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B Armitage

Publications and source records attributed to B Armitage.

14 recordsLinked to original sources
PubMed2001

Recognition of ATGA sequences by the unfused aromatic dication DB293 forming stacked dimers in the DNA minor groove.

Furamidine and related diamidines represent a promising series of drugs active against widespread parasites, in particular the Pneumocystic carinii pathogen. In this series, the phenylfuranbenzimidazole diamidine derivative DB293 was recently identified as the first unfused aromatic dication capable of forming stacked dimers in the DNA minor groove of GC-containing sequences. Here we present a detailed biochemical and biophysical characterization of the DNA sequence recognition properties of DB293. Three complementary footprinting techniques using DNase I, Fe(II)-EDTA, and an anthraquinone photonuclease were employed to locate binding sites for DB293 in different DNA restriction fragments. Two categories of sites were identified by DNase I footprinting: (i) 4/5 bp sequences containing contiguous A.T pairs, such as 5'-AAAA and 5'-ATTA; and (ii) sequences including the motif 5'-ATGA.5'-TCAT. In particular, a 13-bp sequence including two contiguous ATGA motifs provided a highly preferential recognition site for DB293. Quantitative footprinting analysis revealed better occupancy of the 5'-ATGA site compared to the AT-rich sites. Preferential binding of DB293 to ATGA sites was also observed with other DNA fragments and was confirmed independently by means of hydroxyl radical footprinting generated by the Fe(II)-EDTA system, as well as by a photofootprinting approach using the probe anthraquinone-2-sulfonate (AQS). In addition, this photosensitive reagent revealed the presence of sites of enhanced cutting specific to DB293. This molecule, but not other minor groove binders such as netropsin, induces specific local structural changes in DNA near certain binding sites, as independently shown by DNase I and the AQS probe. Recognition of the ATGA sequence by DB293 was investigated further using melting temperature experiments and surface plasmon resonance (SPR). The use of different hairpin oligonucleotides showed that DB293 can interact with AT sites via the formation of 1:1 drug-DNA complexes but binds much more strongly, and cooperatively, to ATGA-containing sequences to form 2:1 drug-DNA complexes. DB293 binds strongly to ATGA sequences with no significant context dependence but is highly sensitive to the orientation of the target sequence. The formation of 2:1 DB293/DNA complexes is abolished by reversing the sequence 5'-ATGA-->3'-ATGA, indicating that directionality plays an important role in the drug-DNA recognition process. Similarly, a single mutation in the A[T-->G]GA sequence is very detrimental to the dimer interactions of DB293. From the complementary footprinting and SPR data, the 5'-ATGA sequence is identified as being a highly favored dimer binding site for DB293. The data provide clues for delineating a recognition code for diamidine-type minor groove binding agents, and ultimately to guide the rational design of gene regulatory molecules targeted to specific sites of the genetic material.

Antifungal Agents↗
PubMed1998

Hairpin-forming peptide nucleic acid oligomers.

A series of partially self-complementary peptide nucleic acid (PNA) oligomers was prepared. Examination of their melting behavior, circular dichroism spectra, and fluorescence properties reveals that these PNA oligomers exist as stem-loop ("hairpin") structures. Fluorescence is readily observed in hairpins containing a covalently linked, emissive acridine derivative which is, at least partially, intercalated in the duplex region of the PNA hairpin. The acridine fluorescence is quenched when an anthraquinone derivative is covalently attached to the PNA so that it is bound near the acridine in the hairpin structure. Acridine fluorescence is restored in hairpins containing both the anthraquinone and the acridine by increasing the temperature and melting the structure to its linear form or by opening the hairpin through formation of a hybrid duplex with complementary DNA. The latter process may form the basis for development of selective and sensitive DNA assays.

Aminacrine↗
PubMed1998

Selective photocleavage of DNA by anthraquinone derivatives: targeting the single-strand region of hairpin structures.

A tetracationic anthraquinone derivative (27AQS2) binds to hairpin DNA and irradiation of the bound quinone leads to selective strand cleavage. NMR spectroscopy reveals that 27AQS2 binds at the loop and to the stem-loop junction of hairpin DNA. UV irradiation of the bound quinone causes cleavage of the DNA in the loop region and at guanines in the stem region. Inclusion of ethidium bromide in the reaction mixture leads to a greatly increased selectivity for loop cleavage. Spectroscopic and chemical evidence suggests a three component mechanism for reaction. The ability to target single-stranded regions of DNA structures is an important property of this photonuclease.

Anthraquinones↗
PubMed1998

Peptide nucleic acid (PNA)/DNA hybrid duplexes: intercalation by an internally linked anthraquinone.

Peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson-Crick base pairing. A set of reporter compounds that bind to DNA by intercalation are known, but these compounds do not intercalate in PNA/DNA hybrid duplexes. Analysis of the hybrid PNA duplexes requires development of reporter compounds that probe their chemical and physical properties. We prepared a series of anthraquinone (AQ) derivatives that are linked to internal positions of a PNA oligomer. These are the first non-nucleobase functional groups that have been incorporated into a PNA. The resulting PNA(AQ) conjugates form stable hybrids with complementary DNA oligomers. We find that when the AQ groups are covalently bound to PNA that they stabilize the hybrid duplex and are, at least partially, intercalated.

Anthraquinones↗
PubMed1997

Peptide nucleic acid-anthraquinone conjugates: strand invasion and photoinduced cleavage of duplex DNA.

