Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

DNA Binding Properties of Bis-linked Netropsin Derivatives with Head-to-Head and Tail-to-Tail Orientations of Two Netropsin Moieties

We have studied the interaction with DNA of bis-linked netropsin derivatives in which two monomers are attached via short linkers in head-to-head and tail-to-tail manners:

Here Py is a N-propylpyrrole amino acid residue. Cis[Pt(NH3)2]2+ is a cis-diammineplatinum (II) residue. Dp is a dimethylaminopropylamine residue. Pim is a pimelic acid residue. Adi is an adipic acid residue. Arrows indicate direction from the N-terminus to the C-terminus in each peptide fragment. We have found that head-to-head bis-netropsins and bind in the extended

conformation and parallel-stranded hairpin form to poly(dA)? poly(dT) at isolated sites and can form self-associated dimer species upon binding to partially overlapped sites on DNA. In contrast, binds only in the extended conformation to poly(dA)? poly(dT).

For DNA fragments containing multiple blocks of (A/T)4 and (T/A)4 separated by zero, one, two and three GC-base pairs, DNase I footprinting and CD spectroscopy studies reveal that 5'-AAAATTTT-3' is the strongest affinity binding site for bis-netropsins and . In contrast,

binds more strongly to DNA sites with the sequence 5'-TTTTAAAA-3' (1). CD studies show

that both and bind in the extended conformation to DNA oligomer

with the sequence 5'-CCAAAATTTTCC-3' (I) and interact in the parallel-stranded hairpin and antiparallel dimer forms with duplexes 5'-CCTATATATACC-3' (II), 5'-CCTTTTTTTTCC-3' (III) and 5'-CCTTTTAAAACC-3' (IV). In contrast, DNA oligomers III and IV serve as the best substrates for binding of in the extended form. Considerable differences are also observed on binding of

the synthetic ligands to DNA oligomers with sequences 5'- CGTATACG-3' (V) and 5'- CCTATATCC -3' (VI). and bind to DNA-oligomers V and VI in the parallel-stranded hairpin

form, whereas interacts with DNA oligomer VI predominantly in a self-associated dimer form.
In system, containing and octamer duplex V, a partially bonded monodentate type of

binding of the synthetic ligand dominates. Our present observations, coupled with literature data, show that mode of binding of synthetic ligands to DNA and their binding affinities depend on the minor groove width and DNA flexibility. Parallel-stranded hairpin polyamides can be used for design and synthesis of new generation of sequence specific DNA-binding ligands.

Supported by the Deutche Volkswagen Stiftung (grant AZI/70409) and Russian Foundation for Basic Research (grant 00-48240).

References and Footnotes
  1. S.L. Grokhovsky, A.N. Surovaya, G. Burkhardt, V.F. Pismensky, B.K. Chernov, Ch. Zimmer and G.V. Gursky, FEBS Lett. 439, 346-350, (1998).

A.N. Surovaya (1), G. Burckhardt (2), S. L. Grokhovsky (1,3), Ch. Zimmer (2) and G. V. Gursky (1)

Engelhardt Institute of Molecular Biology (1), Moscow 119991, Russia Institute of Molecular Biology (2), Friedrich Schiller University, Jena , Germany University of Oslo (3), Centre for Medical Studies, Oslo, Norway E-mail: gursky@genome.eimb.relarn.ru ; Fax: (7) (095) 135-1405