Based on protein-DNA complex crystal structural data in up-to-date Nucleic Acid Database,the related parameters of DNA Kinetic Structure were investigated by Monte-Carlo Multiple Integrals on the base of modified DNA ...Based on protein-DNA complex crystal structural data in up-to-date Nucleic Acid Database,the related parameters of DNA Kinetic Structure were investigated by Monte-Carlo Multiple Integrals on the base of modified DNA structure statistical mechanical model,and time complexity and precision were analyzed on the calculated results.展开更多
To study the kinetics in vivo of a Hantaan virus DNA vaccine, we constructed a fusion DNA vaccine, pEGFP/S, by cloning the S segment of Hantavirus into the vector, pEGFP-C1, which encodes Green fluorescent protein EGF...To study the kinetics in vivo of a Hantaan virus DNA vaccine, we constructed a fusion DNA vaccine, pEGFP/S, by cloning the S segment of Hantavirus into the vector, pEGFP-C1, which encodes Green fluorescent protein EGFP. In this report, we provide evidence that pEGFP/S was distributed and persistently expressed for more than 60 days in several organs after inoculation. Our findings suggest that the persistent immune responses induced by a Hantaan virus DNA vaccine are likely due to the plasmid pEGFP/S deposited in vivo, which acts as a booster immunization.展开更多
We here study the influences of the temperature and solvent ions in solution on the states and properties of DNA by a new dynamical model. This model admits three degrees of freedom per base-pair: two displacement var...We here study the influences of the temperature and solvent ions in solution on the states and properties of DNA by a new dynamical model. This model admits three degrees of freedom per base-pair: two displacement variables related to the vibrations of the hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of each base, which delineate different forms of motion of the hydrogen atom and bases and the relations among them. In this -model we stress specially the important role of the hydrogen atom in the hydrogen bonds of the bases in the dynamics of DNA. According to their properties of motion we give the Hamiltonian of the system and the corresponding equations of motion, and End out their soliton solutions. The solitons formed by the displacements of the hydrogen atoms and bases and their rotations are the excitation states arising from the energy absorbed by the DNA working at the biological temperature. We give further the free energy of the thermal excitation state in DNA system by transfer integral way and End out the corresponding specific heat. The specific heat increases with the increasing of the temperature and concentration of the solvent ions in the solution, but is not linear changes in the region of high temperature. If compared with experimental data, they are approximately consistent. Meanwhile we End that the solvent ion conceptration influences seriously on the stability, states, and configurations of DNA.展开更多
DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar specie...DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar species. Pleuronichthys japonicus has never been found previously in China. However, in this study, we identified both species using DNA barcoding （cytochrome c oxidase subunit I （COI））, the mtDNA control region and cytochrome b. The results reveal that： l） intraspecific variation in the DNA barcode is much less than interspecific variation; 2） the two morphologically similar species were placed into separate clades distinguishable by high bootstrap values; 3） COI barcodes are more powerful for identifying the two species than the other two mtDNA fragments.展开更多
Despite extensive studies on the mechanics of DNA under external constrains, such as tension, torsion, and bending, several important aspects have remained poorly understood. One biologically important example is the ...Despite extensive studies on the mechanics of DNA under external constrains, such as tension, torsion, and bending, several important aspects have remained poorly understood. One biologically important example is the mechanics of DNA under sharp bending conditions, which has been debated for a decade without thorough comprehension. The debate is about the interesting phenomenon raised from a series of different experiments: sharply bent DNA has a surprisingly high apparent bending flexibility that deviates from the canonical bending elasticity of DNA. This finding has motivated various theoretical models, which mainly incorporate the excitation of mechanical defects inside severely bent DNA molecules. Here, we review the recent progress on the understanding of the mechanics of sharply bent DNA and provide our view on this important question by interrogating the theoretical foundation of these experimental measurements.展开更多
Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical confo...Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.展开更多
DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect ...DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics （MD） simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d（CGCGAATTCGCG）2, coion Cl- and counterions Li＋, Na＋, K＋, Rb＋ and Cs~ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. In- creasing KCI concentration in solution hinders the A-DNA^B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K＋ 〈 Rb＋ 〈 Cs＋ 〈 Na＋ 〈 Li＋. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation （MMSA）. The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.展开更多
Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM...Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.展开更多
We are all familiar with DNA as the substance that encodes the genomes of all living things.In addition to genetic function,DNA is one of the smartest building blocks for innovative nanostructures.DNA walker is a kind...We are all familiar with DNA as the substance that encodes the genomes of all living things.In addition to genetic function,DNA is one of the smartest building blocks for innovative nanostructures.DNA walker is a kind of self-assembled molecular machine that mimics the movement of protein motors in living systems.Usually,DNA walker consists of three parts：a single stranded DNA track,展开更多
基金Supported by Inner Mongolia Natural Science Foundation(200711020112)Innovation Fundation of Inner Mongolia University of Science and Technology (2009NC064)~~
文摘Based on protein-DNA complex crystal structural data in up-to-date Nucleic Acid Database,the related parameters of DNA Kinetic Structure were investigated by Monte-Carlo Multiple Integrals on the base of modified DNA structure statistical mechanical model,and time complexity and precision were analyzed on the calculated results.
