Selective Stabilization of Triplex DNA by Anthraquinone Sulfonamide Derivatives

Kan, Yongzhi; Armitage, Bruce A.; Schuster, Gary B.

doi:10.1021/bi962335s

Cited by 32 publications

(22 citation statements)

References 27 publications

(47 reference statements)

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“…Sonicated salmon sperm DNA, poly[d(GC)], poly(dT) (all from Amersham Pharmacia), Escherichia coli tRNA (Sigma), a T 4 -hairpin (5Ј-CGCGCGCGTTTTCGCGC-GCG-3Ј), and the sequence d(T 4 G 4 ) in a double-strand (5Ј-CGCGA ATCGCT T T TGGGGTACCCCA A A AGCGAT T-CGCG-3Ј) (all from Microsynth; Balgach, Switzerland) were dissolved in 50 mM Tris͞50 mM NaCl, pH 7.4. Triplex DNA competitor poly(dT)⅐poly(dA)⅐poly(dT) was prepared as described (24). Phosphatidylcholine (100 mg͞ml, Sigma) was dissolved in hexane.…”

Section: Methodsmentioning

confidence: 99%

In vitrogenerated antibodies specific for telomeric guanine-quadruplex DNA react withStylonychia lemnaemacronuclei

Schaffitzel

Berger

Postberg

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

564

481

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Most eukaryotic telomeres contain a repeating motif with stretches of guanine residues that form a 3 -terminal overhang extending beyond the telomeric duplex region. The telomeric repeat of hypotrichous ciliates, d(T4G4), forms a 16-nucleotide 3 -overhang. Such sequences can adopt parallel-stranded as well as antiparallel-stranded quadruplex conformations in vitro. Although it has been proposed that guanine-quadruplex conformations may have important cellular roles including telomere function, recombination, and transcription, evidence for the existence of this DNA structure in vivo has been elusive to date. We have generated high-affinity single-chain antibody fragment (scFv) probes for the guanine-quadruplex formed by the Stylonychia telomeric repeat, by ribosome display from the Human Combinatorial Antibody Library. Of the scFvs selected, one (Sty3) had an affinity of Kd ‫؍‬ 125 pM for the parallel-stranded guanine-quadruplex and could discriminate with at least 1,000-fold specificity between parallel or antiparallel quadruplex conformations formed by the same sequence motif. A second scFv (Sty49) bound both the parallel and antiparallel quadruplex with similar (Kd ‫؍‬ 3-5 nM) affinity. Indirect immunofluorescence studies show that Sty49 reacts specifically with the macronucleus but not the micronucleus of Stylonychia lemnae. The replication band, the region where replication and telomere elongation take place, was also not stained, suggesting that the guanine-quadruplex is resolved during replication. Our results provide experimental evidence that the telomeres of Stylonychia macronuclei adopt in vivo a guanine-quadruplex structure, indicating that this structure may have an important role for telomere functioning.T elomeres are specialized DNA-protein complexes at the end of eukaryotic chromosomes. They protect the chromosome ends from recombination, from fusion, and from being mistaken as broken ends (1-3). Telomeric DNA consists of simple repetitive DNA sequences ranging in size from 36 nucleotides in hypotrichous ciliates up to 50 kb in mammals. The 3Ј-strand is usually G-rich and extends over the complementary strand. It has been shown that the G-rich overhang can adopt a variety of unusual DNA structures (4), of which guanine-quadruplex DNA and t-loops are stable in vitro under physiological conditions (5-8). Parallel-stranded as well as antiparallel-stranded guaninequadruplex structures have been biophysically and structurally analyzed in detail with synthetic oligonucleotides (6-11). It has been suggested that this structure is also involved in numerous cellular processes, including transcription and recombination, in addition to telomere function (12). However, direct evidence for this DNA structure in vivo has been lacking to date.Ciliated protozoa are a well-suited biological system to study telomere structure and function, and many important processes including telomere sequences and telomerase were first identified in these cells (1-3). Hypotrichous ciliates, such as Oxytricha, Euplotes, or Styl...

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Section: Methodsmentioning

confidence: 99%

In vitrogenerated antibodies specific for telomeric guanine-quadruplex DNA react withStylonychia lemnaemacronuclei

Schaffitzel

Berger

Postberg

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

564

481

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“…This study revealed that the 1,4 compounds destabilize DNA triplexes, leading to dissociation of the third strand, whereas their 2,6 isomeric analogues bind to and stabilize triple-stranded structures. A related study has also shown that selective stabilization of triplex DNA can be achieved with a series of disubstituted anthraquinone sulfonamides and suggested that 2,7-functionalised compounds are more potent than their 2,6 counterparts [117]. We have also compared the activity of four di-substituted and two monosubstituted amidoanthraquinone compounds, and have examined how the position of the cationic substituents affects triplex affinity [118].…”

Section: Triplex Binding Ligandsmentioning

confidence: 98%

Targeting DNA with Triplexes

Fox¹

2000

CMC

191

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The formation of intermolecular DNA triple helices offers the possibility of designing compounds with extensive sequence recognition properties which may be useful as antigene agents or tools in molecular biology. In these structures a third strand oligonucleotide binds in the DNA major groove, making specific contacts with substituents on the exposed faces of the base pairs. Although triplexes form with exquisite specificity their use suffers from several drawbacks. Two limitations of this approach, which are considered in this review are, firstly that conditions of low pH are necessary for formation of the C+*GC triplet, and secondly that these structures are often less stable than their duplex counterparts. This review outlines the strategies that have been employed to overcome these drawbacks. The pH problem is addressed by considering the various DNA base analogues that have been used to recognise GC base pairs in a pH independent fashion, and discusses the benefits and limitations of each analogue. Triplex stability can be increased by using novel base analogues, backbone modifications and the use of triplex-specific binding ligands.

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“…It has helped in the design of one of the most efficient triplex stabilizers to date, BQQ, by suggesting that addition of a new ring to the BfPQ molecule would enhance stacking interactions with the Watson strand of the triple helix [126]. A rationale has been provided for the differential effects of 2,6-, 2,7-and 1,4-disubstituted anthraquinone derivatives on triplex stabilization [127,128]. Molecular modelling has also suggested that neomycin displays a good charge and shape complementarity with the Watson-Hoogsteen groove of triplexes [124,129].…”

Section: Structural Featuresmentioning

confidence: 99%