Mini Thomas

Synthesis of a novel thiazole based dipeptide chemosensor for Cu(II) in water

A thiazole-based novel dipeptide module has been synthesized, which exhibited selective Cu(II) recognition in water in the presence of other competing divalent transition metal ions at micromolar concentrations. This is the first example of an entirely synthetic peptide based chemosensor for Cu(II).

Distamycin Analogues without Leading Amide at Their N-Termini − Comparative Binding Properties to AT- and GC-Rich DNA Sequences

An efficient, simple and general route towards the solution-phase synthesis of four distamycin analogues containing 2-5 N-methylcarboxamide units without the leading amide unit at the N-terminus is described. The binding abilities of these molecules to calf thymus DNA, poly d(AT), poly dA.poly dT and poly d(GC) were evaluated by duplex DNA melting temperature (Tm) analysis, fluorescence probe displacement assay, footprinting studies and induced circular dichroism (ICD) measurements. A minimum of three N-methylpyrrolecarboxamide units was found to be necessary for the onset of DNA binding. The other three analogues exhibited AT-specific footprints on DNA at a salt concentration of 40 mM NaCl. Interestingly, intense ICD spectra were obtained not only with AT-rich DNA tracts, but also with poly d(GC). Though these ICD signals were sensitive to changes in salt concentration of the solution, residual ICD was present even at [NaCl] values as high as 4.8 M, at which poly d(GC) is likely to exist in the Z conformation. This implies that nonelectrostatic interactions are involved in the binding process involving poly d(GC) and also that binding is preserved even with the Z form of DNA. These results have significance on account of the growing interest in polyamide-based minor groove binders as artificial gene regulators and also in view of the increasing evidence for the biological significance of the Z morph of DNA.

Facile synthesis of oligopeptide distamycin analogs devoid of hydrogen bond donors or acceptors at the N-terminus: sequence-specific duplex DNA binding as a function of peptide chain length

The first examples of distamycin analogs, which lack hydrogen bond interactor groups at the N-terminus, have been synthesized. The bispyrrole peptide did not exhibit any detectable binding with double-stranded (ds) DNA. However, all other homologues did bind to ds-DNA strongly, with the binding affinities increasing as a function of the number of repeating pyrrole carboxamide units, implying that a hydrogen bond donor or acceptor atom per se at the N-terminus is not essential for their DNA binding. Studies with poly d(GC) showed that the N-terminal formamide is not a prerequisite for GC binding, contrary to earlier postulations.

Facile synthesis of novel fluorescent distamycin analogues

A facile synthesis of four distamycin analogues that bear the dansyl fluorophore is described. The nature of the linkage between the fluorophore and the sequence recognition element had a dramatic effect on the fluorescence properties of these ligands upon DNA binding.

Novel distamycin analogues: facile synthesis of cholesterol conjugates of distamycin-like oligopeptides

A facile route towards the synthesis of the first examples of cholesterol-conjugated distamycin analogues is described. These compounds retain their strong binding capacity to double-stranded (ds)-DNA. Aqueous suspensions of these analogues exhibited closed, vesicle-like structures under transmission electron microscope.

DNA recognition by the first tail-to-tail linked distamycin-like oligopeptide dimers

Sequence-specific bidentate binding to double-stranded (ds)-DNA by ‘tail-to-tail’ linked dimeric distamycin analogues is described; compared to their monomeric analogues, these dimers exhibit greater affinity and longer binding site size and open up a novel avenue in the design of minor groove binders that overcome the phasing problem.

Unusual DNA binding exhibited by synthetic distamycin analogues lacking the N-terminal amide unit under high salt conditions.

Abstract The binding of three analogues of the minor-groove binding antiviral antibiotic distamycin (Dst) with double-stranded (ds)-DNA were monitored using ds-DNA melting temperature (Tm) measurements, ethidium bromide (EtBr) displacement assay, footprinting analysis and induced circular dichroism (ICD). These compounds contained 3–5 N-methyl-pyrrole-car- boxamide units and lacked the N-terminal formamide unit present in Dst. These experiments suggested that the present analogues did not compromise their AT-specificity despite the deletion of the N-terminal formamide unit. The binding affinities, however, were significantly affected. Interestingly, the analogue with three N-methyl-pyrrole-carboxamide units exhibited an initial decrease in ICD at >40 mM salt concentrations. This was followed by a pronounced recovery of ICD at > 1.6 M salt concentrations, a phenomenon hitherto not observed with any other DNA binding molecules. The pentapyrrole analogue exhibited the highest binding affinity with CT-DNA under normal (40 mM) salt conditions. However, it suffered maximum relative dissociation under high salt conditions and did not exhibit any recovery in ICD at higher NaCl concentrations. The analogues possessing four and five pyrrole rings exhibited intense ICD signals with poly d(GC) in the ligand absorption region in the presence of 40 mM NaCl, unlike the one with three pyrrole rings. These ICD signals were however, highly susceptible to changes in ionic strength. Thus subtle modifications in the ligand molecular structure can have dramatic effect on their DNA binding properties.

Ethyl 2-[N-(tert-butyl­oxy­carbonyl)-l-alanyl­amino]-4-methyl-1,3-thia­zole-5-carboxyl­ate reveals a trans orientation of the preceding amide N—H with respect to the thia­zole-ring sulfur

The title molecule, C(15)H(23)N(3)O(5)S, was prepared as a synthetic precursor to 4-methylthiazole-based DNA minor groove binders which would bear chiral amino acids in the sequence. The crystallographic evidence presented herein shows that the aromatic amide NH group preceding the thiazole ring points away from the direction of sulfur. The molecule is biplanar, with the dihedral angle between the N-terminus peptide moiety and the thiazole-containing plane being 49.7 (5) degrees, with a bend at the Calpha carbon.

DNA binding properties of novel dansylated distamycin analogues in which the fluorophore is directly conjugated to the N-methyl-pyrrole carboxamide backbone

Abstract Polyamides that are structural analogues of the naturally occurring DNA minor groove binding antibiotic distamycin (Dst) are promising candidates as gene modulators. Developing strategies for the large scale screening and monitoring of the cellular distribution of such ligands would aid the faster discovery of molecules, which would have eventual utility in molecular biology and medicine. Attachment of fluorescent tags would be a useful step towards this end. A fundamental question in this connection is whether the tag modifies the DNA binding affinity of the parent compounds. Towards answering this question, we have developed two oligopeptides that bear the dansyl (N, N-dimethylaminonaphthalene sulfonamido fluorophore) coupled directly to the N-terminus of the conjugated N-methylpyrrole carboxamide network, and possess three or four N-methyl pyrrole carboxamide units (abbreviated as Dn3 and Dn4 respectively). DNA binding abilities of these molecules were assessed from fluorescence titration experiments, duplex-DNA Tm analysis (employing both UV and fluorescence spectroscopy), induced circular dichroism measurements (ICD), salt dependence of ICD and apparent binding constant measurements (Kapp) employing ethidium bromide (EtBr) displacement assay. Both these molecules ‘reported’ DNA binding in the form of an enhanced fluorescence emission. As judged from the ICD measurements, salt dependence of ICD, Tm analysis and Kapp measurements, the binding affinities of the molecules that possessed dansyl group at their N-termini were lower than the ones with equivalent number of amide units, but possessed N-methylpyrrole carboxamide unit at their N-ter- mini. These results would have implications in the future design of fluorescent polyamides.