Bibliographie

Auteur·rice

Eric Largy

1.
R. R. Abzalimov, I. A. Kaltashov, Extraction of local hydrogen exchange data from HDX CAD MS measurements by deconvolution of isotopic distributions of fragment ions. J. Am. Soc. Mass Spectrom. 17, 1543–1551 (2006).
2.
R. R. Abzalimov, D. A. Kaplan, M. L. Easterling, I. A. Kaltashov, Protein conformations can be probed in top-down HDX MS experiments utilizing electron transfer dissociation of protein ions without hydrogen scrambling. J. Am. Soc. Mass Spectrom. 20, 1514–1517 (2009).
3.
F. Cantais, A. Catrain, E. Largy, G. Van Vyncht, A. Delobel, “Characterisation of humira adalimumab by high resolution mass spectrometry” (Quality Assitance, Donstiennes, Belgique, 2015).
4.
A. Delobel, E. Largy, F. Cantais, A. Catrain, G. Van Vyncht, “Characterisation of antibody-drug conjugates by high-resolution mass spectrometry” (Quality Assitance, Donstiennes, Belgique, 2016).
5.
C. Altona, M. Sundaralingam, Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation. J. Am. Chem. Soc. 94, 8205–8212 (1972).
6.
A. Ambrus, D. Chen, J. Dai, T. Bialis, R. A. Jones, D. Yang, Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res. 34, 2723–2735 (2006).
7.
J. Anacleto, E. Kabir, M. Blanco, Y. Leblanc, C. Lento, D. J. Wilson, Efficient, zero scrambling fragmentation of deuterium labeled peptides on the ZenoToF 7600 electron activated dissociation platform. J. Am. Soc. Mass Spectrom. 36, 1175–1181 (2025).
8.
Anirban Ghosh, E. Largy, V. Gabelica, G4dbr: A Database of Validated DNA G-quadruplexes Structures in Native Mass Spectrometry Conditions (Zenodo, 2020).
9.
A. Arora, M. Dutkiewicz, V. Scaria, M. Hariharan, S. Maiti, J. Kurreck, Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif. RNA 14, 1290–1296 (2008).
10.
S. Balasubramanian, S. Neidle, G-quadruplex nucleic acids as therapeutic targets. Curr. Opin. Chem. Biol. 13, 345–353 (2009).
11.
G. D. Balkwill, T. P. Garner, H. E. L. Williams, M. S. Searle, Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop. J. Mol. Biol. 385, 1600–1615 (2009).
12.
J.-D. Beaudoin, J.-P. Perreault, 5’-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res. 38, 7022–7036 (2010).
13.
A. Beck, E. Wagner-Rousset, M.-C. Bussat, M. Lokteff, C. Klinguer-Hamour, J.-F. Haeuw, L. Goetsch, T. Wurch, A. Dorsselaer, N. Corvaia, Trends in glycosylation, glycoanalysis and glycoengineering of therapeutic antibodies and fc-fusion proteins. Curr. Pharm. Biotechnol. 9, 482–501 (2008).
14.
A. Beck, E. Wagner-Rousset, D. Ayoub, A. Van Dorsselaer, S. Sanglier-Cianférani, Characterization of therapeutic antibodies and related products. Anal. Chem. 85, 715–736 (2013).
15.
A. Bedrat, L. Lacroix, J.-L. Mergny, Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res. 44, 1746–1759 (2016).
16.
L. Belarif, C. Mary, L. Jacquemont, H. L. Mai, R. Danger, J. Hervouet, D. Minault, V. Thepenier, V. Nerrière-Daguin, E. Nguyen, S. Pengam, E. Largy, A. Delobel, B. Martinet, S. Le Bas-Bernardet, S. Brouard, J.-P. Soulillou, N. Degauque, G. Blancho, B. Vanhove, N. Poirier, IL-7 receptor blockade blunts antigen-specific memory T cell responses and chronic inflammation in primates. Nat. Commun. 9, 4483 (2018).
17.
C. F. Bennett, Therapeutic antisense oligonucleotides are coming of age. Annu. Rev. Med. 70, 307–321 (2019).
18.
A. Berner, R. N. Das, N. Bhuma, J. Golebiewska, A. Abrahamsson, M. Andréasson, N. Chaudhari, M. Doimo, P. P. Bose, K. Chand, R. Strömberg, S. Wanrooij, E. Chorell, G4-ligand-conjugated oligonucleotides mediate selective binding and stabilization of individual G4 DNA structures. J. Am. Chem. Soc. 146, 6926–6935 (2024).
19.
H. Bertrand, S. Bombard, D. Monchaud, M.-P. Teulade-Fichou, A platinum–quinacridine hybrid as a G-quadruplex ligand. JBIC, J. Biol. Inorg. Chem. 12, 1003–1014 (2007).
20.
