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The binding of two hairpin polyamide ligands at adjacent sites on DNA has been studied using NMR spectroscopy. The ligands ImPyPy-γ-PyPyPy-Gly-Dp and Ac-lmPyPy-γ-PyPyPy-Gly-Dp were studied binding to oligomers containing one or two matched binding sites: 5′-XGTTA-3′ and 5′-TAACX[SUBN]GTTA-3′, where X is G, C, or A and N = 0, 1 or 2. At these sites the C-terminal ring shows an equilibrium between normal and inverted conformations. Better binding was observed with the ligand running 5′ to 3′ along the contacted strand than in the opposite direction. Complexes of DNAs with two binding sites indicated that at least one spacing base pair was required, and that the identity of this base pair was not critical. Binding with 5′ to 3′ contact is again preferred. Demonstrated binding at adjacent sites indicates that it may be possible to engineer cooperative binding for enhanced specificity or affinity. [ABSTRACT FROM AUTHOR]

Investigates the kinetic consequences of the DNA binding polyamides covalent linkage. Affinity and specificity of polyamide binding to DNA; Impact of covalent linkage on polyamide affinity and specificity; Description of biological polyamides function; Use of fluorescence-based stopped flow technique in measuring binding kinetic effects.

Focuses on the rate of guanosine 5'-phosphate 2-methylimidazolide (2-MeImpG) dimerization to form the RNA-linked dimer as a function of monomer and of polycytidylate concentration. Dimerization in solution exhibiting a simple second order dependence on 2-MeImpG concentration; Association constants in the dimerization reaction.

Focuses on a study which determined the sequence specificity of the gamma-turn and C-terminal beta-alanine amino acids by footprinting and affinity cleavage of DNA-restriction fragments. Quantitative dinucleotidase I footprinting; Sequence affinity of the gamma-turn and beta-alanine amino acids; Implications for the design of minor groove-binding molecules.

Predicts the sequence specificity of minor groove binding polyamides containing pyrrole and imidazole amino acids. Pairing rules; Quantitative DNase I footprint titrations; Quantitation by storage phosphor technology autoradiography.

Determines the orientation preference of pyrrole-imidazole polyamides in the minor groove of DNA. Synthesis of polyamides from Boc-beta-alanine Pan-resin with the usage of stepwise solid phase methods; Preference of positive charge at the C-terminus; Absence of substitution of an N-terminal imidazole.

Studies the recognition of seven base pair sequences in the minor groove of DNA by ten-ring pyrrole-imidazole polyamide hairpins. Definition of an upper limit of binding site size; Analysis of the DNA binding properties of polyamides; Indications that ten-ring hairpin polyamides have binding affinities similar to eight-ring hairpin polyamides.

Studies the discrimination of six base pair DNA sequences containing four contiguous G,C base pairs by eight-ring hairpin polyamides in the minor groove of DNA. Analysis of DNA binding properties of three polyamides; Expansion of the DNA sequence repertoire targeted by pyrrole-imidazole polyamides; Identification of sequence composition effects.

Describes the use of pyrrole-imidazole polyamides for the recognition of core 5'-GGG-3' sequences in the minor groove of double stranded DNA. Identification of binding site size and orientation by MPE-Fe(II) footprinting and affinity cleaving; Synthesis of polyamides; Determination of binding affinities by quantitative DNase I footprinting.

Explores the sequence-specific recognition of the minor groove of DNA by pyrrole-imidazole polyamides. Analysis of a series of four hairpin pyrrole-imidazole polyamides with respect to DNA binding affinity and sequence specificity; Binding activity.

Explores the recognition of 5'-(A,T)GG(A,T)2-3' sequences in the minor groove of DNA by hairpin polyamides. Analysis of a series of four hairpin pyrrole-imidazole polyamides with respect to DNA binding affinity and sequence specificity; Results of quantitative DNase I footprint titration experiments.

Presents a method for optimizing the hairpin design for ligands which bind the minor groove of DNA. Preparation of four pyrrole-imidazole polyamides substituted at the C-terminus with aliphatic amino acids using solid phase synthetic methodology; Effect of adding a C-terminal beta-alanine residue; Addition of a C-terminal glycine residue.

Describes the solid phase synthesis of sequence specific DNA binding polyamides containing N-methylimidazole and N-methylpyrrole amino acids. Preparation of two monomer building blocks, Boc-Py-OBt ester and Boc-Im acid, on a 50 gram scale without column chromatography; Optimization of cycling protocols to afford high stepwise coupling yields; Deprotection by aminolysis.

Investigates the reactivity of the natural polyamines, spermine and spermidine using guanosine 5'-phosphate 2-methylimidazolide, a labile phosphoimidazolide analog of guanosine triphosphate. Product analysis by high-pressure liquid chromatography; Rationalization of variations in product ratio; Kinetic determination of nucleophilicity.

Presents chemical information pertaining to the stereochemical control of the deoxyribonucleic acid (DNA) binding affinity. Analysis of the DNA binding properties of two enatiometric polyamides; Demonstration of the quantitative footprint titrations; Modulation of effects.

Introduces a powerful class of small molecules for sequence-specific recognition of double-helical DNA. Considering the broad range of sequences that can be specifically targeted with pyrrole-imidazole polyamides, coupled with an efficient solid-phase synthesis methodology; DNA-binding affinity pyrrole-imidazole polyamides; Minor-groove-binding; Regulating affininty with placement of a C-H.

Focuses on the compensation for the sequence composition effects for recognition of minor groove of deoxyribonucleic acid (DNA), in connection with the selective placement of an aliphatic beta-alanine (beta) residue paired with a pyrole (PY) or imidazole (Im) aromatic amino acid. Preparation of a series of polyamides; Regulation of the binding affinities and specificities of these polyamides; Indication of modeling.

Eight-ring hairpin polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids have been shown to bind with subnanomolar affinity to discrete DNA sites and to modulate a variety of DNA-dependent biological processes. We show here that addition of a second positive charge at the C terminus of an 8-ring hairpin polyamide confers activity against a number of clinically relevant fungal strains in vitro, and activity against Candida albicans in a mouse model. Control experiments indicate that the observed antifungal activity results from a DNA binding mechanism-of-action that does not involve DNA damage or disruption of chromosomal integrity. Hairpin activity is shown to be proportional to yeast DNA content (ploidy). Transcriptional interference is proposed as the likely explanation for fungal cytotoxicity. Experiments with sensitized yeast strains indicate the potential for discrete sites of action rather than global effects. [Copyright &y& Elsevier]

An efficient synthesis of DNA binding molecules consisting of four heterocyclic carboxamide units and various substituents at both termini is described. The minor-groove binding ligands showed excellent activity against a broad range of Gram-positive bacteria; no cross-resistance to known antibacterial drugs was observed. [Copyright &y& Elsevier]

Presents research which added a new aromatic amino acid, 3-hydroxypyrrole (Hp), to test pairings to distinguish all four Watson-Crick base pairs in the minor groove of DNA. Design of synthetic ligands; Oligodeoxy nucleotides and targeting of predetermined DNA sequences; Pairing rules for minor-groove binding polyamides; Findings.