A bis-peptide nucleic acid (PNA)-anthraquinone imide (AQI) conjugate has been synthesized and shown to form strand invasion complexes with a duplex DNA target. The two arms of the bis-PNA each consist of five consecutive thymine residues and are linked by a flexible, hydrophilic spacer. Probing with potassium permanganate reveals that the bis-PNA complexes to duplex DNA at A5.T5sites with local displacement of the T5DNA strand. The 5 bp sequence targeted by the PNA is the shortest strand invasion complex reported to date. Irradiation of the strand invasion complex results in asymmetric cleavage of the displaced strand, with more efficient cleavage at the 3'-end of the loop. This result indicates that the bis-PNA binds to the DNA such that the C-terminal T5sequence forms the strand invasion complex, leaving the N-terminal T5sequence to bind by triplex formation, thereby placing the AQI closer to the 3'-end of the displaced strand, consistent with the observed photocleavage pattern. The ability of the PNA to directly report its binding site by photoinduced cleavage could have significant utility in mapping the secondary and tertiary structure of nucleic acids.

Anthraquinones↗
PubMed1997

Peptide nucleic acid-DNA duplexes: long range hole migration from an internally linked anthraquinone.

The discovery that peptide nucleic acids (PNA) mimic DNA and RNA by forming complementary duplex structures following Watson-Crick base pairing rules opens fields in biochemistry, diagnostics, and medicine for exploration. Progress requires the development of modified PNA duplexes having unique and well defined properties. We find that anthraquinone groups bound to internal positions of a PNA oligomer intercalate in the PNA-DNA hybrid. Their irradiation with near-UV light leads to electron transfer and oxidative damage at remote GG doublets on the complementary DNA strand. This behavior mimics that observed in related DNA duplexes and provides the first evidence for long range electron (hole) transport in PNA-DNA hybrid. Analysis of the mechanism for electron transport supports hole hopping.

Animals↗
PubMed1997

Selective stabilization of triplex DNA by anthraquinone sulfonamide derivatives.

A series of cationic anthraquinone derivatives was investigated for their ability to stabilize duplex and triplex DNA. Thermal denaturation experiments demonstrate that each of these compounds stabilizes the [poly(dT) x poly(dA) x poly(dT)] triplex without significantly affecting the [poly(dT) x poly(dA)] duplex. The amount of stabilization is determined by the number and placement of the cationic substituents on the anthraquinone skeleton. The stabilization arises primarily from higher affinity binding of the quinones to the triplex relative to the duplex structures. Phosphorescence quenching and viscometric titrations indicate that the quinones bind to the triplex by intercalation.

Anthraquinones↗
PubMed1997

Anthraquinone photonucleases: a surprising role for chloride in the sequence-neutral cleavage of DNA and the footprinting of minor groove-bound ligands.

Irradiation of water-soluble anthraquinone (AQ) reagents in the presence of chloride ions results in the spontaneous, sequence-neutral cleavage of DNA. Mechanistic studies indicate that cleavage is initiated by chlorine atoms, produced by charge transfer interaction between chloride anion and AQ triplet states. High-resolution gel electrophoresis suggests that cleavage arises from abstraction of a hydrogen atom from C-4' of deoxyribose units. The targeting of this hydrogen, which is located in the minor groove of duplex DNA, can be effectively blocked by netropsin and, to a lesser degree, berenil, leading to photofootprinting of these minor groove-binding drugs.

Anthraquinones↗
PubMed1997

Variation in fertility between different types of local area.

Trends in fertility at the national level have been described in a recent article in the Population Review series. This article examines variations in the pattern of fertility experienced in different kinds of area within England and Wales. For this purpose use is made of the new ONS classification of local authorities into 11 groups and 29 clusters of areas with similar socio-economic characteristics. The classification was developed from statistics collected in the 1991 Census of Population. Although proportions of residents aged 0-4, 5-14, and 25-44 were among the 37 Census variables used to define groups and clusters of similar areas, the analysis did not make direct use of any measure of fertility related to ages of women at childbirth.

Adolescent↗
PubMed1996

Population review: (4). Trends in fertility.

Fertility in the United Kingdom has now been at a level below that needed for natural replacement of the population (TPFR of 2.1) for more than twenty years. Whilst fertility in many parts of the world (eg most of Europe, and much of the developing world) has declined sharply in recent years, the overall rate in the United Kingdom has been fairly stable (TPFR about 1.8) since 1980. Women are having their children at older ages: fertility rates have been falling for women aged under 30 and rising for women above that age. The mean age at motherhood rose by 1.4 years to 28.4 in England and Wales between 1984 and 1994. The proportion of women in England and Wales who were still childless at age 45 rose to 13 per cent in 1994, and will increase further in the future. One third of births are now to women who are not married, but the recent rapid increase in this proportion may not continue. The percentage of all births which are both outside marriage and registered solely by the mother has been fairly stable (around 7 per cent) for several years. Fertility rates are higher in Northern Ireland than in the rest of the United Kingdom, and lowest in Scotland and in the North of England. Northern Ireland has the lowest proportion of births outside marriage.

Adolescent↗
PubMed1995

Population review. Structure and distribution of the population.

This article is the first in a series of articles reviewing the changing composition of the population of the United Kingdom. The series is a follow-up to the demographic reviews published in the mid-1970s and mid-1980s (see In Brief, page 2). This first article gives a summary view of the changes since the early Seventies in the structure and distribution of the UK population, and also takes account of population projections for future years. It begins by describing changes in the total population. The review then goes on to consider changes in sex ratios, age distribution, marital status, the regional distribution of the UK resident population, population density, ethnicity and household composition.

Adolescent↗