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DNA

Faculty of Science - Papers (Archive)

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Desiccation Protects Antarctic Mosses From Ultraviolet-B Induced Dna Damage, Johanna Turnbull, Sharon A. Robinson, Simon J. Leslie Jan 2009

Desiccation Protects Antarctic Mosses From Ultraviolet-B Induced Dna Damage, Johanna Turnbull, Sharon A. Robinson, Simon J. Leslie

Faculty of Science - Papers (Archive)

Antarctic mosses live in a frozen desert, and are characterised by the ability to survive desiccation. They can tolerate multiple desiccation-rehydration events over the summer growing season. As a result of recent ozone depletion, such mosses may also be exposed to ultraviolet-B radiation while desiccated. The ultraviolet-B susceptibility of Antarctic moss species was examined in a laboratory experiment that tested whether desiccated or hydrated mosses accumulated more DNA damage under enhanced ultraviolet-B radiation. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (64) pyrimidone dimers was measured in moss samples collected from the field and then exposed to ultraviolet-B radiation in either ...


Site-Specific Covalent Attachment Of Dna To Proteins Using A Photoactivatable Tus-Ter Complex, Dahdah B. Dahdah, Isabelle Morin, Morgane Moreau, Nicholas E. Dixon, Patrick M. Schaeffer Jan 2009

Site-Specific Covalent Attachment Of Dna To Proteins Using A Photoactivatable Tus-Ter Complex, Dahdah B. Dahdah, Isabelle Morin, Morgane Moreau, Nicholas E. Dixon, Patrick M. Schaeffer

Faculty of Science - Papers (Archive)

Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.


Real-Time Single-Molecule Observation Of Rolling-Circle Dna Replication, Nathan A. Tanner, Joseph J. Loparo, Samir M. Hamdan, Slobodan Jergic, Nicholas E. Dixon, Antoine M. Van Oijen Jan 2009

Real-Time Single-Molecule Observation Of Rolling-Circle Dna Replication, Nathan A. Tanner, Joseph J. Loparo, Samir M. Hamdan, Slobodan Jergic, Nicholas E. Dixon, Antoine M. Van Oijen

Faculty of Science - Papers (Archive)

We present a simple technique for visualizing replication of individual DNA molecules in real time. By attaching a rolling-circle substrate to a TIRF microscope-mounted flow chamber, we are able to monitor the progression of single-DNA synthesis events and accurately measure rates and processivities of single T7 and Escherichia coli replisomes as they replicate DNA. This method allows for rapid and precise characterization of the kinetics of DNA synthesis and the effects of replication inhibitors.


The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting Jan 2008

The Proofreading Exonuclease Subunit E Of Escherichia Coli Dna Polymerase Iii Is Tethered To The Polymerase Subunit A Via A Flexible Linker, Kiyoshi Ozawa, Slobodan Jergic, Ah-Young Park, Nicholas E. Dixon, Gottfried Otting

Faculty of Science - Papers (Archive)

Escherichia coli DNA polymerase III holoenzyme is composed of 10 different subunits linked by noncovalent interactions. The polymerase activity resides in the α-subunit. The ε-subunit, which contains the proofreading exonuclease site within its N-terminal 185 residues, binds to α via a segment of 57 additional C-terminal residues, and also to θ, whose function is less well defined. The present study shows that θ greatly enhances the solubility of ε during cell-free synthesis. In addition, synthesis of ε in the presence of θ and α resulted in a soluble ternary complex that could readily be purified and analyzed by NMR ...


Nanofiber Mats From Dna, Swnts, And Poly(Ethylene Oxide) And Their Application In Glucose Biosensors, Jun Chen, Chee O. Too, Gordon G. Wallace, Tuan A Nguyen, Violetta Misoska, Yong Liu Jan 2008

Nanofiber Mats From Dna, Swnts, And Poly(Ethylene Oxide) And Their Application In Glucose Biosensors, Jun Chen, Chee O. Too, Gordon G. Wallace, Tuan A Nguyen, Violetta Misoska, Yong Liu

Faculty of Science - Papers (Archive)

Ultrafine fibers with diameters ranging from 50 to 300 nm were prepared from DNA/single-walled carbon nanotubes (SWNTs)/poly(ethylene oxide) blended dispersion. Well-defined electrospun fibers were obtained by good control of key dispersion properties related to electrospinning, such as ionic conductivity, surface tension, and viscosity. Raman spectroscopy confirmed the presence of SWNT in the resulting fibers, indicating good interaction between DNA and SWNT. The resulting fibers also exhibited electroactive behavior and could be used as an immobilization matrix for a glucose oxidase enzyme biosensor. The sensor response was linear up to 20 mM glucose with a sensitivity of 2 ...


