DNA photolyase is a photoreactivation enzyme which has a role in the mechanism of DNA repair. The existence of DNA photolyase gene could affect the success of mutation process. SM026H is a drought tolerance branching ...DNA photolyase is a photoreactivation enzyme which has a role in the mechanism of DNA repair. The existence of DNA photolyase gene could affect the success of mutation process. SM026H is a drought tolerance branching line of kenaf identified by Research Institute for Tobacco and Fibre Crops, Karangploso, Malang, Indonesia which has a potential as a source for mutation breeding. In this research, cloning and sequencing of the DNA photolyase gene of line SM026H were conducted. The DNA of SM026H leaves was isolated using DNeasy Kit, then was amplified by Polymerase Chain Reaction (PCR) using AC1 as a forward primer, paired with AC3R or AC4R as reverse primers and checked using electrophoresis on a 0.7% agarose gel. The AC1-AC3R primer pair produced a DNA fragment with a size of 750 bp, whereas the AC1-AC4R primer pair produced a DNA fragment of 1000 bp in size. Cloning of the AC1-AC3R and AC1-AC4R fragments was done prior to sequencing. Preparation for cloning was done by running and extracting the PCR products from a 0.7% Low Melting Agarose (LMA), and then ligating them to a pCR21 plasmid using an electroporation method. Two sub-fragments of each AC1-AC3R and AC1-AC4R fragments were identified. They were 600 bp and 500 bp, resulting from the AC1-AC3R fragment, and 1300 bp and 500 bp, resulting from the AC1-AC4R fragment. The sequencing result of those sub-fragments was analyzed using a Basic Local Alignment Search Tool (BLAST) program. It was shown that the sequences have a degree of homology to DNA photolyase sequence of Arabidopsis thaliana A. thaliana, Cucumis sativus, Spinacia oleracea, Stellaria longipes and Oryza sativa. These suggested that the kenaf line SM0026H possesses the DNA photolyase gene. However, further study needs to be done to ascertain that the gene was not the cryptochrome.展开更多
A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a ...A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.展开更多
The crystal structure of the title compound （C34H47NTO9, Mr = 697.79） has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000（8）, b = 11.360（10）...The crystal structure of the title compound （C34H47NTO9, Mr = 697.79） has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000（8）, b = 11.360（10）, c = 17.841（15.）/k, β = 97.083（14）°, V = 1810（3）A^3, Z = 2, F（000） = 744, D,.= 1.280 g/cm^3,/t = 0.094 mm^-1, the final R = 0.0721 and wR = 0.1942 for 2479 observed reflections with I 〉 2σ（I）. The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond （N（6）-H（6）…O（8）） introduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.展开更多
Sunlight has an indispensable importance for living things in nature[1-3].However,the direct absorption of UV will lead to the formation of pyrimidine dimers between adjacent pyrimidines in DNA strands usually in the ...Sunlight has an indispensable importance for living things in nature[1-3].However,the direct absorption of UV will lead to the formation of pyrimidine dimers between adjacent pyrimidines in DNA strands usually in the form of cyclobutene pyrimidine dimers(CPDs)and pyrimidine(6-4)pyrimidone photoproducts(6-4PPs)which causes great damage[4-6].A DNA repair system,known as photoreactivation,can effectively repair the dimers using photolyase[7-9],which has currently been found in plants,prokaryotic and eukaryotic cells[10-12].This study was carried out to determine whether photolyase DNA repair can be observed in yeast.Several yeast Petri dishes were treated with ultraviolet radiation,different treatments were then added to them,and the colonies were counted after culturing,hence verifying that yeasts can use the photoreactivation process.展开更多