H. Bertrand, D. Monchaud, A. De Cian, R. Guillot, J.-L. Mergny, M.-P. Teulade-Fichou, The importance of metal geometry in the recognition of G-quadruplex-DNA by metal-terpyridine complexes. Org. Biomol. Chem. 5, 2555 (2007).
21.
H. Bertrand, S. Bombard, D. Monchaud, M.-P. Teulade-Fichou, New platinum(II) complexes targeting the loops of the human telomeric G-quadruplex. Nucleic Acids Symp. Ser. 52, 163–164 (2008).
22.
H. Bertrand, S. Bombard, D. Monchaud, E. Talbot, A. Guédin, J.-L. Mergny, R. Grünert, P. J. Bednarski, M.-P. Teulade-Fichou, Exclusive platination of loop adenines in the human telomeric G-quadruplex. Org. Biomol. Chem. 7, 2864 (2009).
23.
H. Bertrand, A. Granzhan, D. Monchaud, N. Saettel, R. Guillot, S. Clifford, A. Guédin, J.-L. Mergny, M.-P. Teulade-Fichou, Recognition of G-quadruplex DNA by triangular star-shaped compounds: With or without side chains? Chem. – Eur. J. 17, 4529–4539 (2011).
24.
F. Besselièvre, F. Mahuteau-Betzer, D. S. Grierson, S. Piguel, Ligandless microwave-assisted pd/Cu-catalyzed direct arylation of oxazoles. J. Org. Chem. 73, 3278–3280 (2008).
25.
G. Biffi, D. Tannahill, J. McCafferty, S. Balasubramanian, Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013).
26.
B. Bobály, V. D’Atri, A. Beck, D. Guillarme, S. Fekete, Analysis of recombinant monoclonal antibodies in hydrophilic interaction chromatography: A generic method development approach. J. Pharm. Biomed. Anal. 145, 24–32 (2017).
27.
D. L. Boger, B. E. Fink, M. P. Hedrick, Total synthesis of distamycin a and 2640 analogues: A solution-phase combinatorial approach to the discovery of new, bioactive DNA binding agents and development of a rapid, high-throughput screen for determining relative DNA binding affinity or DNA binding sequence selectivity. J. Am. Chem. Soc. 122, 6382–6394 (2000).
28.
D. Boger, Thiazole orange as the fluorescent intercalator in a high resolution fid assay for determining DNA binding affinity and sequence selectivity of small molecules. Bioorg. Med. Chem. 9, 2511–2518 (2001).
29.
D. Bouyssié, J. Lesne, M. Locard-Paulet, R. Albigot, O. Burlet-Schiltz, J. Marcoux, HDX-viewer: Interactive 3D visualization of hydrogen–deuterium exchange data. Bioinformatics 35, 5331–5333 (2019).
30.
N. Branda, G. Kurz, J.-M. Lehn, JANUS WEDGES: A new approach towards nucleobase-pair recognition. Chem. Commun., 2443 (1996).
31.
B. Brauer, M. K. Kesharwani, J. M. L. Martin, Some observations on counterpoise corrections for explicitly correlated calculations on noncovalent interactions. J. Chem. Theory Comput. 10, 3791–3799 (2014).
32.
R. M. Brosh, Put on your thinking cap: G-quadruplexes, helicases, and telomeres. Aging (Milano) 3, 332–335 (2011).
33.
C. I. Butré, E. Largy, A. Delobel, “Profiling of n-linked oligosaccharides of a glycoprotein by UPLC-FLR-ESI-MS after derivatization with fluorescent anthranilamide” (Springer US, 2021), pp. 179–188.
34.
C. I. Butré, E. Largy, F. Cantais, A. Delobel, “Profiling, relative quantification, and identification of sialylated n-linked oligosaccharides by UPLC-FLR-ESI/MS after derivatization with fluorescent anthranilamide” (Springer US, 2021), pp. 237–247.
35.
C. Cajot, A. Delobel, E. Largy, Epitope mapping of an interleukin receptor for three therapeutic antibodies by hydrogen-deuterium exchange mass spectrometry. LCGC: Spec. Issues 16, 8–14 (2018).
36.
N. H. Campbell, G. N. Parkinson, A. P. Reszka, S. Neidle, Structural basis of DNA quadruplex recognition by an acridine drug. J. Am. Chem. Soc. 130, 6722–6724 (2008).
37.
D. A. Case, H. M. Aktulga, K. Belfon, D. S. Cerutti, G. A. Cisneros, V. W. D. Cruzeiro, N. Forouzesh, T. J. Giese, A. W. Götz, H. Gohlke, S. Izadi, K. Kasavajhala, M. C. Kaymak, E. King, T. Kurtzman, T.-S. Lee, P. Li, J. Liu, T. Luchko, R. Luo, M. Manathunga, M. R. Machado, H. M. Nguyen, K. A. O’Hearn, A. V. Onufriev, F. Pan, S. Pantano, R. Qi, A. Rahnamoun, A. Risheh, S. Schott-Verdugo, A. Shajan, J. Swails, J. Wang, H. Wei, X. Wu, Y. Wu, S. Zhang, S. Zhao, Q. Zhu, T. E. Cheatham, D. R. Roe, A. Roitberg, C. Simmerling, D. M. York, M. C. Nagan, K. M. Merz, AmberTools. J. Chem. Inf. Model. 63, 6183–6191 (2023).