Comparison Of Mass Spectrometry And Other Techniques For Probing Interactions Between Metal Complexes And Dna, Thitima Urathamakul, Daniel J. Waller, Jennifer L. Beck, Janice Aldrich-Wright, Stephen F. Ralph Jan 2008

Comparison Of Mass Spectrometry And Other Techniques For Probing Interactions Between Metal Complexes And Dna, Thitima Urathamakul, Daniel J. Waller, Jennifer L. Beck, Janice Aldrich-Wright, Stephen F. Ralph

Faculty of Science - Papers (Archive)

Electrospray ionization mass spectrometry (ESI-MS) was used to study the binding interactions of two series of ruthenium complexes, [Ru(phen)2L]2+ and [RuL′2(dpqC)]2+, to a double stranded DNA hexadecamer, and derive orders of relative binding affinity. These were shown to be in good agreement with orders of relative binding affinity derived from absorption and circular dichroism (CD) spectroscopic examination of the same systems and from DNA melting curves. However, the extent of luminescence enhancement caused by the addition of DNA to solutions of the ruthenium complexes showed little correlation with orders of binding affinity derived from ...


Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting Jan 2007

Solution Structure Of Domains Iva And V Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii And Interaction With The Alpha Subunit, Xun-Cheng Su, Slobodan Jergic, Max A Keniry, Nicholas E. Dixon, Gottfried Otting

Faculty of Science - Papers (Archive)

The solution structure of the C-terminal Domain V of the τ subunit of E. coli DNA polymerase III was determined by nuclear magnetic resonance (NMR) spectroscopy. The fold is unique to τ subunits. Amino acid sequence conservation is pronounced for hydrophobic residues that form the structural core of the protein, indicating that the fold is representative for τ subunits from a wide range of different bacteria. The interaction between the polymerase subunits τ and α was studied by NMR experiments where α was incubated with full-length C-terminal domain (τC16), and domains shortened at the C-terminus by 11 and ...


The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon Jan 2007

The Unstructured C-Terminus Of The Tau Subunit Of Escherichia Coli Dna Polymerase Iii Holoenzyme Is The Site Of Interaction With The Alpha Subunit, Slobodan Jergic, Kiyoshi Ozawa, Neal K. Williams, Xun-Cheng Su, Daniel D. Scott, Samir M. Hamdan, Jeffrey A. Crowther, Gottfried Otting, Nicholas E. Dixon

Faculty of Science - Papers (Archive)

The τ subunit of Escherichia coli DNA polymerase III holoenzyme interacts with the α subunit through its C-terminal Domain V, τC16. We show that the extreme C-terminal region of τC16 constitutes the site of interaction with α. The τC16 domain, but not a derivative of it with a C-terminal deletion of seven residues (τC16Δ7), forms an isolable complex with α. Surface plasmon resonance measurements were used to determine the dissociation constant (KD) of the α−τC16 complex to be ∼260 pM. Competition with immobilized τC16 by τ ...


Polyamide Platinum Anti-Cancer Complexes Designed To Target Specific Dna Sequences, David Jaramillo, Nial J. Wheate, Stephen F. Ralph, Warren A. Howard, Yitzhak Tor, Janice Aldrich-Wright Jan 2006

Polyamide Platinum Anti-Cancer Complexes Designed To Target Specific Dna Sequences, David Jaramillo, Nial J. Wheate, Stephen F. Ralph, Warren A. Howard, Yitzhak Tor, Janice Aldrich-Wright

Faculty of Science - Papers (Archive)

Two new platinum complexes, trans-chlorodiammine[N-(2-aminoethyl)-4-[4-(N-methylimidazole-2-carboxamido)-N-methylpyrrole-2-carboxamido]-N-methylpyrrole-2-carboxamide]platinum(II) chloride (DJ1953-2) and trans-chlorodiammine[N-(6-aminohexyl)-4-[4-(N-methylimidazole-2-carboxamido)-N-methylpyrrole-2-carboxamido]-N-methylpyrrole-2-carboxamide]platinum(II) chloride (DJ1953-6) have been synthesized as proof-of-concept molecules in the design of agents that can specifically target genes in DNA. Coordinate covalent binding to DNA was demonstrated with electrospray ionization mass spectrometry. Using circular dichroism, these complexes were found to show greater DNA binding affinity to the target sequence:  d(CATTGTCAGAC)2, than toward either d(GTCTGTCAATG)2, which contains different flanking sequences, or d(CATTGAGAGAC)2, which contains a double base pair ...


Proteomic Dissection Of Dna Polymerization, Jennifer L. Beck, Thitima Urathamakul, Stephen James Watt, Margaret Sheil, Patrick M. Schaeffer, Nicholas E. Dixon Jan 2006

Proteomic Dissection Of Dna Polymerization, Jennifer L. Beck, Thitima Urathamakul, Stephen James Watt, Margaret Sheil, Patrick M. Schaeffer, Nicholas E. Dixon

Faculty of Science - Papers (Archive)

DNA polymerases replicate the genome by associating with a range of other proteins that enable rapid, high-fidelity copying of DNA. This complex of proteins and nucleic acids is called the replisome. Proteins of the replisome must interact with other networks of proteins, such as those involved in DNA repair. Many of the proteins involved in DNA polymerisation and the accessory proteins are known, but the array of proteins they interact with, and the spatial and temporal arrangement of these interactions is a current research topic. Mass spectrometry is a technique that can be used to identify the sites of these ...