文摘DNA photolyase is a photoreactivation enzyme which has a role in the mechanism of DNA repair. The existence of DNA photolyase gene could affect the success of mutation process. SM026H is a drought tolerance branching line of kenaf identified by Research Institute for Tobacco and Fibre Crops, Karangploso, Malang, Indonesia which has a potential as a source for mutation breeding. In this research, cloning and sequencing of the DNA photolyase gene of line SM026H were conducted. The DNA of SM026H leaves was isolated using DNeasy Kit, then was amplified by Polymerase Chain Reaction (PCR) using AC1 as a forward primer, paired with AC3R or AC4R as reverse primers and checked using electrophoresis on a 0.7% agarose gel. The AC1-AC3R primer pair produced a DNA fragment with a size of 750 bp, whereas the AC1-AC4R primer pair produced a DNA fragment of 1000 bp in size. Cloning of the AC1-AC3R and AC1-AC4R fragments was done prior to sequencing. Preparation for cloning was done by running and extracting the PCR products from a 0.7% Low Melting Agarose (LMA), and then ligating them to a pCR21 plasmid using an electroporation method. Two sub-fragments of each AC1-AC3R and AC1-AC4R fragments were identified. They were 600 bp and 500 bp, resulting from the AC1-AC3R fragment, and 1300 bp and 500 bp, resulting from the AC1-AC4R fragment. The sequencing result of those sub-fragments was analyzed using a Basic Local Alignment Search Tool (BLAST) program. It was shown that the sequences have a degree of homology to DNA photolyase sequence of Arabidopsis thaliana A. thaliana, Cucumis sativus, Spinacia oleracea, Stellaria longipes and Oryza sativa. These suggested that the kenaf line SM0026H possesses the DNA photolyase gene. However, further study needs to be done to ascertain that the gene was not the cryptochrome.
文摘A molecular dynamics (MD) simulation is performed on a DNA photolyase to study the conformational behavior of the photoactive cofactor flavin adenine dinucleotide (FAD) inside the enzyme pocket. A DNA photolyase is a highly efficient light-driven enzyme that repairs the UV-induced cyclobutane pyrimidine dimer in damaged DNA. In this work, the FAD conformational and dynamic changes were studied within the total complex structure of a DNA photolyase protein (containing FADH–, MTHF, and DNA molecules) embedded in a water solvent. We aimed to compare the conformational changes of the FAD cofactor and other constituent fragments of the molecular system under consideration. The obtained results were discussed to gain insight into the light-driven mechanism of DNA repair by a DNA photolyase enzyme—based on the enzyme structure, the FAD mobility, and conformation shape.
基金This work was supported by the National Natural Science Foundation of China (Nos. 30470444, 20672106)
文摘The crystal structure of the title compound （C34H47NTO9, Mr = 697.79） has been determined by single-crystal X-ray diffraction. The crystal belongs to monoclinic, space group P21 with a = 9.000（8）, b = 11.360（10）, c = 17.841（15.）/k, β = 97.083（14）°, V = 1810（3）A^3, Z = 2, F（000） = 744, D,.= 1.280 g/cm^3,/t = 0.094 mm^-1, the final R = 0.0721 and wR = 0.1942 for 2479 observed reflections with I 〉 2σ（I）. The two methyl groups attached to the cyclobutane ring are cis oriented. An intramolecular hydrogen bond （N（6）-H（6）…O（8）） introduces rigidity into the title molecule and the crystal structure is stabilized by intermolecular N-H…O hydrogen bonds.
文摘Sunlight has an indispensable importance for living things in nature[1-3].However,the direct absorption of UV will lead to the formation of pyrimidine dimers between adjacent pyrimidines in DNA strands usually in the form of cyclobutene pyrimidine dimers(CPDs)and pyrimidine(6-4)pyrimidone photoproducts(6-4PPs)which causes great damage[4-6].A DNA repair system,known as photoreactivation,can effectively repair the dimers using photolyase[7-9],which has currently been found in plants,prokaryotic and eukaryotic cells[10-12].This study was carried out to determine whether photolyase DNA repair can be observed in yeast.Several yeast Petri dishes were treated with ultraviolet radiation,different treatments were then added to them,and the colonies were counted after culturing,hence verifying that yeasts can use the photoreactivation process.
