Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli (2004)
Peter, Brian J, Arsuaga, Javier, Breier, Adam M, Khodursky, Arkady B, Brown, Patrick O, Cozzarelli, Nicholas R
Abstract Background The chromosome of Escherichia coli is maintained in a negatively supercoiled state, and supercoiling levels are affected by growth phase and a variety of environmental stimuli. In...
Using Graph Theory to Describe and Model Chromosome Aberrations (2002)
Rainer K. Sachs, Javier Arsuaga, Mariel Vázquez, Lynn Hlatky, Philip Hahnfeldt
Sachs, R. K., Arsuaga, J., Vázquez, M., Hlatky, L. and Hahnfeldt, P. Using Graph Theory to Describe and Model Chromosome Aberrations. Radiat. Res. 158, 556–567 (2002). A comprehensive description...
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis
Trigueros, Sonia, Arsuaga, Javier, Vazquez, Maria E., Sumners, De Witt, Roca, Joaquim
We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate...
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
Arsuaga, Javier, Vázquez, Mariel, Trigueros, Sonia, Sumners, De Witt, Roca, Joaquim
When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled....
Topological domain structure of the Escherichia coli chromosome
Postow, Lisa, Hardy, Christine D., Arsuaga, Javier, Cozzarelli, Nicholas R.
The circular chromosome of Escherichia coli is organized into independently supercoiled loops, or topological domains. We investigated the organization and size of these domains in vivo and in vitro....
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
Peter, Brian J, Arsuaga, Javier, Breier, Adam M, Khodursky, Arkady B, Brown, Patrick O, Cozzarelli, Nicholas R
Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, suggesting that supercoiling transmits regulatory signals from the...
DNA knots reveal a chiral organization of DNA in phage capsids
Arsuaga, Javier, Vazquez, Mariel, McGuirk, Paul, Trigueros, Sonia, Sumners, De Witt, Roca, Joaquim
Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some...
Novel display of knotted DNA molecules by two-dimensional gel electrophoresis
Trigueros, Sonia, Arsuaga, Javier, Vazquez, Maria E., Sumners, De Witt, Roca, Joaquim
We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate...
Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
Arsuaga, Javier, Vázquez, Mariel, Trigueros, Sonia, Sumners, De Witt, Roca, Joaquim
When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled....
Topological domain structure of the Escherichia coli chromosome
Postow, Lisa, Hardy, Christine D., Arsuaga, Javier, Cozzarelli, Nicholas R.
The circular chromosome of Escherichia coli is organized into independently supercoiled loops, or topological domains. We investigated the organization and size of these domains in vivo and in vitro....
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
Peter, Brian J, Arsuaga, Javier, Breier, Adam M, Khodursky, Arkady B, Brown, Patrick O, Cozzarelli, Nicholas R
Microarray analysis shows that transcription of 306 E. Coli genes is affected by changes in the level of chromosome supercoiling, suggesting that supercoiling transmits regulatory signals from the...
DNA knots reveal a chiral organization of DNA in phage capsids
Arsuaga, Javier, Vazquez, Mariel, McGuirk, Paul, Trigueros, Sonia, Sumners, De Witt, Roca, Joaquim
Icosahedral bacteriophages pack their double-stranded DNA genomes to near-crystalline density and achieve one of the highest levels of DNA condensation found in nature. Despite numerous studies, some...
Chromosomes are predominantly located randomly with respect to each other in interphase human cells
Cornforth, Michael N., Greulich-Bode, Karin M., Loucas, Bradford D., Arsuaga, Javier, Vázquez, Mariel, Sachs, Rainer K., ...
To test quantitatively whether there are systematic chromosome–chromosome associations within human interphase nuclei, interchanges between all possible heterologous pairs of chromosomes were...