23-bp genus-level nucleotide signature (GTCCGGTCCGCCTCGGCGGTGCG) was developed for the identification of the whole genus. The specific primers MH-1F/1R were designed, and 125 individuals of twelve Ephedra species/varieties were gathered for applicability verification of the nucleotide signature. Additionally, seven batches of Chinese patent medicines containing Ephedra herbs were used to test the application of the nucleotide signature in complex and highly processed materials. The results demonstrated that the 23-bp molecular marker was unique to Ephedra and conserved within the genus. It can be successfully utilized for the detection of Ephedra components in complex preparations and processed products with severe DNA degradation. The method developed in this study could undoubtedly serve as a strong support for the supervision of illegal circulation of Ephedra-containing products.