Shape selective recognition of T·A base pairs by hairpin polyamides containing N-Terminal 3-Methoxy (and 3-Chloro) thiophene residues

Foister, Shane; Marques, Michael A.; Doss, Raymond M.; Dervan, Peter B.

doi:10.1016/s0968-0896(03)00502-9

Cited by 35 publications

(37 citation statements)

References 15 publications

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“…Based on the pairing rules, match polyamide 1 targets sequences of the type 5Ј-WTWCGW -3Ј (where W ϭ A or T), whereas mismatch polyamide 2 targets sequences of the type 5Ј-WGGWCW-3Ј. The 3-chlorothiophene ring at the N terminus of polyamide 1 provides specificity for a T•A base pair (22). We mapped the detailed binding sites for both match and mismatch polyamides on the VEGF promoter fragment that encompasses the HRE.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist

Olenyuk

Zhang

Klco

et al. 2004

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

205

180

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Section: Resultsmentioning

confidence: 99%

“…Synthetic oligomers containing N-methylpyrrole and N-methylimidazole amino acids conjugated to a fluorescein dye represent a modular molecular recognition toolkit with properties that satisfy these criteria. DNA sequence specificity is programmed by a simple code created by pairs of aromatic rings (19)(20)(21)(22).…”

mentioning

confidence: 99%

Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist

Olenyuk

Zhang

Klco

et al. 2004

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

205

180

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“…From a series of thiophene caps including 3-H, -CH 3 , -NH 2 , -NHAc, -OH, -OCH 3 , -F and -Cl, it was found that N-terminal 3-methoxy (Mt) and 3-chloro (Ct) thiophene-2-carboxamide residues, when paired with Py, demonstrate selectivity for T•A versus A•T [39] (Fig. 6).…”

Section: Table 1 Specific Py Im and Hp Pairingsmentioning

confidence: 99%

Programmable DNA Binding Oligomers for Control of Transcription

Dervan¹,

Doss²,

Marques³

2005

CMCACA

116

115

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Mapping and sequencing the genetic blueprint in human, mice, yeast and other model organisms has created challenges and opportunities for chemistry, biology and human medicine. An understanding of the function of each of the approximately 25,000 genes in humans, and the biological circuitry that controls these genes will be driven in part by new technologies from the world of chemistry. Many cellular events that lead to cancer and the progression of human disease represent aberrant gene expression. Small molecules that can be programmed to mimic transcription factors and bind a large repertoire of DNA sequences in the human genome would be useful tools in biology and potentially in human medicine. Polyamides are synthetic oligomers programmed to read the DNA double helix. They are cell permeable, bind chromatin and have been shown to downregulate endogenous genes in cell culture.

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“…Note that the C-terminal pyrrole is located in the inverted conformation and the tail is out of the groove (modified from [31] In an effort to explore the sequence specificity of new ring pairs in eight-ring hairpin polyamides containing 3-substituted thiophene-2-carboxamide residues at the Nterminus new hairpin lexitropsins were synthesized by standard solid-phase techniques (Fig. (6)) [32]. Quantitative DNase I footprinting titration and molecular modelling studies (Spartan Essential software) gave rise to interesting binding models in the minor groove of the DNA.…”

Section: Fig (3)mentioning

confidence: 99%

Advances in DNA-Ligands with Groove Binding, Intercalating and/or Alkylating Activity: Chemistry, DNA-Binding and Biology

Pindur¹,

Jansen²,

Lemster

2005

CMC

105

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It is known that DNA is a well-characterized intracellular target but its size and sequential characteristics make it an elusive target for selective drug action. Binding of low molecular weight ligands to DNA causes a variety of significant biological responses. In this context the main consideration is given to recent developments in DNA sequence selective binding agents bearing conjugated effectors because of their potential application in treatment of cancers, in diagnosis as well as in molecular biology. In the present review recent results about analogues of netropsins, distamycin A and of some lexitropsins and combilexins or related hybrid molecules with sequence reading, intercalating or alkylating activity are described and evaluated for prospective applications. Furthermore there exists DNA minor groove binder with different basic structures which does not possess the typical polyamide chain, including dimeric intercalating chromophores. Finally new results about peptide nucleic acids and related nucleic acid bases linked with polyamides are reported. In pronounced examples the structural chemistry, synthesis, DNA binding with several biophysical methods, molecular aspects, structure activity relationship, topoisomerase inhibition, antitumour and antibacterial effects are discussed in detail.

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Shape selective recognition of T·A base pairs by hairpin polyamides containing N-Terminal 3-Methoxy (and 3-Chloro) thiophene residues

Cited by 35 publications

References 15 publications

Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist

Inhibition of vascular endothelial growth factor with a sequence-specific hypoxia response element antagonist

Programmable DNA Binding Oligomers for Control of Transcription

Advances in DNA-Ligands with Groove Binding, Intercalating and/or Alkylating Activity: Chemistry, DNA-Binding and Biology

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