Rusling, David A., Broughton-Head, Victoria J., Tuck, Alex, Khairallah, Hannah, Osborne, Sadie D., Brown, Tom, ...
We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very...
Brennan, Lavinia, Peng, Guomei, Srinivasan, Natarajan, Fox, Keith R., Brown, Tom
The nucleoside analogues 2'-O-dimethylaminoethoxy uridine and 5-dimethylaminopropargyl deoxyuridine have been synthesised and incorporated into oligonucleotides. Their triplex-stabilising properties...
Gerrard, Simon R., Srinivasan, Natarajan, Fox, Keith R., Brown, Tom
Triplex-mediated recognition of Py.Pu base pairs in DNA is a greater challenge than for Pu.Py base pairs as fewer hydrogen bonds are presented for binding in the major groove. Initial studies on...
Li, Hong, Broughton-Head, Victoria J., Fox, Keith R., Brown, Tom
Stable triplexes have been generated under near-physiological conditions by the introduction of the C and T base analogues 3-methyl-2-aminopyridine-2 '-deoxyriboside and...
Synthesis of anthraquinone oligonucleotides for triplex stabilization (2007)
Zhao, Zhengyun, Peng, Guomei, Michels, Jan, Fox, Keith R., Brown, Tom
The synthesis of two anthraquinone phosphoramidites is described. In both cases the anthraquinone moiety is attached via a linker to the 5-position of a uracil base, allowing incorporation at any...
Hampshire, Andrew J., Rusling, David A., Broughton-Head, Victoria J., Fox, Keith R.
Footprinting is a simple method for assessing the sequence selectivity of DNA-binding ligands. The method is based on the ability of the ligand to protect DNA from cleavage at its binding site. This...
Sequence effects of single base loops in intramolecular quadruplex DNA (2007)
Rachwal, Phillip A., Brown, Tom, Fox, Keith R.
We have examined the properties of intramolecular G-quadruplexes in which the G3 tracts are separated by single base loops. The most stable complex contained 1′,2′-dideoxyribose in all three...
Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes (2007)
Rachwal, Philip A., Brown, Tom, Fox, Keith R.
G-Rich sequences are known to form four-stranded structures that are based on stacks of G-quartets, and sequences with the potential to adopt these structures are common in eukaryotic genomes....
Li, Hong, Broughton-Head, Victoria J., Peng, Guomei, Powers, Vicki E.C., Ovens, Matthew J., Fox, Keith R.., ...
A method has been developed to attach 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen to the 5 position of thymine bases during solid-phase oligonucleotide synthesis. UV irradiation of triplex-forming...
DNA triple-helix formation at target sites containing duplex mismatches (2006)
Rusling, David A., Brown, Tom, Fox, Keith R.
We have studied the formation of DNA triple helices at target sites that contain mismatches in the duplex target. Fluorescence melting studies were used to examine a series of parallel triple helices...
Hampshire, Andrew J., Khairallah, Hannah, Khalaf, Abedawn I., Ebrahimabadi, Abdolrasoul H., Waigh, Roger D., Suckling, Colin J., ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence specific binding of an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B) to DNA....
A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA (2006)
Caesar, Christina.E.B., Johnsson, Richard., Ellervik, Ulf, Fox, Keith.R., Lincoln, Per, Norden, Bengt
We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific...
A fast algorithm for the construction of universal footprinting templates in DNA (2006)
Anderson, James W., Fox, Keith R., Niblo, Graham A.
We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the...
Hampshire, Andrew J., Khairallah, Hannah, Khalaf, Abedawn I., Ebrahimabadi, Abdolrasoul H., Waigh, Roger D., Suckling, Colin J., ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence specific binding of an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B) to DNA....
Rusling, David A., Le Strat, Loic, Powers, Vicki E.C., Broughton-Head, Victoria J., Booth, James, Lack, Oliver, ...
We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine oligopyrimidine sequence, using oligonucleotides that contain combinations of...
Rusling, David A., Le Strat, Loic, Powers, Vicki E.C., Broughton-Head, Victoria J., Booth, James, Lack, Oliver, ...
We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine · oligopyrimidine sequence, using oligonucleotides that contain combinations of...
Brown, Nicholas M., Rachwal, Phillip A., Brown, Tom, Fox, Keith R.
We examined the stability and kinetics of folding of the Oxytricha telomeric repeat sequence (G4T4)4. Fluorescence melting experiments show that this intramolecular quadruplex, which is more stable...
