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Processes of dna condensation induced by multivalent cations: Approximate annealing experiments and molecular dynamics simulations

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Chinese Physics B 2013年第9期22卷 648-655页

作者：柴爱华冉诗勇张冬蒋杨伟杨光参章林溪 Department of Physics Zhejiang University College of Mathematics Physics and Information EngineeringJiaxing University Department of Physics Wenzhou University

The condensation of dna induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the dna solutions in different numbers of steps, and we find that the process of dna condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the dna aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed dna structure will be. This investigation can help us to control dna condensation and understand the complicated structures of dna--cation complexes.

关键词： dna condensation multivalent cations molecular dynamics simulation

Syntheses of bifunctional molecules containing [12]aneN_3 and carbazol moieties as effective dna condensation agents

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Science China Chemistry 2014年第2期57卷 296-306页

作者： YAN Hao YUE Pan LI ZhiFen GUO ZhiFo LU ZhongLin Key Laboratory of Theoretical and Computational Photochemistry Ministry of Education College of Chemistry Beijing Normal University

Bifunctional molecules containing macrocyclic polyamine [12]aneN3 and carbazol units, 1-4, have been efficiently synthe sized and fully characterized. Through gel electrophoresis, atomic force microscopy, and dynamic light scattering experiments, compounds 3 and 4b bearing both [12]aneN3 and carbazol moieties showed effective dna condensation ability at the concen- tration of 80 jaM. Investigations from EB displacement fluorescence spectra, viscosity titration, and ionic strength effects re vealed that the effective dna condensation comes from the appropriate combination of carbazol and [12]aneN3 units in the bifunctional molecules, and the dna condensation process is reversible. The incorporation of triazole units in the molecules clearly reduced the cytotoxicity.

关键词： dna condensation macrocyclic polyamines carbazoles triazole gel electrophoresis AFM

A multi-field approach to dna condensation

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Chinese Physics B 2015年第12期24卷 28-37页

作者：冉诗勇贾俊丽 Department of Physics Wenzhou University

dna condensation is an important process in many fields including life sciences, polymer physics, and applied technology. In the nucleus, dna is condensed into chromosomes. In polymer physics, dna is treated as a semi-flexible molecule and a polyelectrolyte. Many agents, including multi-valent cations, surfactants, and neutral poor solvents, can cause dna condensation, also referred to as coil–globule transition. Moreover, dna condensation has been used for extraction and gene delivery in applied technology. Many physical theories have been presented to elucidate the mechanism underlying dna condensation, including the counterion correlation theory, the electrostatic zipper theory, and the hydration force theory. Recently several single-molecule studies have focused on dna condensation, shedding new light on old concepts. In this document, the multi-field concepts and theories related to dna condensation are introduced and clarified as well as the advances and considerations of single-molecule dna condensation experiments are introduced.

关键词： dna condensation coil–globule transition polyelectrolyte Manning theory counterion correlation hydration force single-molecule magnetic tweezers

Synthesis of Zidovudine derived [12]aneN3 Compounds and Their Interaction with dna

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Synthesis of Zidovudine derived [12]aneN3 Compounds and Thei...

Synthesis and In Vitro Study of Carbamate-Linked Cationic Lipid for Gene Delivery

中国化学会第30届学术年会-第二十八分会：化学生物学

作者： Uzair Alam Zhong-Lin,Lu College of Chemistry Beijing Normal University

In human body,dna carries genetic information,its cleavage,protection and delivery plays an important role in treating both congenital and acquired *** medicine,main application of dna condensation is gene delivery in gene therapy but it can also be helpful in dna transcription and gene *** nucleases and gene vectors are aimed to find some new tools which can selectively recognize and cleave the abnormal gene and deliver the therapeutic gene to cell *** this in mind,four different highly functionalized zidovudine based[12]aneN derivatives were designed and *** the substitution reaction and then copper-mediated click reactions were used for the combination of base and macrocyclic polyamine[12]aneN unit and all of four compounds were characterized by H NMR,C NMR,MS and *** retardation assays were performed to assess the condensation ability towards *** an ethidium bromide(EB)displacement assay was carried out to further evaluate the binding capability of the four compounds with ***,to validate the four compounds as non-viral gene carrier,condensation reversibility experiment is under investigation.

关键词： aneN3 dna condensation Artificial nucleases Gene Therapy Non-viral Gene Vectors

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Synthesis and In Vitro Study of Carbamate-Linked Cationic Li...