38.
S. Ceschi, E. Largy, V. Gabelica, C. Sissi, A two-quartet G-quadruplex topology of human KIT2 is conformationally selected by a perylene derivative. Biochimie 179, 77–84 (2020).
39.
D. Chen, Meena, S. K. Sharma, L. W. McLaughlin, Formation and stability of a janus-wedge type of DNA triplex. J. Am. Chem. Soc. 126, 70–71 (2004).
40.
A. Cheng, C. Liu, W. Ye, D. Huang, W. She, X. Liu, C. P. Fung, N. Xu, M. C. Suen, W. Ye, H. H. Y. Sung, I. D. Williams, G. Zhu, P.-Y. Qian, Selective C9orf72 G-quadruplex-binding small molecules ameliorate pathological signatures of ALS/FTD models. J. Med. Chem. 65, 12825–12837 (2022).
41.
J. K. Chik, J. L. Vande Graaf, D. C. Schriemer, Quantitating the statistical distribution of deuterium incorporation to extend the utility of H/D exchange MS data. Anal. Chem. 78, 207–214 (2006).
42.
G. W. Collie, G. N. Parkinson, S. Neidle, F. Rosu, E. De Pauw, V. Gabelica, Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures. J. Am. Chem. Soc. 132, 9328–9334 (2010).
43.
A. Cucchiarini, M. Dobrovolná, V. Brázda, J.-L. Mergny, Analysis of quadruplex propensity of aptamer sequences. Nucleic Acids Res. 53, gkaf424 (2025).
44.
S. D. Cummings, Platinum complexes of terpyridine: Synthesis, structure and reactivity. Coord. Chem. Rev. 253, 449–478 (2009).
45.
J. Dai, C. Punchihewa, A. Ambrus, D. Chen, R. A. Jones, D. Yang, Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation. Nucleic Acids Res. 35, 2440–2450 (2007).
46.
J. Dai, M. Carver, C. Punchihewa, R. A. Jones, D. Yang, Structure of the hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: Insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res. 35, 4927–4940 (2007).
47.
J. Dai, E. Hatzakis, L. H. Hurley, D. Yang, I-motif structures formed in the human c-MYC promoter are highly dynamic–insights into sequence redundancy and I-motif stability. PLOS One 5, e11647 (2010).
48.
V. D’Atri, D. Guillarme, “Characterization of glycosylated proteins at subunit level by HILIC/MS” (Springer US, 2021), pp. 85–95.
49.
A. De Cian, L. Guittat, K. Shin-ya, J.-F. Riou, J.-L. Mergny, Affinity and selectivity of G4 ligands measured by FRET. Nucleic Acids Symp. Ser. 49, 235–236 (2005).
50.
A. De Cian, L. Lacroix, C. Douarre, N. Temime-Smaali, C. Trentesaux, J.-F. Riou, J.-L. Mergny, Targeting telomeres and telomerase. Biochimie 90, 131–155 (2008).
51.
F. Debaene, A. Bœuf, E. Wagner-Rousset, O. Colas, D. Ayoub, N. Corvaïa, A. Van Dorsselaer, A. Beck, S. Cianférani, Innovative native MS methodologies for antibody drug conjugate characterization: High resolution native MS and IM-MS for average DAR and DAR distribution assessment. Anal. Chem. 86, 10674–10683 (2014).
52.
A. De Cian, E. DeLemos, J.-L. Mergny, M.-P. Teulade-Fichou, D. Monchaud, Highly efficient G-quadruplex recognition by bisquinolinium compounds. J. Am. Chem. Soc. 129, 1856–1857 (2007).
53.
R. Del Villar-Guerra, R. D. Gray, J. B. Chaires, Characterization of quadruplex DNA structure by circular dichroism. Curr. Protoc. Nucleic Acid Chem. 68 (2017).
54.
R. del Villar-Guerra, J. O. Trent, J. B. Chaires, G-quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew. Chem. Int. Ed. 57, 7171–7175 (2018).
55.
P. B. Dervan, Design of sequence-specific DNA-binding molecules. Science 232, 464–471 (1986).
56.
A. Kabbara, C. Buré, A. Guedin, B. Kauffmann, E. Largy, J. Marquevielle, P. Bonnafous, Z. Mdarhri, Y. Ferrand, V. Gabelica, F. Rosu, M.-L. Andreola, C. Olivier, S. Amrane, Dibenzoacridinium derivatives as a new class of G-quadruplex ligands with anti-HIV-1 properties. NAR Mol. Med. (submitted).
