Intrinsic dynamics of DNA plays a crucial role in DNA-protein interactions and has been emphasized as a possible key component for in vivo chromatin organization. We have prepared an entangled DNA microtube above the overlap concentration by exploiting the complementary cohesive ends of λ-phage DNA, which is confirmed by atomic force microscopy and agarose gel electrophoresis. Photon correlation spectroscopy further confirmed that the entangled solutions are found to exhibit the classical hydrodynamics of a single chain segment on length scales smaller than the hydrodynamic length scale of single λ-phage DNA molecule. We also observed that in 41.6% (gm water/gm DNA) hydrated state, λ-phage DNA exhibits a dynamic transition temperature (T(dt)) at 187 K and a crossover temperature (T(c)) at 246 K. Computational insight reveals that the observed structure and dynamics of entangled λ-phage DNA are distinctively different from the behavior of the corresponding unentangled DNA with open cohesive ends, which is reminiscent with our experimental observation.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3391602 | PMC |
http://dx.doi.org/10.1021/jp2108363 | DOI Listing |
Viruses
November 2024
Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD 20993, USA.
To better understand host-phage interactions and the genetic bases of phage resistance in a model system relevant to potential phage therapy, we isolated several spontaneous mutants of the USA300 clinical isolate NRS384 that were resistant to phage K. Six of these had a single missense mutation in the host gene, which encodes the RNA polymerase β' subunit. To examine the hypothesis that mutations in the host RNA polymerase affect the transcription of phage genes, we performed RNA-seq analysis on total RNA samples collected from NRS384 wild-type (WT) and mutant cultures infected with phage K, at different timepoints after infection.
View Article and Find Full Text PDFNature
December 2024
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Host-pathogen conflicts are crucibles of molecular innovation. Selection for immunity to pathogens has driven the evolution of sophisticated immunity mechanisms throughout biology, including in bacterial defence against bacteriophages. Here we characterize the widely distributed anti-phage defence system CmdTAC, which provides robust defence against infection by the T-even family of phages.
View Article and Find Full Text PDFJ Bacteriol
September 2024
Department of Microbiology, Genetics, & Immunology, Michigan State University, East Lansing, Michigan, USA.
A major challenge faced by is constant predation by bacteriophage (phage) in aquatic reservoirs and during infection of human hosts. To overcome phage predation, has acquired and/or evolved a myriad of phage defense systems. Although several novel defense systems have been discovered, we hypothesized that more were encoded in given the low diversity of phages that have been isolated, which infect this species.
View Article and Find Full Text PDFJ Biol Chem
September 2024
Department of Chemistry, Johns Hopkins University, Baltimore, Maryland, USA. Electronic address:
Fapy•dG (N6-(2-deoxy-α,β-D-erythro-pentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine) and 8-OxodGuo (8-oxo-7,8-dihydro-2'-deoxyguanosine) are major products of 2'-deoxyguanosine oxidation. Fapy•dG is unusual in that it exists as a dynamic mixture of anomers. Much less is known about the effects of Fapy•dG than 8-OxodGuo on transcriptional bypass.
View Article and Find Full Text PDFCell Rep
August 2024
Research Department, New England Biolabs, 240 County Road, Ipswich, MA 01938, USA. Electronic address:
Enzymatic modification of DNA nucleobases can coordinate gene expression, nuclease protection, or mutagenesis. We recently discovered a clade of phage-specific cytosine methyltransferase (MT) and 5-methylpyrimidine dioxygenase (5mYOX) enzymes that produce 5-hydroxymethylcytosine (5hmC) as a precursor for enzymatic hypermodifications on viral genomes. Here, we identify phage MT- and 5mYOX-associated glycosyltransferases (GTs) that catalyze linkage of diverse sugars to 5hmC nucleobase substrates.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!