An extra dimension in nucleic acid sequence recognition (2005)
Introduction 312 Triple helices in DNA 312 Chemically modified TFOs 313 Further development 316 Recognition of GC base pairs 316 Recognition of TA base pairs 316 Recognition of AT base pairs 317...
Smith, Matt J., Alharbi, Khalid K., Chen, Xiao-he, Day, Ian N.M., Fox, Keith R.
Various physical mutation-scanning methods have been developed to avoid unnecessary resequencing of long stretches of DNA (1)(2)(3)(4)(5)(6). Protein-based mutation-scanning techniques include...
Four base recognition by triplex-forming oligonucleotides at physiological pH (2005)
Rusling, David A., Powers, Vicki E.C., Ranasinghe, Rohan T., Wang, Yang, Osborne, Sadie D., Brown, Tom, ...
We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU...
Kinetic stability of intermolecular DNA quadruplexes (2005)
Merkina, Elena.E., Fox, Keith.R.
Fluorescently labeled oligodeoxyribonucleotides containing a single tract of four successive guanines have been used to study the thermodynamic and kinetic properties of short intermolecular DNA...
Wang, Yang, Rusling, David A., Powers, Vicki E.C., Lack, Oliver, Osborne, Sadie D., Fox, Keith R., ...
We have prepared the 2'-aminoethoxy derivative of the S nucleoside (S-2AE) and incorporated it into triplex-forming oligonucleotides for recognition of TA interruptions within a target oligopurine...
Wang, Yang, Rusling, David A., Powers, Vicki E.C., Lack, Oliver, Osborne, Sadie D., Fox, Keith R., ...
We have prepared the 2'-aminoethoxy derivative of the S nucleoside (2AES) and incorporated it into triplex-forming oligonucleotides for recognition of TA interruptions within a target oligopurine...
Four base recognition by triplex-forming oligonucleotides at physiological pH (2005)
Rusling, David.A., Powers, Vicki .E.C., Ranasinghe, Rohan .T., Wang, Yang, Osborne, Sadie .D., Brown, Tom., ...
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for...
Ranasinghe, Rohan T., Rusling, David A., Powers, Vicki E.C., Fox, Keith R., Brown, Tom
Substituted 3H-pyrrolo[2,3-d] pyrimidin-2(7H)-one nucleoside analogues have been synthesised from 5-alkynyl-uridine derivatives, incorporated into triplex forming oligonucleotides (TFOs) and found to...
Four base recognition by triplex-forming oligonucleotides at physiological pH (2005)
Rusling, David A., Powers, Vicki E.C., Ranasinghe, Rohan T., Wang, Yang, Osborne, Sadie D., Brown, Tom, ...
We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU...
Smith, Matt J., Alharbi, Khalid K., Chen, Xiao-he, Day, Ian N.M., Fox, Keith R.
Various physical mutation-scanning methods have been developed to avoid unnecessary resequencing of long stretches of DNA (1–6). Protein-based mutation-scanning techniques include enzymatic...
Essay. An extra dimension in nucleic acid sequence recognition (2005)
Watson-Crick base pairing is a natural molecular recognition process that has been exploited in molecular biology and universally adopted in many fields. An additional mode of nucleic acid sequence...
Effects of a hairpin polyamide on DNA melting: comparison with distamycin and Hoechst 33258 (2004)
James, Peter L., Le Strat, Loic, Ellervik, Ulf, Bratwall, Christina, Nordén, Bengt, Brown, Tom, ...
We have used DNase I footprinting and fluorescence melting studies to study the interaction of the hairpin polyamide Im-Py-Py-Py-(R)(H2N)gamma-Im`-PY-PY-PY-beta-Dp with its preferred binding sites...
DNA sequence recognition by an isopropyl substituted thiazole polyamide (2004)
James, Peter L., Merkina, Elena E., Khalaf, Abedawn I., Suckling, Colin J., Waigh, Roger D., Brown, Tom, ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted...
DNA sequence recognition by an isopropyl substituted thiazole polyamide (2004)
James, Peter L., Merkina, Elena E., Khalaf, Abedawn I., Suckling, Colin J., Waigh, Roger D., Brown, Tom, ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted...
Osborne, Sadie D., Powers, Vicki E.C., Rusling, David A., Lack, Oliver, Fox, Keith R., Brown, Tom
We have used DNase I footprinting, fluorescence and ultraviolet (UV) melting experiments and circular dichroism to demonstrate that, in the parallel triplex binding motif,...
DNA sequence specificity of triplex-binding ligands (2003)
Keppler, Melanie D., James, Peter L., Neidle, Stephen, Brown, Tom, Fox, Keith R.