57.
N. Q. Do, K. W. Lim, M. H. Teo, B. Heddi, A. T. Phan, Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity. Nucleic Acids Res. 39, 9448–9457 (2011).
58.
M. Dong, T. E. Mürdter, U. Klotz, Telomeres and telomerase as novel drug targets: Reflections on the 2009 nobel prize in physiology or medicine. Eur. J. Clin. Pharmacol. 66, 1–3 (2010).
59.
B. L. Duivelshof, S. Denorme, K. Sandra, X. Liu, A. Beck, M. A. Lauber, D. Guillarme, V. D’Atri, Quantitative N-glycan profiling of therapeutic monoclonal antibodies performed by middle-up level HILIC-HRMS analysis. Pharmaceutics 13, 1744 (2021).
60.
B. L. Duivelshof, A. Beck, D. Guillarme, V. D’Atri, Bispecific antibody characterization by a combination of intact and site-specific/chain-specific LC/MS techniques. Talanta 236, 122836 (2022).
61.
B. Dumat, G. Bordeau, E. Faurel-Paul, F. Mahuteau-Betzer, N. Saettel, M. Bombled, G. Metgé, F. Charra, C. Fiorini-Debuisschert, M.-P. Teulade-Fichou, N-phenyl-carbazole-based two-photon fluorescent probes: Strong sequence dependence of the duplex vs quadruplex selectivity. Biochimie 93, 1209–1218 (2011).
62.
S. A. Dvorkin, A. I. Karsisiotis, M. Webba Da Silva, Encoding canonical DNA quadruplex structure. Sci. Adv. 4, eaat3007 (2018).
63.
K. Elimelech-Zohar, Y. Orenstein, An overview on nucleic-acid G-quadruplex prediction: From rule-based methods to deep neural networks. Briefings Bioinf. 24, bbad252 (2023).
64.
A. Delobel, E. Largy, F. Cantais, G. Van Vyncht, “Characterisation of the glycosylation of enbrel: Etanercept by high resolution mass spectrometry” (Quality Assitance, Donstiennes, Belgique, 2016).
65.
J. R. Engen, T. Botzanowski, D. Peterle, F. Georgescauld, T. E. Wales, Developments in hydrogen/deuterium exchange mass spectrometry. Anal. Chem. 93, 567–582 (2021).
66.
E. Largy, C. Cajot, A. Delobel, “Epitope mapping of an interleukin receptor for three therapeutic antibodies by hydrogen-deuterium exchange mass spectrometry (HDX-MS)” (Quality Assitance, Donstiennes, Belgique, 2017).
67.
M. M. Fay, S. M. Lyons, P. Ivanov, RNA G-quadruplexes in biology: Principles and molecular mechanisms. J. Mol. Biol. 429, 2127–2147 (2017).
68.
P. L. Ferguson, J. Pan, D. J. Wilson, B. Dempsey, G. Lajoie, B. Shilton, L. Konermann, Hydrogen/deuterium scrambling during quadrupole time-of-flight MS/MS analysis of a zinc-binding protein domain. Anal. Chem. 79, 153–160 (2007).
69.
H. Fernando, A. P. Reszka, J. Huppert, S. Ladame, S. Rankin, A. R. Venkitaraman, S. Neidle, S. Balasubramanian, A conserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. Biochemistry 45, 7854–7860 (2006).
70.
M. Folini, L. Venturini, G. Cimino-Reale, N. Zaffaroni, Telomeres as targets for anticancer therapies. Expert Opin. Ther. Targets 15, 579–593 (2011).
71.
T. Fornstedt, M. Enmark, Separation of therapeutic oligonucleotides using ion-pair reversed-phase chromatography based on fundamental separation science. J. Chromatogr. Open 3, 100079 (2023).
72.
P. Froidevaux, J. M. Harrowfield, A. N. Sobolev, Calixarenes as scaffolds: Introduction of tridentate rare earth metal binding units into calix[4]arene. Inorg. Chem. 39, 4678–4687 (2000).
73.
S. Neidle, S. Balasubramanian, Eds., “Fundamentals of quadruplex structures” (The Royal Society of Chemistry, 2006), pp. 1–30.
74.
A. Funke, K. Weisz, Thermodynamic signature of indoloquinolines interacting with G-quadruplexes: Impact of ligand side chain. Biochimie 157, 142–148 (2019).
75.
V. Gabelica, E. Marklund, Fundamentals of ion mobility spectrometry. Curr. Opin. Chem. Biol. 42, 51–59 (2018).
76.
J. Gao, H. A. Pickett, Targeting telomeres: Advances in telomere maintenance mechanism-specific cancer therapies. Nat. Rev. Cancer 22, 515–532 (2022).
77.
