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1. Conformational Change in a Four‐Tetrad DNA G‐Quadruplex upon Intercalation of a Small‐Molecule Ligand PyDH2

   https://doi.org/10.1002/ange.202501443  

   Martin, Kailey N; Lam, Gwendolyn; Reznichenko, Oksana; Brunner, Kyle E; Zdilla, Michael J; McCarthy, Sawyer E; Granzhan, Anton; Yatsunyk, Liliya A (July 2025, Angewandte Chemie)

   Abstract G‐quadruplexes (G4s) are non‐canonical DNA structures implicated in a number of biological processes. Small‐molecule ligands can alter stability and folding of G4s, which can potentially be exploited for therapeutic purposes. In this work, we investigate the interaction of telomeric DNA fragment fromTetrahymena thermophila(TET25, 5′‐G(TTGGGG)_4‐3′) with a G4 ligand PyDH2 belonging to the bisquinolinium family. When alone, TET25 adopts a mixture of three conformations, with the most abundant being a four‐tetrad hybrid G4. In the presence of PyDH2, surprisingly, TET25 folds into an antiparallel chair G4, with PyDH2 intercalated between G‐tetrads 2 and 3, according to our crystal structure. The structure represents the second example, and the first crystallographic evidence, of ligand intercalation into a G4. In solution, the interaction of PyDH2 and TET25 leads to a number of complexes differing by G4 topology and binding stoichiometry, strong stabilization of G4 (∆T_m = 12.4 °C in the presence of one equiv. of PyDH2) and large hysteresis of ∼10 °C, suggesting that ligand binding and G4 folding processes are complex. 

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2. Slow G-Quadruplex Conformation Rearrangement and Accessibility Change Induced by Potassium in Human Telomeric Single-Stranded DNA

   https://doi.org/10.1021/acs.jpcb.4c00719  

   Lacen, Arianna N; Symasek, Andrew; Gunter, Alan; Lee, Hui-Ting (June 2024, The Journal of Physical Chemistry B)

   The guanine-rich telomeric repeats can form G-quadruplexes (G4s) that alter the accessibility of the single-stranded telomeric overhang. In this study, we investigated the effects of Na+ and K+ on G4 folding and accessibility through cation introduction and exchange. We combined differential scanning calorimetry (DSC), circular dichroism (CD), and single molecule Förster resonance energy transfer (smFRET) to monitor the stability, conformational dynamics, and complementary strand binding accessibility of G4 formed by single-stranded telomeric DNA. Our data showed that G4 formed through heating and slow cooling in K+ solution exhibited fewer conformational dynamics than G4 formed in Na+ solution, which is consistent with the higher thermal stability of G4 in K+. Monitoring cation exchange with real time smFRET at room temperature shows that Na+ and K+ can replace each other in G4. When encountering high K+ at room or body temperature, G4 undergoes a slow conformational rearrangement process which is mostly complete by 2 h. The slow conformational rearrangement ends with a stable G4 that is unable to be unfolded by a complementary strand. This study provides new insights into the accessibility of G4 forming sequences at different time points after introduction to a high K+ environment in cells, which may affect how the nascent telomeric overhang interacts with proteins and telomerase. 

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3. 8-Oxoguanine Disrupts G-Quadruplex DNA Stability and Modulates FANCJ AKKQ Peptide Binding

   https://doi.org/10.3390/molecules30163424  

   Campbell, Laura; Lowran, Kaitlin; Cismas, Emma; Wu, Colin G (August 2025, Molecules)

