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Int J Biol Macromol. 2019 May 10;134:422-434. doi: 10.1016/j.ijbiomac.2019.05.063. [Epub ahead of print]

DNA/RNA recognition controlled by the glycine linker and the guanidine moiety of phenanthridine peptides.

Author information

1
Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, 10002 Zagreb, Croatia.
2
Faculty of Food Technology and Biotechnology, University of Zagreb, Pierrotijeva 6, 10000 Zagreb, Croatia.
3
Fidelta d.o.o., Prilaz Baruna Filipovića 29, 10000 Zagreb, Croatia.
4
Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
5
Division of Molecular Biology, Ruđer Bošković Institute, P. O. Box 180, 10002 Zagreb, Croatia.
6
Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, P. O. Box 180, 10002 Zagreb, Croatia. Electronic address: mradic@irb.hr.

Abstract

The binding of four phenanthridine-guanidine peptides to DNA/RNA was evaluated via spectrophotometric/microcalorimetric methods and computations. The minor structural modifications-the type of the guanidine group (pyrrole guanidine (GCP) and arginine) and the linker length (presence or absence of glycine)-greatly affected the conformation of compounds and consequently the binding to double- (ds-) and single-stranded (ss-) polynucleotides. GCP peptide with shorter linker was able to distinguish between RNA (A-helix) and DNA (B-helix) by different circular dichroism response at 295 nm and thus can be used as a chiral probe. Opposed to the dominant stretched conformation of GCP peptide with shorter linker, the more flexible and longer linker of its analogue enabled the molecule to adopt the intramolecularly stacked form which resulted in weaker yet selective binding to DNA. Beside efficient organization of ss-polynucleotide structures, GCP peptide with shorter linker bound stronger to ss-DNA/RNA compared to arginine peptides which emphasize the importance of GCP unit.

KEYWORDS:

DNA/RNA chiral probe; DNA/RNA recognition; Pyrrole guanidine peptide

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