J.-M. Garant, J.-P. Perreault, M. S. Scott, G4RNA screener web server: User focused interface for RNA G-quadruplex prediction. Biochimie 151, 115–118 (2018).
78.
R. F. Gesteland, T. Cech, J. F. Atkins, The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World (Cold Spring Harbor Laboratory Press, 2006)Cold spring harbor monograph series.
79.
A. Ghosh, E. Largy, V. Gabelica, DNA G-quadruplexes for native mass spectrometry in potassium: A database of validated structures in electrospray-compatible conditions. Nucleic Acids Res. 49, 2333–2345 (2021).
80.
E. Largy, F. Cantais, G. Van Vyncht, A. Delobel, “Characterisation of the glycosylation of humira (adalimumab) and erbitux (cetuximab) by high resolution mass spectrometry” (Quality Assitance, Donstiennes, Belgique, 2016).
81.
A. Goga, M. Stoffel, Therapeutic RNA-silencing oligonucleotides in metabolic diseases. Nat. Rev. Drug Discovery 21, 417–439 (2022).
82.
A. W. Götz, M. J. Williamson, D. Xu, D. Poole, S. Le Grand, R. C. Walker, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born. J. Chem. Theory Comput. 8, 1542–1555 (2012).
83.
C. Granotier, Preferential binding of a G-quadruplex ligand to human chromosome ends. Nucleic Acids Res. 33, 4182–4190 (2005).
84.
A. Granzhan, E. Largy, N. Saettel, M.-P. Teulade-Fichou, Macrocyclic DNA-mismatch-binding ligands: Structural determinants of selectivity. Chem. – Eur. J. 16, 878–889 (2010).
85.
S. Grimme, J. Antony, T. Schwabe, C. Mück-Lichtenfeld, Density functional theory with dispersion corrections for supramolecular structures, aggregates, and complexes of (bio)organic molecules. Org, Biomol, Chem, 5, 741–758 (2007).
86.
A. Guédin, J. Gros, P. Alberti, J.-L. Mergny, How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res. 38, 7858–7868 (2010).
87.
J. Guillon, C. Denevault-Sabourin, E. Chevret, M. Brachet-Botineau, V. Milano, A. Guédin-Beaurepaire, S. Moreau, L. Ronga, S. Savrimoutou, S. Rubio, J. Ferrer, J. Lamarche, J.-L. Mergny, M.-C. Viaud-Massuard, M. Ranz, E. Largy, V. Gabelica, F. Rosu, F. Gouilleux, V. Desplat, Design, synthesis, and antiproliferative effect of 2,9-bis[4-(pyridinylalkylaminomethyl)phenyl]-1,10-phenanthroline derivatives on human leukemic cells by targeting G-quadruplex. Arch. Pharm. 354, 2000450 (2021).
88.
J. Guillon, A. Cohen, C. Boudot, S. Monic, S. Savrimoutou, S. Moreau, S. Albenque-Rubio, C. Lafon-Schmaltz, A. Dassonville-Klimpt, J.-L. Mergny, L. Ronga, M. Bernabeu De Maria, J. Lamarche, C. D. Lago, E. Largy, V. Gabelica, S. Moukha, P. Dozolme, P. Agnamey, N. Azas, C. Mullié, B. Courtioux, P. Sonnet, Design, synthesis, and antiprotozoal evaluation of new promising 2,9-bis[(substituted-aminomethyl)]-4,7-phenyl-1,10-phenanthroline derivatives, a potential alternative scaffold to drug efflux. Pathogens 11, 1339 (2022).
89.
J. Guillon, M. Le Borgne, V. Milano, A. Guédin-Beaurepaire, S. Moreau, N. Pinaud, L. Ronga, S. Savrimoutou, S. Albenque-Rubio, M. Marchivie, H. Kalout, C. Walker, L. Chevallier, C. Buré, E. Largy, V. Gabelica, J.-L. Mergny, V. Baylot, J. Ferrer, Y. Idrissi, E. Chevret, D. Cappellen, V. Desplat, Z. Schelz, I. Zupkó, New 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinazoline and 2,4-bis[(substituted-aminomethyl)phenyl]phenylquinoline derivatives: Synthesis and biological evaluation as novel anticancer agents by targeting G-quadruplex. Pharmaceuticals 17, 30 (2023).
90.
M. Guttman, D. D. Weis, J. R. Engen, K. K. Lee, Analysis of overlapped and noisy hydrogen/deuterium exchange mass spectra. J. Am. Soc. Mass Spectrom. 24, 1906–1912 (2013).
91.
S. Haider, G. N. Parkinson, S. Neidle, Crystal structure of the potassium form of an oxytricha nova G-quadruplex. J. Mol. Biol. 320, 189–200 (2002).
92.
K. Halder, M. Wieland, J. S. Hartig, Predictable suppression of gene expression by 5′-UTR-based RNA quadruplexes. Nucleic Acids Res. 37, 6811–6817 (2009).
