Resolution of undistorted symmetric immobile DNA junctions by vaccinia topoisomerase I. 2004

Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
Department of Chemistry, New York University, New York, New York 10003, USA.

Holliday junctions are intermediates in genetic recombination. They consist of four strands of DNA that flank a branch point. In natural systems, their sequences have 2-fold (homologous) sequence symmetry. This symmetry enables the molecules to undergo an isomerization, known as branch migration, that relocates the site of the branch point. Branch migration leads to polydispersity, which makes it difficult to characterize the physical properties of the junction and the effects of the sequence context flanking the branch point. Previous studies have reported two symmetric junctions that do not branch migrate: one that is immobilized by coupling to an asymmetric junction in a double crossover context, and a second that is based on molecules containing 5',5' and 3',3' linkages. Both are flawed by distorting the structure of the symmetric junction from its natural conformation. Here, we report an undistorted symmetric immobile junction based on the use of DNA parallelogram structures. We have used a series of these junctions to characterize the junction resolution reaction catalyzed by vaccinia virus DNA topoisomerase. The resolution reaction entails cleavage and rejoining at CCCTT/N recognition sites arrayed on opposing sides of the four-arm junction. We find that resolution is optimal when the scissile phosphodiester (Tp/N) is located two nucleotides 5' to the branch point on the helical strand. Covalent topoisomerase-DNA adducts are precursors to recombinant strands in all reactions, as expected. Kinetic analysis suggests a rate limiting step after the first-strand cleavage.

UI MeSH Term Description Entries
D008956 Models, Chemical Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment. Chemical Models,Chemical Model,Model, Chemical
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D011995 Recombination, Genetic Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses. Genetic Recombination,Recombination,Genetic Recombinations,Recombinations,Recombinations, Genetic
D004264 DNA Topoisomerases, Type I DNA TOPOISOMERASES that catalyze ATP-independent breakage of one of the two strands of DNA, passage of the unbroken strand through the break, and rejoining of the broken strand. DNA Topoisomerases, Type I enzymes reduce the topological stress in the DNA structure by relaxing the superhelical turns and knotted rings in the DNA helix. DNA Nicking-Closing Protein,DNA Relaxing Enzyme,DNA Relaxing Protein,DNA Topoisomerase,DNA Topoisomerase I,DNA Topoisomerase III,DNA Topoisomerase III alpha,DNA Topoisomerase III beta,DNA Untwisting Enzyme,DNA Untwisting Protein,TOP3 Topoisomerase,TOP3alpha,TOPO IIIalpha,Topo III,Topoisomerase III,Topoisomerase III beta,Topoisomerase IIIalpha,Topoisomerase IIIbeta,DNA Nicking-Closing Proteins,DNA Relaxing Enzymes,DNA Type 1 Topoisomerase,DNA Untwisting Enzymes,DNA Untwisting Proteins,Topoisomerase I,Type I DNA Topoisomerase,III beta, Topoisomerase,III, DNA Topoisomerase,III, Topo,III, Topoisomerase,IIIalpha, TOPO,IIIalpha, Topoisomerase,IIIbeta, Topoisomerase,Topoisomerase III, DNA,Topoisomerase, TOP3,beta, Topoisomerase III
D004274 DNA, Recombinant Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected. Genes, Spliced,Recombinant DNA,Spliced Gene,Recombinant DNA Research,Recombination Joint,DNA Research, Recombinant,Gene, Spliced,Joint, Recombination,Research, Recombinant DNA,Spliced Genes
D004279 DNA, Viral Deoxyribonucleic acid that makes up the genetic material of viruses. Viral DNA
D001483 Base Sequence The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence. DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D014616 Vaccinia virus The type species of ORTHOPOXVIRUS, related to COWPOX VIRUS, but whose true origin is unknown. It has been used as a live vaccine against SMALLPOX. It is also used as a vector for inserting foreign DNA into animals. Rabbitpox virus is a subspecies of VACCINIA VIRUS. Buffalopox virus,Poxvirus officinale,Rabbitpox virus,Buffalo Pox Virus,Rabbit Pox Virus,Buffalo Pox Viruses,Buffalopox viruses,Rabbit Pox Viruses,Rabbitpox viruses,Vaccinia viruses,Virus, Buffalo Pox,Viruses, Buffalo Pox,virus, Buffalopox
D017665 Hydroxyl Radical The univalent radical OH. Hydroxyl radical is a potent oxidizing agent.

Related Publications

Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
August 1993, Biochemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
January 1996, Proceedings of the National Academy of Sciences of the United States of America,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
October 2000, Biochemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
September 2004, Journal of molecular biology,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
April 1992, The Journal of biological chemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
October 1990, The Journal of biological chemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
August 1992, The Journal of biological chemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
September 2002, Biochemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
January 2007, Biochemistry,
Shiping Liao, and Chengde Mao, and Jens J Birktoft, and Stewart Shuman, and Nadrian C Seeman
August 1992, The Journal of biological chemistry,
Copied contents to your clipboard!