文摘To study the kinetics in vivo of a Hantaan virus DNA vaccine, we constructed a fusion DNA vaccine, pEGFP/S, by cloning the S segment of Hantavirus into the vector, pEGFP-C1, which encodes Green fluorescent protein EGFP. In this report, we provide evidence that pEGFP/S was distributed and persistently expressed for more than 60 days in several organs after inoculation. Our findings suggest that the persistent immune responses induced by a Hantaan virus DNA vaccine are likely due to the plasmid pEGFP/S deposited in vivo, which acts as a booster immunization.
文摘We here study the influences of the temperature and solvent ions in solution on the states and properties of DNA by a new dynamical model. This model admits three degrees of freedom per base-pair: two displacement variables related to the vibrations of the hydrogen atom in the hydrogen bonds and base (nucleotide), respectively, and an angular variable related to the rotation of each base, which delineate different forms of motion of the hydrogen atom and bases and the relations among them. In this -model we stress specially the important role of the hydrogen atom in the hydrogen bonds of the bases in the dynamics of DNA. According to their properties of motion we give the Hamiltonian of the system and the corresponding equations of motion, and End out their soliton solutions. The solitons formed by the displacements of the hydrogen atoms and bases and their rotations are the excitation states arising from the energy absorbed by the DNA working at the biological temperature. We give further the free energy of the thermal excitation state in DNA system by transfer integral way and End out the corresponding specific heat. The specific heat increases with the increasing of the temperature and concentration of the solvent ions in the solution, but is not linear changes in the region of high temperature. If compared with experimental data, they are approximately consistent. Meanwhile we End that the solvent ion conceptration influences seriously on the stability, states, and configurations of DNA.
基金Supported by the Special Fund for Agro-scientific Research in the Public Interest (No. 201003068)Special Key Program of Zhejiang Provincial Department of Science and Technology (No. 2008C12011)
文摘DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar species. Pleuronichthys japonicus has never been found previously in China. However, in this study, we identified both species using DNA barcoding （cytochrome c oxidase subunit I （COI））, the mtDNA control region and cytochrome b. The results reveal that： l） intraspecific variation in the DNA barcode is much less than interspecific variation; 2） the two morphologically similar species were placed into separate clades distinguishable by high bootstrap values; 3） COI barcodes are more powerful for identifying the two species than the other two mtDNA fragments.
基金supported by the Mechanobiology Institute at National University of Singapore and Singapore Ministry of Education Academic Research Fund Tier 2 (Grant No. MOE2013-T2-1-154)
文摘Despite extensive studies on the mechanics of DNA under external constrains, such as tension, torsion, and bending, several important aspects have remained poorly understood. One biologically important example is the mechanics of DNA under sharp bending conditions, which has been debated for a decade without thorough comprehension. The debate is about the interesting phenomenon raised from a series of different experiments: sharply bent DNA has a surprisingly high apparent bending flexibility that deviates from the canonical bending elasticity of DNA. This finding has motivated various theoretical models, which mainly incorporate the excitation of mechanical defects inside severely bent DNA molecules. Here, we review the recent progress on the understanding of the mechanics of sharply bent DNA and provide our view on this important question by interrogating the theoretical foundation of these experimental measurements.