93.
K. Halder, E. Largy, M. Benzler, M.-P. Teulade-Fichou, J. S. Hartig, Efficient suppression of gene expression by targeting 5′-UTR-based RNA quadruplexes with bisquinolinium compounds. ChemBioChem 12, 1663–1668 (2011).
94.
R. Halder, J.-F. Riou, M.-P. Teulade-Fichou, T. Frickey, J. S. Hartig, Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. BMC Res. Notes 5, 138 (2012).
95.
Y.-W. Ham, W. C. Tse, D. L. Boger, High-resolution assessment of protein DNA binding affinity and selectivity utilizing a fluorescent intercalator displacement (FID) assay. Bioorg. Med. Chem. Lett. 13, 3805–3807 (2003).
96.
F. Hamon, E. Largy, A. Guédin-Beaurepaire, M. Rouchon-Dagois, A. Sidibe, D. Monchaud, J.-L. Mergny, J.-F. Riou, C.-H. Nguyen, M.-P. Teulade-Fichou, An acyclic oligoheteroaryle that discriminates strongly between diverse G-quadruplex topologies. Angew. Chem. Int. Ed. 50, 8745–8749 (2011).
97.
B. Helmich-Paris, B. De Souza, F. Neese, R. Izsák, An improved chain of spheres for exchange algorithm. J. Chem. Phys. 155, 104109 (2021).
98.
E. Henderson, C. C. Hardin, S. K. Walk, I. Tinoco, E. H. Blackburn, Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine⋅guanine base pairs. Cell 51, 899–908 (1987).
99.
M. Hernandes, S. M. Cavalcanti, D. R. Moreira, W. De Azevedo Junior, A. C. Leite, Halogen atoms in the modern medicinal chemistry: Hints for the drug design. Curr. Drug Targets 11, 303–314 (2010).
100.
D. J. Hill, M. J. Mio, R. B. Prince, T. S. Hughes, J. S. Moore, A field guide to foldamers. Chem. Rev. 101, 3893–4012 (2001).
101.
J. Hon, T. Martínek, J. Zendulka, M. Lexa, Pqsfinder: An exhaustive and imperfection-tolerant search tool for potential quadruplex-forming sequences in R. Bioinformatics 33, 3373–3379 (2017).
102.
M. P. Horvath, S. C. Schultz, DNA G-quartets in a 1.86 Å resolution structure of an oxytricha nova telomeric protein-DNA complex. J. Mol. Biol. 310, 367–377 (2001).
103.
B. M. Hossain, L. Konermann, Pulsed hydrogen/deuterium exchange MS/MS for studying the relationship between noncovalent protein complexes in solution and in the gas phase after electrospray ionization. Anal. Chem. 78, 1613–1619 (2006).
104.
V. Hourdel, S. Volant, D. P. O’Brien, A. Chenal, J. Chamot-Rooke, M.-A. Dillies, S. Brier, MEMHDX: An interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. Bioinformatics 32, 3413–3419 (2016).
105.
H. Wickham, Httr2: Perform HTTP requests and process the responses. (2023).
106.
J. L. Huppert, S. Balasubramanian, Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908–2916 (2005).
107.
P. K. Iyer, J. B. Beck, C. Weder, S. J. Rowan, Synthesis and optical properties of metallo-supramolecular polymers. Chem. Commun., 319 (2005).
108.
R. R. Iyer, A. Pluciennik, V. Burdett, P. L. Modrich, DNA mismatch repair: Functions and mechanisms. Chem. Rev. 106, 302–323 (2006).
109.
S. Izadi, R. Anandakrishnan, A. V. Onufriev, Building water models: A different approach. J. Phys. Chem. Lett. 5, 3863–3871 (2014).
110.
N. Jain, S. W. Smith, S. Ghone, B. Tomczuk, Current ADC linker chemistry. Pharm. Res. 32, 3526–3540 (2015).
111.
M. K. Janowska, K. Reiter, P. Magala, M. Guttman, R. E. Klevit, HDXBoxeR: An R package for statistical analysis and visualization of multiple hydrogen–deuterium exchange mass-spectrometry datasets of different protein states. Bioinformatics 40, btae479 (2024).
112.
P. V. Jena, P. S. Shirude, B. Okumus, K. Laxmi-Reddy, F. Godde, I. Huc, S. Balasubramanian, T. Ha, G-quadruplex DNA bound by a synthetic ligand is highly dynamic. J. Am. Chem. Soc. 131, 12522–12523 (2009).
113.
J. Jerbi, R. F. Fink, J. Peña-García, D. Arias-Olivares, J. Contreras-García, J. P. Cerón-Carrasco, Quantum effects explain the twist angle in the helical structure of DNA. ChemPhysChem 25, e202400372 (2024).
114.
