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1.
Chemical modification or radiation can cause DNA damage, which plays a crucial role for mutagenesis of DNA, carcinogenesis, and aging. DNA damage can also alter the fine structure of DNA that may serve as a recognition signal for DNA repair enzymes. A new, advanced sampling replica-exchange method has been developed to specifically enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) simulations. The approach employs specific biasing potentials acting on pairs of pseudodihedral angles of the nucleic acid backbone that are added in the replica simulations to promote transitions of the most common substates of the DNA backbone. The sampled states can exchange with a reference simulation under the control of the original force field. The application to 7,8-dihydro-8oxo-guanosine, one of the most common oxidative damage in DNA indicated better convergence of sampled states during 10 ns simulations compared to 20 times longer standard MD simulations. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions, including explicit solvent and ions. The biasing potential-replica exchange MD simulations indicated significant differences in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine compared to a regular guanosine in the same sequence context. This concerns both the ratio of the B-DNA substates BI and BII associated with the backbone dihedral angles ε and ζ but also coupled changes in the backbone dihedral angles α and γ. Such differences may play a crucial role in the initial recognition of damaged DNA by repair enzymes. 相似文献
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Sohel Md Mahmodul Hasan Akyuz Bilal Konca Yusuf Arslan Korhan Gurbulak Kutlay Abay Murat Kaliber Mahmut Cinar Mehmet Ulas 《Mammalian genome》2020,31(9-12):309-324
Mammalian Genome - Maternal nutrition during pregnancy is one of the major intrauterine environmental factors that influence fetal development by significantly altering the expression of genes that... 相似文献
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环境因素在物种进化和遗传变异过程中起着非常重要的作用。为探讨新疆鹅喉羚遗传多样性与环境因子的关系,本研究采用聚合酶链式反应(PCR)和直接测序的方法,测定了新疆鹅喉羚11个群体84份样本的线粒体DNA Cyt b基因(1140 bp)和D-loop区(1100 bp)序列,分析各群体遗传多样性及环境因子对遗传多样性的影响。结果显示新疆鹅喉羚具有较高的单倍型多样性,较低的核苷酸多样性,表明其遗传多样性处于较低水平。环境因子与群体遗传多样性的相关性分析结果表明,海拔、年均降水量、年均气温、人口数量是影响新疆鹅喉羚遗传多样性的主要环境因子,其中海拔是最关键的环境因子。本研究结论为新疆鹅喉羚群体有效合理的保护与管理提供理论依据。 相似文献
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Yu Zhiming Wang Yue Mei Fengling Yan Haiting Jin Zhenhui Zhang Pengcheng Zhang Xian Tr Mahmut Jackson Stephen Shi Nongnong Hong Yiguo 《Functional & integrative genomics》2022,22(3):423-428
Functional & Integrative Genomics - Spinach RNA-mimicking GFP (S-RMG) has been successfully used to monitor cellular RNAs including microRNAs in bacterium, yeast, and human cells. However,... 相似文献
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In this study, effects of different starches (tapioca (TS), wheat (WS), corn (CS), potato (PS), modified corn (MCS) and modified
potato (MPS)) and gums (xanthan gum (XG), guar gum (GG), alginate (A), salep (S), locust bean gum (LBG) and carrageen (C))
on the rheological properties of model hot chocolate beverage were studied. Swelling power (SP) of the starches and water
absorption capacity (WAC) of the gums were determined. Hot chocolate beverages showed pseudoplastic behaviour. Ostwald de
Waele model accurately described flow behaviour of each beverage sample. K, n, R
2 values for Ostwald model were in the range of 4.8–160.3 mPa.sn, 0.5117–0.9745, 0.9972–0.9998, respectively. The highest synergic effect in the model was observed between the interaction
of MCS and XG. The XG-PS, XG-TS, XG-CS combinations showed the highest K and viscosity values, respectively. 相似文献
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Özgür Aykut Kara Altan Gökşen Tosun Nazan Tekin Şaban Gökçe İsa 《Molecular biology reports》2021,48(4):3439-3449
Molecular Biology Reports - Heat shock protein 90 (Hsp90) is a key chaperone that is abnormally expressed in cancer cells, and therefore, designing novel compounds to inhibit chaperone activities... 相似文献