Beyond the Double Helix: NMR Adventures into Dynamic DNA Structures 

Prof. Peter Plavec (Slovenian NMR Center, Ljubljana/SVN)

Mittwoch, 3. Dezember 2025, 17:15 Uhr

Technische Universität Graz, HS H "Ulrich Santner"

Kopernikusgasse 24, EG, 8010 Graz

Abstract:

The structure of nucleic acids continues to unveil layers of unexpected structural diversity and complexity. Advanced techniques, particularly nuclear magnetic resonance (NMR) spectroscopy, have shown that DNA oligonucleotides exhibit far greater polymorphism than the traditional canonical double helix model suggests. Emerging research demonstrates that guanine-rich (G-rich) sequences often serve as hotspots for both methylation instability and the formation of G-quadruplexes (G4s). Through solution-state NMR studies, we identified a distinct, sequence-specific influence of 5-methylcytosine (Cm) on the folding dynamics of bcl2Mid, a GC-rich segment within the promoter region of the BCL2 gene. When cytosine at position C6 is replaced with its methylated analogue (C6m), the G4 folding process becomes noticeably slower, and the equilibrium between the dominant and minor structural forms shifts in the presence of K⁺ ions. Remarkably, the inclusion of a single Cm residue triggers localized structural rearrangements within the major [3+1] hybrid G4 conformation and simultaneously diminishes its overall thermodynamic stability. This shift favors the accumulation of the minor G4 species, which was subsequently characterized as a parallel-stranded G4 containing a distinctive snapback motif that occupies a vacancy in the external G-quartet. Interestingly, the zinc finger 3 motif of the transcription factor Sp1 displays a clear preferential affinity for this minor G4 conformation.

G-rich DNA sequences are especially susceptible to oxidative damage due to the inherently low redox potential of guanine bases. Such oxidative lesions disrupt the normal configuration of hydrogen-bond donors and acceptors, thereby interfering with the proper formation and stability of G4 structures. The consequences of guanine oxidation using well-defined model systems composed of a G-rich strand paired with its complementary C-rich strand were followed to evaluate how oxidative damage destabilizes canonical double-stranded DNA and promotes the emergence of alternative G4 structures. Our findings reveal that, despite the presence of oxidative lesions, the damaged constructs retain the ability to form G4 structures, as spare or redundant G-tracts can compensate for compromised guanine runs through complete or partial structural substitution. Nevertheless, the majority of these G4 exist as kinetically trapped intermediates rather than stable products, with the overall thermodynamic equilibrium remaining biased toward the double-stranded DNA form.

Biography:

Janez Plavec is the Head of the Slovenian NMR Centre at the National Institute of Chemistry and Professor of Structural Biology at the University of Ljubljana (UL). He obtained his Ph.D. from Uppsala University, Sweden, in 1995. In 2002, he was a Fulbright Fellow at the Georgia Institute of Technology, Atlanta, USA. He has led the Slovenian NMR Centre since 1996 and coordinated the establishment of the EN-FIST Centre of Excellence. He also serves as a member of the Board of Directors of CERIC-ERIC. Janez Plavec is co-author of over 330 original scientific papers, over 170 invited lectures at international conferences and 110 seminars at universities and academic institutions worldwide.