PHD Student no​/ICHB​/PSD

Institute of Bioorganic Chemistry Polish Academy of Sciences

Organisation/Company Institute of Bioorganic Chemistry Polish Academy of Sciences Department Poznań Doctoral School of the Institutes of the Polish Academy of Sciences Research Field Biological sciences » Biology Researcher Profile First Stage Researcher (R1) Positions PhD Positions Country Poland Final date to receive applications 31 Jan 2026 - 23:59 (Europe/Brussels) Type of Contract Temporary Job Status Full-time Hours Per Week 40 Is the job funded through the EU Research Framework Programme?

Not funded by a EU programme Reference Number 25/2025/ICHB/PSD Is the Job related to staff position within a Research Infrastructure? No

KEY WORDS: G-quadruplex, DNA aptamer, hairpin, thrombin

Research topic:
Modified nucleotide residues as potential tool to increase aptamer - target protein interaction

Aptamers are a diverse group of single-stranded oligonucleotides whose sequence determines folding into a specific structure, which is a key factor enabling binding to a target protein and thus modulating its activity. Examples of the structural diversity of aptamers include the oligonucleotides RE31, RV66, and Toggle-25t, which adopt, respectively, a G-quadruplex structure with an additional duplex fragment, a parallel G-quadruplex with 5’ and 3’ flanking regions, and a hairpin-type structure with an internal loop.

Although aptamers have found numerous applications, the low diversity of modified nucleotide residues compared to amino acids is a major limitation in enhancing their affinity and binding strength to target proteins. The development of nucleotide residue modifications (SOMA-DNA) that better mimic amino acid residues and can significantly improve aptamer binding strength due to additional hydrophobic interactions represented a major advancement in this field.

These observations provided both the scientific foundation and the impetus for the creation of our novel modifications, termed specifically functionalized nucleic acids with increased ribose ring lability (Slow Off-Rate Unlocked Nucleic Acids, SUNAs). Other modifications that may improve protein–aptamer interactions include the introduction of a sulfur atom into the inter‑nucleotide bond or at the C4 position of uridine, as well as replacing the ribose ring with a 2’-fluoroarabinose residue.

In this project, we propose to expand knowledge regarding the usefulness of these modifications for developing variants of RE31, RV66, and Toggle-25t aptamers with enhanced affinity for target proteins. A detailed understanding of these processes and mechanisms at the molecular level could enable the design of new versions of known inhibitors, which, in turn, could contribute to the improvement of therapeutic methods.

Additional information:

• Research and doctoral theses shall be carried out within the project number 2024/55/D/NZ7/02686, entitled “Modified nucleotide residues as potential tool to increase aptamer - target protein interaction”, funded by National Science Center
• PhD students shall receive a stipend in the gross amount of ca4300 PLN for the period of 24 months with the possibility of extending up to 4 8 months, and with the possibility of increasing the amount of the stipend after the mid‑term evaluation (in accordance with the current regulation of the Minister - 5340.90 PLN gross).
• PhD students shall be subject to social insurance, pursuant to article. 6 section 1 passage 7b of the act of October 13th, 1998 on the social insurance system (Journal of Laws of 2019, item 300, 303 and 730).
• Possibility to apply for funding for short‑term international research trips (NAWA PROM)
• Possibility of using the Multisport card, group insurance, social benefits (co‑financing of holiday leave, refund of tickets for cultural events).

PhD students shall receive a stipend in the gross amount of ca 4300 PLN

• MSc degree in biology or a related field, or fulfilling the conditions stipulated in article 186, section 2 of the act of July 20th, 2018 Law on Higher Education and Science (Journal of Laws of 2018, item 1668, as amended).
• Experience in laboratory…