We construct a system of magnetic tweezers and apply it to study the interaction between histones and DNA. The condensation of DNA by purified histones at low ionic strengths is directly monitored by recording the len...We construct a system of magnetic tweezers and apply it to study the interaction between histones and DNA. The condensation of DNA by purified histones at low ionic strengths is directly monitored by recording the length of the DNA as a function of elapsed time. It is found that DNA condensates in a dynamic manner. The binding of hist, ones to DNA is energetically favoured, but the ten,sion applied on DNA tends to unravel the DNA-histone complex, The competition between the two processes determiners the rate of the DNA condensation.展开更多
Plant RNA N-glycosidase specifically hydrolyzes the N-C glycosidic bond of a conserved adenosine in the sarcin/ricin domain of the largest RNA in ribosome, releasing an adenine base and thus inhibiting protein synthes...Plant RNA N-glycosidase specifically hydrolyzes the N-C glycosidic bond of a conserved adenosine in the sarcin/ricin domain of the largest RNA in ribosome, releasing an adenine base and thus inhibiting protein synthesis. This substrate specificity was challenged later by discovery that various RNA derivatives and DNAs, especially the double-stranded supercoiled DNA could be used as substrate by RNA N-glycosidase. Thus, it was argued whether the DNA-cleaving activity was an intrinsic feature of RNA N-glycosidase or it was contaminated by DNase. In this article, several lines of evidence are presented to show that RNA N-glycosidase can really release the adenine base from the double-stranded supercoi/ed DNA. It was proposed that the cleavage mechanism of supercoiled DNA was the phosphodiester bonds in enzymatically deadenylated regions of the supercoiled DNA would become fragile and liable to produce nicked or linear form owing to the existence of tension in the supercoiled DNA molecule, not direct result of enzymatic action on the phosphodiester bond.展开更多
Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we em...Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.展开更多
In view of the growing interest for the synthesis of metal complexes and their interaction with DNA, we have synthesized and characterized two complexes containing ruthenium as metal center. The complexes are of the t...In view of the growing interest for the synthesis of metal complexes and their interaction with DNA, we have synthesized and characterized two complexes containing ruthenium as metal center. The complexes are of the type [Ru（dppz）L4]（C104）2 where L are biologically important ligands such as pyrazole and dimethylpyrazole. The characterization of these complexes is done by 1 H NMR, 13C NMR, elemental analysis and mass spectroscopy. The interaction of these complexes with CT DNA was monitored and binding constants were determined using absorption and fluorescence spectroscopy. The mode of binding was found to be intercalative for both complexes and was determined using hydrodynamic viscosity studies. The complexes were further studied for photocleavage studies with supercoiled plasmid pBR322 DNA.展开更多
基金Supported by the National Natural Science Foundation of China under Grant No 10334100. The authors acknowledge the help of Professor .J. Yan of the National University of Singapore in setting up the instrument.
文摘We construct a system of magnetic tweezers and apply it to study the interaction between histones and DNA. The condensation of DNA by purified histones at low ionic strengths is directly monitored by recording the length of the DNA as a function of elapsed time. It is found that DNA condensates in a dynamic manner. The binding of hist, ones to DNA is energetically favoured, but the ten,sion applied on DNA tends to unravel the DNA-histone complex, The competition between the two processes determiners the rate of the DNA condensation.
文摘Plant RNA N-glycosidase specifically hydrolyzes the N-C glycosidic bond of a conserved adenosine in the sarcin/ricin domain of the largest RNA in ribosome, releasing an adenine base and thus inhibiting protein synthesis. This substrate specificity was challenged later by discovery that various RNA derivatives and DNAs, especially the double-stranded supercoiled DNA could be used as substrate by RNA N-glycosidase. Thus, it was argued whether the DNA-cleaving activity was an intrinsic feature of RNA N-glycosidase or it was contaminated by DNase. In this article, several lines of evidence are presented to show that RNA N-glycosidase can really release the adenine base from the double-stranded supercoi/ed DNA. It was proposed that the cleavage mechanism of supercoiled DNA was the phosphodiester bonds in enzymatically deadenylated regions of the supercoiled DNA would become fragile and liable to produce nicked or linear form owing to the existence of tension in the supercoiled DNA molecule, not direct result of enzymatic action on the phosphodiester bond.
基金supported by the National Natural Science Foundation of China(Nos.12274212,12347102 and 12174184).
文摘Understanding how supercoiled DNA releases intramolecular stress is essential for its functional realization.However,the molecular mechanism underlying the relaxation process remains insufficiently explored.Here we employed MD simulations based on the oxDNA2 model to investigate the relaxation process of a 336-base pair supercoiled minicircular DNA under double-strand breaks with two fixed endpoints.Our simulations show that the conformational changes in the DNA occur continuously,with intramolecular stress release happening abruptly only when the DNA chain traverses the breakage site.The relaxation process is influenced not only by the separation distance between the fixed ends but also their angle.Importantly,we observe an inhibitory effect on the relaxation characterized by small angles,where short terminal loops impede DNA conformational adjustments,preserving the supercoiled structure.These findings elucidate the intricate interplay between DNA conformational change,DNA motion and intramolecular stress release,shedding light on the mechanisms governing the relaxation of supercoiled DNA at the molecular level.
文摘In view of the growing interest for the synthesis of metal complexes and their interaction with DNA, we have synthesized and characterized two complexes containing ruthenium as metal center. The complexes are of the type [Ru（dppz）L4]（C104）2 where L are biologically important ligands such as pyrazole and dimethylpyrazole. The characterization of these complexes is done by 1 H NMR, 13C NMR, elemental analysis and mass spectroscopy. The interaction of these complexes with CT DNA was monitored and binding constants were determined using absorption and fluorescence spectroscopy. The mode of binding was found to be intercalative for both complexes and was determined using hydrodynamic viscosity studies. The complexes were further studied for photocleavage studies with supercoiled plasmid pBR322 DNA.