A. Kabir, M. Bhattarai, K. Ø. Rasmussen, A. Shehu, A. Usheva, A. R. Bishop, B. Alexandrov, Examining DNA breathing with pyDNA-EPBD. Bioinformatics 39, btad699 (2023).
115.
Y. A. Kaiyum, E. Hoi Pui Chao, L. Dhar, A. A. Shoara, M.-D. Nguyen, C. D. Mackereth, P. Dauphin-Ducharme, P. E. Johnson, Ligand-induced folding in a dopamine-binding DNA aptamer. ChemBioChem 25, e202400493 (2024).
116.
Z.-y. Kan, Y. Lin, F. Wang, X.-y. Zhuang, Y. Zhao, D.-w. Pang, Y.-h. Hao, Z. Tan, G-quadruplex formation in human telomeric (TTAGGG)4 sequence with complementary strand in close vicinity under molecularly crowded condition. Nucleic Acids Res. 35, 3646–3653 (2007).
117.
Z.-Y. Kan, L. Mayne, P. Sevugan Chetty, S. W. Englander, ExMS: Data analysis for HX-MS experiments. J. Am. Soc. Mass Spectrom. 22, s13361-11-236-3 (2011).
118.
Z. Kan, X. Ye, J. J. Skinner, L. Mayne, S. W. Englander, ExMS2: An integrated solution for hydrogen–deuterium exchange mass spectrometry data analysis. Anal. Chem. 91, 7474–7481 (2019).
119.
Z. Kan, X. Ye, J. J. Skinner, L. Mayne, S. W. Englander, ExMS2: An integrated solution for hydrogen–deuterium exchange mass spectrometry data analysis. Anal. Chem. 91, 7474–7481 (2019).
120.
B. Karg, S. Mohr, K. Weisz, Duplex-guided refolding into novel G-quadruplex (3+1) hybrid conformations. Angew. Chem. Int. Ed. 58, 11068–11071 (2019).
121.
H. G. Kazemier, K. Paeschke, P. M. Lansdorp, Guanine quadruplex monoclonal antibody 1H6 cross-reacts with restrained thymidine-rich single stranded DNA. Nucleic Acids Res. 45, 5913–5919 (2017).
122.
I. Kejnovská, D. Renčiuk, J. Palacký, M. Vorlíčková, “CD study of the g-quadruplex conformation” (Springer New York, 2019), pp. 25–44.
123.
P. Kharel, S. Balaratnam, N. Beals, S. Basu, The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WIREs RNA 11, e1568 (2020).
124.
N. Khristenko, F. Rosu, E. Largy, J. Haustant, C. Mesmin, V. Gabelica, Native electrospray ionization of multi-domain proteins via a bead ejection mechanism. J. Am. Chem. Soc. 145, 498–506 (2023).
125.
N. Khristenko, F. Rosu, E. Largy, J. Haustant, C. Mesmin, V. Gabelica, Native electrospray ionization of multi-domain proteins via a bead ejection mechanism. J. Am. Chem. Soc. 145, 498–506 (2023).
126.
O. Kikin, L. D’Antonio, P. S. Bagga, QGRS mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34, W676–W682 (2006).
127.
M.-Y. Kim, H. Vankayalapati, K. Shin-ya, K. Wierzba, L. H. Hurley, Telomestatin, a potent telomerase inhibitor that interacts quite specifically with the human telomeric intramolecular G-quadruplex. J. Am. Chem. Soc. 124, 2098–2099 (2002).
128.
J. Kim, S. Woo, C. M. De Gusmao, B. Zhao, D. H. Chin, R. L. DiDonato, M. A. Nguyen, T. Nakayama, C. A. Hu, A. Soucy, A. Kuniholm, J. K. Thornton, O. Riccardi, D. A. Friedman, C. M. El Achkar, Z. Dash, L. Cornelissen, C. Donado, K. N. W. Faour, L. W. Bush, V. Suslovitch, C. Lentucci, P. J. Park, E. A. Lee, A. Patterson, A. A. Philippakis, B. Margus, C. B. Berde, T. W. Yu, A framework for individualized splice-switching oligonucleotide therapy. Nature 619, 828–836 (2023).
129.
D. Knapton, M. Burnworth, S. J. Rowan, C. Weder, Fluorescent organometallic sensors for the detection of chemical-warfare-agent mimics. Angew. Chem. 118, 5957–5961 (2006).
130.
F. Koeppel, Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quadruplexes. Nucleic Acids Res. 29, 1087–1096 (2001).
131.
D. Koirala, S. Dhakal, B. Ashbridge, Y. Sannohe, R. Rodriguez, H. Sugiyama, S. Balasubramanian, H. Mao, A single-molecule platform for investigation of interactions between G-quadruplexes and small-molecule ligands. Nat. Chem. 3, 782–787 (2011).
132.
A. König, V. Laffilé, S. Thore, C. D. Mackereth, L. Yatsunyk, Y. Ferrand, E. Largy, V. Gabelica, Helical aromatic oligoamide foldamers as selective G- quadruplex ligands (accepted).