We have examined the ability of naphthylquinoline, a 2,7-disubstituted anthraquinone and BePI, a benzo[e]pyridoindole derivative, to stabilize parallel DNA triplexes of different base composition....
James, Peter L., Brown, Tom, Fox, Keith R.
We have used oligonucleotides containing appropriately placed fluorophores and quenchers to measure the stability of 15mer intermolecular triplexes with third strands consisting of repeats of TTT,...
Stability of intramolecular DNA quadruplexes: comparison with DNA duplexes (2003)
Risitano, Antonina, Fox, Keith R.
We have determined the stability of intramolecular quadruplexes that are formed by a variety of G-rich sequences, using oligonucleotides containing appropriately placed fluorophores and quenchers....
Cleavage of fragments containing DNA mismatches by enzymic and chemical probes (2003)
Brown, James, Brown, Tom, Fox, Keith R.
We prepared synthetic 50-mer DNA duplexes, each containing four mismatched base-pairs in similar positions. We examined their cleavage by DNases I and II, micrococcal nuclease (MNase),...
Sequence-dependent folding of DNA three-way junctions (2002)
Assenberg, Rene, Weston, Anthony, Cardy, Don L.N., Fox, Keith R.
Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined...
Sollogoub, Matthieu, Darby, Richard A.J., Cuenoud, Bernard, Brown, Tom, Fox, Keith R.
We have prepared oligonucleotides containing the novel base analogue 2'-aminoethoxy,5-proparaylamino-U in place of thymidine and examined their ability to form intermolecular and intramolecular...
Darby, Richard A.J., Sollogoub, Matthieu, McKeen, Catherine, Brown, Lynda, Risitano, Antonina, Brown, Nicholas, ...
We have used oligonucleotides containing molecular beacons to determine melting profiles for intramolecular DNA duplexes, triplexes and quadruplexes (tetraplexes). The synthetic oligonucleotides used...
Leslie, Kris D., Fox, Keith R.
We have examined the interaction of Hoechst 33258 and echinomycin with nucleosomal DNA fragments which contain isolated ligand binding sites. A 145 base pair fragment was prepared on the basis of the...
Sequence-dependent folding of DNA three-way junctions (2002)
Assenberg, René, Weston, Anthony, Cardy, Don L. N., Fox, Keith R.
Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined...
Stabilisation of TG- and AG-containing antiparallel DNA triplexes by tripler-binding ligands (2001)
Keppler, Melanie D., Neidle, Stephen, Fox, Keith R.
We have used DNase I footprinting to examine the interaction of several triplex-binding ligands with antiparallel TG- and AG-containing triplexes. We find that although a 17mer TG-containing...
Affinity of mismatch-binding protein MutS for heteroduplexes containing different mismatches (2001)
Brown, James, Brown, Tom, Fox, Keith R.
We have used bandshift analysis to measure the interaction between the Escherichia coli mismatch-binding protein MutS and synthetic DNA fragments containing all possible DNA mismatches as well as an...
Fox, Keith R., Flashman, Emily, Gowers, Darren
We have used DNase I footprinting to examine the binding of five different 17-mer oligonucleotides to a 53-base oligopurine tract containing four pyrimidine interruptions. Although all the expected...
Stabilisation of TG- and AG-containing antiparallel DNA triplexes by triplex-binding ligands
Keppler, Melanie D., Neidle, Stephen, Fox, Keith R.
We have used DNase I footprinting to examine the interaction of several triplex-binding ligands with antiparallel TG- and AG-containing triplexes. We find that although a 17mer TG-containing...
Recognition of GT mismatches by Vsr mismatch endonuclease
Fox, Keith R., Allinson, Sarah L., Sahagun-Krause, Heidi, Brown, Tom
The Vsr mismatch endonuclease recognises the sequence CTWGG (W = A or T) in which the underlined thymine is paired with guanine and nicks the DNA backbone on the 5′-side of the mispaired thymine....
Darby, Richard A. J., Sollogoub, Matthieu, McKeen, Catherine, Brown, Lynda, Risitano, Antonina, Brown, Nicholas, ...
We have used oligonucleotides containing molecular beacons to determine melting profiles for intramolecular DNA duplexes, triplexes and quadruplexes (tetraplexes). The synthetic oligonucleotides used...
Sequence-dependent folding of DNA three-way junctions
Assenberg, René, Weston, Anthony, Cardy, Don L. N., Fox, Keith R.
Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined...
James, Peter L., Brown, Tom, Fox, Keith R.
We have used oligonucleotides containing appropriately placed fluorophores and quenchers to measure the stability of 15mer intermolecular triplexes with third strands consisting of repeats of TTT,...
