Netropsin antibiotic

Increasing concentrations in the range 0-10 molecules/100 bp, of both Distamycin and Netropsin-antibiotics which bind in the minor groove of DNA without intercalation — lead to a broadening of the 0.05 nm interference band, reflecting a broadening of the distribution of internucleosomal distances. A parallel decrease in the M/L is also observed. Above 20 molecules/100 bp denaturation takes place... 

Nature provides examples of sequence-selective minor groove binding, such as antibiotics including netropsin, distamycin, anthelvencin, and kikumycin. 

We first describe the NMR parameters for the duplex to strand transition of the synthetic DNA poly(dA-dT) (18) with occasional reference to poly(dA-dU) (24) and poly(dA- brdU) and the corresponding synthetic RNA poly(A-U) (24). This is followed by a comparison of the NMR parameters of the synthetic DNA in the presence of 1 M Na ion and 1 M tetramethylammonium ion in an attempt to investigate the effect of counterion on the conformation and stability of DNA. We next outline structural and dynamical aspects of the complexes of poly(dA-dT) with the mutagen proflavine (25) and the anti-tumor agent daunomycin (26) which intercalate between base pairs and the peptide antibiotic netropsin (27) which binds in the groove of DNA. 

Antibiotic Resonances The protons on the N-methylpyrrole rings of netropsin can be detected in the 1 antibiotic per 5 base pair netropsin poly(dA-dT) complex at 87°C (Figure 41). The proton line widths indicate that the entire complex is intact at this... 

The exchangeable and nonexchangeable netropsin protons have been monitored in detail for the 1 antibiotic per dG-dG-dA-dA-dT-dT-dC-dC octanucleotide duplex complex in our laboratory (9 7). 

Summary High resolution proton NMR spectroscopy has been utilized to probe the opening of antibiotic-free base pair regions (t 2L 61°C) and those centered about bound netropsin (t 90°C) in the biphasic dissociation of the 1 netropsin per 25 base pair poly(dA-dT) complex in 0.1 M buffer solution with temperature. 

The observation of selective complexation shifts in the nucleic acid resonances of the synthetic DNA demonstrate a change in the glycosidic torsion angles of the adenosine and thymidine residues and a minimal perturbation in the base pair overlaps on addition of netropsin. These structural perturbations at the antibiotic binding site are propagated to adjacent antibiotic-free base pair regions at low netropsin concentrations. 

We observe that netropsin binds tightly to DNA and stabilizes 5 base pairs centered about its binding site. The opening rates of the intervening base pair stretches during the dissociation of the antibiotic-free base pair regions in the Nuc/D = 50 complex are slower by an order of magnitude compared to the dissociation rates for the duplex to strand transition of poly(dA-dT) alone in 0.1 M buffer solution. 

The NMR data demonstrate a decreased segmental mobility of antibiotic-free strand regions anchored at one or both ends by netropsin-bound base pair regions in the partially melted out Nuc/D = 50 complex between 65° and 90°C. The migration of the antibiotic along the partially opened structure is slow between 60° and 70°C but the migration rate increases between 75° and 90°C. 

In the search for simpler analogues of netropsine and distamycin A, which are DNA minor groove binding antibiotics, pyrazoles (316) and (317) have been synthesized <89JOC428). The x-ray structure of (316) was reported. 

Finally, a very large and exciting field of polymer nmr studies is that of the structure and dynamics of biomolecules. Here, proton spectroscopy (at superconducting frequencies) remains dominant. I illustrate this by an example of Dinshaw Patel s studies of nucleic acids and oligonucleotides, which shows the use of H— H nuclear Overhauser enhancement (NOE) to explore the binding site of the antibiotic netropsin... 

Any compound that shows promise can be drawn on a computer display, along with the three-dimensional image of a receptor site. For example, the binding of netropsin, an antibiotic with a wide range of antimicrobial activity, to the minor groove of DNA is shown in Figure 30.1. 

The antibiotic netropsin (turquoise atoms) bound in the minor groove of DNA. 

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