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Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modeling

Project Description

The work will be focused on detailed structural characterisation of short purine oligonucleotides clipped by proper sequential motifs that induce parallel orientation of DNA strands.
For this purpose, NMR experiments combined with MD simulations will be employed. The effect of modifications of selected nucleotides on the structural properties of designed models will be investigated to gain deeper understanding of key noncovalent interactions that contribute to the folding of such systems.

Keywords: oligonucleotides, MD simulations, molecular modelling, NMR spectroscopy

HOW TO APPLY: Register for this call using the registration form at and submit required documents to receive support with the preparation of the application and all formalities. Your application package will be forwarded to the supervisor for preliminary revision.
Applicants who wish to pursue a degree at the CEITEC PhD program must hold the equivalent of a Master’s degree (MSc) in a similar field (four- or five-year undergraduate degree). The application can be submitted before obtaining the Master’s degree; however, the applicant should obtain a degree within five months after the application deadline.

Funding Notes

Admission for studies, student registration for the full-time study program, and proper fulfillment of student duties constitute the student’s right to a regular income of 22 000 CZK (850 EUR). Information is available at View Website

Living costs and other practicalities available at View Website


William Copp, Alexey Y. Denisov, Jingwei Xie, Anne M. Noronha, Christopher Liczner, Nozhat Safaee, Christopher J. Wilds, Kalle Gehring; Influence of nucleotide modifications at the C2’ position on the Hoogsteen base-paired parallel-stranded duplex of poly(A) RNA. Nucleic Acids Research, 2017, 45(17),10321–1033.

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