Formation propensity of pseudo-circular G-hairpins

Beková Kateřina1,*, Lenarčič Živković Martina1,3, Gajarský Martin1, Stadlbauer Petr2, Šponer Jiří2, Vicherek Lukáš1, Fiala Radovan1, Rosenberg Ivan3, Petrová Magdaléna3, Plavec Janez3, Trantírek Lukáš 1

1 Central European Institute of Technology, Masaryk University, Brno, Czech Republic

2 Institute of Biophysics of the AS CR, v.v.i., Brno, Czech Republic

3 Kemijski institute - National Institute of Chemistry, Ljubljana, Slovenia

4 Institute of Organic Chemistry and Biochemistry of the ASCR, v.v.i, Praha, Czech Republic

*email: katerina.bekova@ceitec.muni.cz, lukas.trantirek@ceitec.muni.cz

 

Recently, Gajarsky et al. [1] showed that 11-nt long sequence, 5´- d(GTGTGGGTGTG)-3´ (SC11) from telomeric DNA of Saccharomyces cerevisiae3, adopts novel type of mixed parallel/antiparallel foldback DNA structure stabilized by G:G base pairs, referred to as pseudo-circular G-hairpin (PGH).

Here, we analyzed the PGH structure and its primary sequence to identify the minimal sequence requirements for PGH formation. We discovered more than ten SC11 sequence variants that are able to form PGHs. Our bioinformatics analysis revealed that the sequences with PGH-formation potential are both abundant and nonrandomly distributed in metazoan genomes. These sequences are overrepresented at evolutionarily conserved regulatory genomic foci, particularly in gene introns, which suggests their active biological role(s). Most importantly, by determining the high-resolution structure of extended SC11 sequence, we show for the first time that pseudo-circular G-hairpins might exist in at least two distinct topological forms. The structure of the novel topological form reveals unprecedented atomistic details of the junction between the protruding single stranded DNA and the pseudo-circular element of the PGH. Altogether, our data provide novel insight into the principles of the folding of G-rich oligonucleotides that could be applied to the prediction of natural and/or the design of artificial DNA recognition elements.

1. Gajarský, M., Živković, M. L., Stadlbauer, P., Pagano, B., Fiala, R., Amato, J., ... & Trantírek, L. (2017). Structure of a stable G-Hairpin. Journal of the American Chemical Society, 139(10), 3591-3594.

This project was supported by grants from the Czech Science Foundation (19-26041X), project SYMBIT (CZ.02.1.01/0.0/0.0/15_003/0000477) funded by the Europe-an Regional Development Fund and Ministry of Education, Youth, and Sports (MEYS) of the Czech Republic and by the grant from Ministry of Health of the Czech Republic (NV19-08-00450). This project was also supported by the project MSCAfellow2@MUNI (CZ.02.2.69/0.0/0.0/18_070/0009846) funded by MEYS. MEYS is also acknowledged for their support of access to research infrastructure (CEITEC 2020 LQ1601; CIISB-LM2018127; Czech-BioImaging LM2015062; EATRIS-CZ LM2015064). This project was supported by NCBR, Faculty of Science, Masaryk University. Computational resources were supplied by the project "e-Infrastruktura CZ" (e-INFRA LM2018140) provided within the program Projects of Large Research, Development and Innovations Infrastructures.