基金supported by the Fundamental Research Funds for the Central Universities(Grant No.2013121005)the National Natural Science Foundation of China(Grant Nos.11474237 and 11574310)+1 种基金the 111 Project (Grant No.B16029)the National Research Foundation of Singapore through the NRF Investigatorship and the Mechanobiology Institute
文摘Deoxyribonucleic acid(DNA) carries the genetic information in all living organisms. It consists of two interwound single-stranded(ss) strands, forming a double-stranded(ds) DNA with a right-handed double-helical conformation. The two strands are held together by highly specific basepairing interactions and are further stabilized by stacking between adjacent basepairs. A transition from a dsDNA to two separated ssDNA is called melting and the reverse transition is called hybridization. Applying a tensile force to a dsDNA can result in a particular type of DNA melting, during which one ssDNA strand is peeled away from the other. In this work, we studied the kinetics of strand-peeling and hybridization of short DNA under tensile forces. Our results show that the force-dependent strand-peeling and hybridization can be described with a simple two-state model. Importantly, detailed analysis of the force-dependent transition rates revealed that the transition state consists of several basepairs dsDNA.
基金supported by the National Natural Science Foundation of China(21176132 and 20876083)Specialized Research Fund for the Doctoral Program of Higher Education(20100002110024)
文摘DNA and its conformational transition can be used to design nanometer-scale structures, nano-tweezers and nanomechanical devices. Experiments and molecular simulations have been used to study the concentration effect on the A-DNA→B-DNA conformational transition, but a systematical investigation on counterion effect on the dynamics of this transition has not been reported up to now. In present work, restrained and unrestrained molecular dynamics （MD） simulations have been performed to characterize the stability of DNA conformations and the dynamics of A-DNA→B-DNA transitions in aqueous solutions with different alkali metal counterions. The DNA duplex d（CGCGAATTCGCG）2, coion Cl- and counterions Li＋, Na＋, K＋, Rb＋ and Cs~ as well as water molecule were considered using the PARM99 force field in the AMBER8 package. It was found that B-form DNA is more stable than A-form DNA in aqueous electrolyte solutions with different alkali metal counterions. In- creasing KCI concentration in solution hinders the A-DNA^B-DNA transition and the transition times for different alkali metal counterions conform to neither the simple sequence related to naked ion size nor to hydrated diameter, but an apparently abnormal sequence of K＋ 〈 Rb＋ 〈 Cs＋ 〈 Na＋ 〈 Li＋. This abnormal sequence can be well understood in terms of an electrostatic model based on the effective cation diameters and the modified mean-spherical approximation （MMSA）. The present results provide valuable information for the design of DNA-based nanomaterials and nanodevices.
基金support from the National Natural Science Foundation of China (21176132)the Specialized Research Fund for the Doctoral Program of Higher Education (2010000211024)
文摘Unrestrained molecular dynamics （MD） simulations have been carded out to characterize the stability of DNA conformations and the dynamics of A-DNA^B-DNA conformational transitions in aqueous RbC1 solutions. The PARM99 force field in the AMBER8 package was used to investigate the effect of RbC1 concentration on the dynamics of the A^B conformational tran- sition in the DNA duplex d（CGCGAATTCGCG）2. Canonical A- and B-form DNA were assumed for the initial conformation and the final conformation had a length per complete turn that matched the canonical B-DNA. The DNA structure was moni- tored for 3.0 ns and the distances between the C5＇ atoms were obtained from the simulations. It was found that all of the double stranded DNA strands of A-DNA converged to the structure of B-form DNA within 1.0 ns during the unrestrained MD simula- tions. In addition, increasing the RbC1 concentration in aqueous solution hindered the A^B conformational transition and the transition in aqueous RbC1 solution was faster than that in aqueous NaC1 solution for the same electrolyte strength. The effects of the types and concentrations of counterions on the dynamics of the A^B conformational transition can be understood in terms of the variation in water activity and the number of accumulated counterions in the major grooves of A-DNA. The ru- bidium ion distributions around both fixed A-DNA and B-DNA were obtained using the restrained MD simulations to help ex- plain the effect of RbC1 concentration on the dynamics of the A^B conformational transition.
文摘We are all familiar with DNA as the substance that encodes the genomes of all living things.In addition to genetic function,DNA is one of the smartest building blocks for innovative nanostructures.DNA walker is a kind of self-assembled molecular machine that mimics the movement of protein motors in living systems.Usually,DNA walker consists of three parts：a single stranded DNA track,