   Guanine-rich nucleic acid sequences can adopt G-quadruplex (G4) structures, which pose barriers to DNA replication and repair. The FANCJ helicase contributes to genome stability by resolving these structures, a function linked to its G4-binding site that features an AKKQ amino acid motif. This site is thought to recognize oxidatively damaged G4, specifically those containing 8-oxoguanine (8oxoG) modifications. We hypothesize that FANCJ AKKQ recognition of 8oxoG-modified G4s (8oxoG4s) depends on the sequence context, the position of the lesion within the G4, and overall structural stability. Using fluorescence spectroscopy, we measured the binding affinities of a FANCJ AKKQ peptide for G4s formed by (GGGT)4, (GGGTT)4, and (TTAGGG)4 sequences. G4 conformation and thermal stability were assessed by circular dichroism spectroscopy. Each sequence was modified to include a single 8oxoG at the first (8oxo1), third (8oxo3), or fifth (8oxo5) guanine position. In potassium chloride (KCl), the most destabilized structures were (GGGT)4 8oxo1, (GGGTT)4 8oxo1, and (TTAGGG)4 8oxo5. In sodium chloride (NaCl), the most destabilized were (GGGT)4 8oxo1, (GGGTT)4 8oxo5, and (TTAGGG)4 8oxo5. FANCJ AKKQ binding affinities varied according to damage position and sequence context, with notable differences for (GGGT)4 in KCl and (TTAGGG)4 in NaCl. These findings support a model in which FANCJ binding to G4 and 8oxoG4 structures is modulated by both the oxidative damage position and the G4 local sequence environment. 

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4. Effects of ribonucleotides on telomeric G4 formation, dynamics, and initiation of ribonucleotide excision repair by RNase H2

   https://doi.org/10.1093/nar/gkaf1501  

   Cortez, Luis M; Rahman, Md_Ibnul Rifat; Welfer, Griffin A; Riva, Fillipo; Buettner, Kristen J; Lee, Hui-Ting; Freudenthal, Bret D (January 2026, Nucleic Acids Research)

   Abstract Human telomeres are composed of TTAGGG repeats that can fold into G-quadruplexes (G4s). G4s can form several different conformations, including parallel, antiparallel 2 + 2 chair, antiparallel 2 + 2 basket, and 3 + 1 parallel/antiparallel. Telomeres are composed of deoxyribonucleotide monophosphates; however, telomerase has been shown to insert ribonucleotide monophosphates (rNMPs) as efficiently as replicative DNA polymerases. Non-telomeric rNMP insertions are deleterious, but the effect on telomeres remains under explored. We systematically investigated 16 variants of the G4-forming telomeric sequence (TTAGGG)4 containing a single rNMP substitution. We generally found that rNMP substitution of the first dG in a repeat (TTAGGG)4 altered the G4 conformation. Incorporation of a rNMP also perturbed G4 folding dynamics, decreasing the population of stably folded molecules and promoting rapid structural transitions. Depending on the rNMP position, we further observed a reduction in overall thermal stability. Additionally, RNase H2, the initiator of ribonucleotide excision repair, had reduced cleavage of rNMPs in G4s, and could only cleave rNMPs at more accessible positions within the G4. Cumulatively, we show that the insertion of rNMPs in telomeric sequences alters the conformation and stability of G4s. This could lead to deleterious effects on telomeric integrity, and these changes may persist due to the difficulty of repairing rNMPs within G4s. 

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5. Single-molecule fluorescence detection of a tricyclic nucleoside analogue

   https://doi.org/10.1039/D0SC03903A  

   Samaan, George N.; Wyllie, Mckenzie K.; Cizmic, Julian M.; Needham, Lisa-Maria; Nobis, David; Ngo, Katrina; Andersen, Susan; Magennis, Steven W.; Lee, Steven F.; Purse, Byron W. (February 2021, Chemical Science)

   null (Ed.)

   Fluorescent nucleobase surrogates capable of Watson–Crick hydrogen bonding are essential probes of nucleic acid structure and dynamics, but their limited brightness and short absorption and emission wavelengths have rendered them unsuitable for single-molecule detection. Aiming to improve on these properties, we designed a new tricyclic pyrimidine nucleoside analogue with a push–pull conjugated system and synthesized it in seven sequential steps. The resulting C -linked 8-(diethylamino)benzo[ b ][1,8]naphthyridin-2(1 H )-one nucleoside, which we name ABN, exhibits ε 442 = 20 000 M −1 cm −1 and Φ em,540 = 0.39 in water, increasing to Φ em = 0.50–0.53 when base paired with adenine in duplex DNA oligonucleotides. Single-molecule fluorescence measurements of ABN using both one-photon and two-photon excitation demonstrate its excellent photostability and indicate that the nucleoside is present to > 95% in a bright state with count rates of at least 15 kHz per molecule. This new fluorescent nucleobase analogue, which, in duplex DNA, is the brightest and most red-shifted known, is the first to offer robust and accessible single-molecule fluorescence detection capabilities. 

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