Influence of loop size on the stability of intramolecular DNA quadruplexes
Risitano, Antonina, Fox, Keith R.
We have determined the stability of intramolecular DNA quadruplexes in which the four G3-tracts are connected by non-nucleosidic linkers containing propanediol, octanediol or hexaethylene glycol,...
DNA sequence recognition by an isopropyl substituted thiazole polyamide
James, Peter L., Merkina, Elena E., Khalaf, Abedawn I., Suckling, Colin J., Waigh, Roger D., Brown, Tom, ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted...
Osborne, Sadie D., Powers, Vicki E. C., Rusling, David A., Lack, Oliver, Fox, Keith R., Brown, Tom
We have used DNase I footprinting, fluorescence and ultraviolet (UV) melting experiments and circular dichroism to demonstrate that, in the parallel triplex binding motif,...
Four base recognition by triplex-forming oligonucleotides at physiological pH
Rusling, David A., Powers, Vicki E. C., Ranasinghe, Rohan T., Wang, Yang, Osborne, Sadie D., Brown, Tom, ...
We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU...
Cleavage of fragments containing DNA mismatches by enzymic and chemical probes.
Brown, James, Brown, Tom, Fox, Keith R
We prepared synthetic 50-mer DNA duplexes, each containing four mismatched base-pairs in similar positions. We examined their cleavage by DNases I and II, micrococcal nuclease (MNase),...
Kinetic Stability of Intermolecular DNA Quadruplexes
Merkina, Elena E., Fox, Keith R.
Fluorescently labeled oligodeoxyribonucleotides containing a single tract of four successive guanines have been used to study the thermodynamic and kinetic properties of short intermolecular DNA...
Stabilisation of TG- and AG-containing antiparallel DNA triplexes by triplex-binding ligands
Keppler, Melanie D., Neidle, Stephen, Fox, Keith R.
We have used DNase I footprinting to examine the interaction of several triplex-binding ligands with antiparallel TG- and AG-containing triplexes. We find that although a 17mer TG-containing...
Recognition of GT mismatches by Vsr mismatch endonuclease
Fox, Keith R., Allinson, Sarah L., Sahagun-Krause, Heidi, Brown, Tom
The Vsr mismatch endonuclease recognises the sequence CTWGG (W = A or T) in which the underlined thymine is paired with guanine and nicks the DNA backbone on the 5′-side of the mispaired thymine....
Darby, Richard A. J., Sollogoub, Matthieu, McKeen, Catherine, Brown, Lynda, Risitano, Antonina, Brown, Nicholas, ...
We have used oligonucleotides containing molecular beacons to determine melting profiles for intramolecular DNA duplexes, triplexes and quadruplexes (tetraplexes). The synthetic oligonucleotides used...
Sequence-dependent folding of DNA three-way junctions
Assenberg, René, Weston, Anthony, Cardy, Don L. N., Fox, Keith R.
Three-way DNA junctions can adopt several different conformers, which differ in the coaxial stacking of the arms. These structural variants are often dominated by one conformer, which is determined...
James, Peter L., Brown, Tom, Fox, Keith R.
We have used oligonucleotides containing appropriately placed fluorophores and quenchers to measure the stability of 15mer intermolecular triplexes with third strands consisting of repeats of TTT,...
Influence of loop size on the stability of intramolecular DNA quadruplexes
Risitano, Antonina, Fox, Keith R.
We have determined the stability of intramolecular DNA quadruplexes in which the four G3-tracts are connected by non-nucleosidic linkers containing propanediol, octanediol or hexaethylene glycol,...
DNA sequence recognition by an isopropyl substituted thiazole polyamide
James, Peter L., Merkina, Elena E., Khalaf, Abedawn I., Suckling, Colin J., Waigh, Roger D., Brown, Tom, ...
We have used DNA footprinting and fluorescence melting experiments to study the sequence-specific binding of a novel minor groove binding ligand (thiazotropsin A), containing an isopropyl substituted...
Osborne, Sadie D., Powers, Vicki E. C., Rusling, David A., Lack, Oliver, Fox, Keith R., Brown, Tom
We have used DNase I footprinting, fluorescence and ultraviolet (UV) melting experiments and circular dichroism to demonstrate that, in the parallel triplex binding motif,...
Four base recognition by triplex-forming oligonucleotides at physiological pH
Rusling, David A., Powers, Vicki E. C., Ranasinghe, Rohan T., Wang, Yang, Osborne, Sadie D., Brown, Tom, ...
We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU...