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Biomedical subjects

G B Schuster

Publications and source records attributed to G B Schuster.

At least 19 recordsLinked to original sources
PubMed2001

Charge migration in DNA: ion-gated transport.

Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counterions, is described here. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations reveal that different counterion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge localization. Stochastic dynamic fluctuations between such ionic configurations can induce correlated changes in the spatial distribution of the hole, with concomitant transport along the DNA double helix. Comparative ultraviolet light-induced cleavage experiments on native B DNA oligomers and on ones modified to contain counterion (Na(+))-starved bridges between damage-susceptible hole-trapping sites called GG steps show in the latter a reduction in damage at the distal step. This reduction indicates a reduced mobility of the hole across the modified bridge as predicted theoretically.

Cations↗
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↗
PubMed2000

Long-range charge transfer in DNA: transient structural distortions control the distance dependence.

Damage to DNA is often caused by oxidative reactions. In one such process, an electron is lost from a base, forming its radical cation. Further reaction of the radical cation can lead to permanent change, which results in mutation. This Account is a report on oxidative damage to DNA caused by irradiation of anthraquinone derivatives, which are either randomly bound to the DNA or attached to it covalently at specific locations. Radical cations introduced in the DNA by the excited quinone cause damage both near to it and far away. We describe a mechanism for long-range charge transport in DNA that depends on its spontaneous structural distortion, which we call phonon-assisted polaron hopping. This mechanism, and its extension, provides a framework for understanding the reactions and charge-transport properties of DNA.

Anthraquinones↗
PubMed1999

Long-distance charge transport in duplex DNA: the phonon-assisted polaron-like hopping mechanism.

An anthraquinone-linked duplex DNA oligomer containing 60 base pairs was synthesized by PCR. The strand complementary to the quinone-containing strand has four isolated GG steps, which serve as traps for a migrating radical cation. Irradiation of the quinone leads to electron transfer from the DNA to the quinone forming the anthraquinone radical anion and a base radical cation. The radical cation migrates through the DNA, causing reaction at GG steps revealed as strand breaks. The efficiency of strand cleavage falls off exponentially with distance from the quinone (slope = -0.02 A(-1)). This finding necessitates reinterpretation of mechanisms proposed for radical cation migration in DNA. We propose that radical cations form self-trapped polarons that migrate by thermally activated hopping.

Anthraquinones↗
PubMed1999

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

A tetracationic anthraquinone derivative (27AQS2) binds to hairpin DNA and RNA. Ultraviolet irradiation of the bound quinone causes cleavage in the loop region of both oligonucleotides and at guanines in the stem region of the DNA hairpin. The absence of observable strand cleavage at guanines in the RNA hairpin suggests that either aniline treatment does not cause cleavage at damaged guanines in RNA or that radical cation migration does not occur readily in RNA duplexes. The ability to target the single-stranded regions of DNA and RNA structures is an important property of this photonuclease.

Anthraquinones↗
PubMed1998

Enzymatic reaction with unnatural substrates: DNA photolyase (Escherichia coli) recognizes and reverses thymine [2+2] dimers in the DNA strand of a DNA/PNA hybrid duplex.

Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson-Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.

Base Sequence↗
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

Structural modification changes the DNA binding mode of cation-substituted anthraquinone photonucleases: association by intercalation or minor groove binding determines the DNA cleavage efficiency.

The mode of binding anthraquinone derivatives, bearing positively charged ammonium side chains, to duplex DNA was investigated by optical and NMR spectroscopy. Absorption, circular dichroism, emission, and one- and two-dimensional homonuclear NMR spectroscopy show that mono- and dication-substituted quinones, AQS and 27AQS, bind primarily by intercalation. In contrast, these experiments indicate that the tetracationic anthraquinone 27AQS2 is bound nonintercalatively to duplex DNA. In particular, analysis of the NMR spectrum of 27AQS2 bound to a specially designed synthetic self-complementary dodecanucleotide (5'-CGCGAATTCGCG-3') shows it to be associated primarily with the minor groove of the central AATT sequence. The change in the DNA binding mode greatly affects the photophysical and photochemical properties of these photonucleases with DNA.

Anthraquinones↗
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↗
PubMed1993

Photocleavage of DNA: irradiation of quinone-containing reagents converts supercoiled to linear DNA.

Irradiation (350 nm) of air-saturated solutions of reagents containing an anthraquinone group linked to quaternary alkyl ammonium groups converts supercoiled DNA to circular and to linear DNA. Generation of linear DNA does not occur by accumulation of numerous single-strand cuts but by coincident-site double-strand cleavage of DNA. Irradiation forms the triplet state of the anthraquinone, which reacts either by hydrogen atom abstraction from a sugar of DNA or by electron transfer from a base of the DNA. Subsequent reactions result in chain scission. The quinone is apparently reformed after this sequence and reirradiation leads to double-strand cleavage.

DNA Damage↗
PubMed1990

The photochemistry of acetyl-substituted aroyl azides: the design of photolabeling agents for inert sites in hydrophobic regions.

The photochemistry, photophysics and hydrolytic stability of three substituted aroyl azides were investigated. The azides were selected as model compounds for potential photolabeling agents based on the extreme electrophilic reactivity of aroylnitrenes. Each of the azides studied is a derivative of benzoyl azide containing an acyl group to act as an internal triplet sensitizer and an additional functional group useful for linking the azide to a site-selecting probe molecule. The findings show that benzoyl azides containing the three substituents in a 1,3,5-pattern might be useful for labeling of lipophilic molecules.

Acetylation↗