133.
N. Kosiol, S. Juranek, P. Brossart, A. Heine, K. Paeschke, G-quadruplexes: A promising target for cancer therapy. Mol. Cancer 20, 40 (2021).
134.
A. Kotar, R. Rigo, C. Sissi, J. Plavec, Two-quartet kit* G-quadruplex is formed via double-stranded pre-folded structure. Nucleic Acids Res. 47, 2641–2653 (2019).
135.
R. C. Kretsch, R. Albrecht, E. S. Andersen, H.-A. Chen, W. Chiu, R. Das, J. G. Gezelle, M. D. Hartmann, C. Höbartner, Y. Hu, S. Jadhav, P. E. Johnson, C. P. Jones, D. Koirala, E. L. Kristoffersen, E. Largy, A. Lewicka, C. D. Mackereth, M. Marcia, M. Nigro, M. Ojha, J. A. Piccirilli, P. A. Rice, H. Shin, A.-L. Steckelberg, Z. Su, Y. Srivastava, L. Wang, Y. Wu, J. Xie, N. H. Zwergius, J. Moult, A. Kryshtafovych, Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers. Proteins (2025).
136.
F. Kröhnke, The specific synthesis of pyridines and Oligopyridines1. Synthesis 1976, 1–24 (1976).
137.
S. Kumar, S. P. P. Pany, S. Sudhakar, S. B. Singh, C. S. Todankar, P. I. Pradeepkumar, Targeting parallel topology of G-quadruplex structures by indole- fused quindoline scaffolds. Biochemistry 61, 2546–2559 (2022).
138.
S. Kumari, A. Bugaut, J. L. Huppert, S. Balasubramanian, An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 3, 218–221 (2007).
139.
V. Kuryavyi, A. Majumdar, A. Shallop, N. Chernichenko, E. Skripkin, R. Jones, D. J. Patel, A double chain reversal loop and two diagonal loops define the architecture of unimolecular DNA quadruplex containing a pair of stacked G(syn)⋅G(syn)⋅G(anti)⋅G(anti) tetrads flanked by a G⋅(T-T) triad and a T⋅T⋅T triple11Edited by M. F. Summers. J. Mol. Biol. 310, 181–194 (2001).
140.
P. Kuzmič, Program DYNAFIT for the analysis of enzyme kinetic data: Application to HIV proteinase. Anal. Biochem. 237, 260–273 (1996).
141.
P. Kuzmič, “DynaFit—a software package for enzymology” (Elsevier, 2009), pp. 247–280.
142.
J. Kypr, I. Kejnovska, D. Renciuk, M. Vorlickova, Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37, 1713–1725 (2009).
143.
D. Labudová, J. Hon, M. Lexa, Pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm. Bioinformatics 36, 2584–2586 (2020).
144.
E. Y. N. Lam, D. Beraldi, D. Tannahill, S. Balasubramanian, G-quadruplex structures are stable and detectable in human genomic DNA. Nat. Commun. 4, 1796 (2013).
145.
H. Lardeux, D. Guillarme, V. D’Atri, Comprehensive evaluation of zwitterionic hydrophilic liquid chromatography stationary phases for oligonucleotide characterization. J. Chromatogr. A 1690, 463785 (2023).
146.
E. Largy, F. Hamon, F. Rosu, V. Gabelica, E. De Pauw, A. Guédin, J.-L. Mergny, M.-P. Teulade-Fichou, Tridentate N-donor palladium(II) complexes as efficient coordinating quadruplex DNA binders. Chem. – Eur. J. 17, 13274–13283 (2011).
147.
E. Largy, F. Hamon, M.-P. Teulade-Fichou, Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures. Anal. Bioanal. Chem. 400, 3419–3427 (2011).
148.
E. Largy, F. Hamon, M.-P. Teulade-Fichou, A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes. Methods 57, 129–137 (2012).
149.
E. Largy, N. Saettel, F. Hamon, S. Dubruille, M.-P. Teulade-Fichou, Screening of a chemical library by HT-G4-FID for discovery of selective G-quadruplex binders. Curr. Pharm. Des. 18, 1992–2001 (2012).
150.
E. Largy, M.-P. Teulade-Fichou, “Screening for quadruplex binding ligands: A game of chance?” (Royal Society of Chemistry, 2012), pp. 248–262.
151.
E. Largy, A. Granzhan, F. Hamon, D. Verga, M.-P. Teulade-Fichou, “Visualizing the quadruplex: From fluorescent ligands to light-up probes” (Springer Berlin Heidelberg, 2012), pp. 111–177.
152.
E. Largy, W. Liu, A. Hasan, D. M. Perrin, Base-pairing behavior of a carbocyclic janus-AT nucleoside analogue capable of recognizing a and T within a DNA duplex. ChemBioChem 14, 2199–2208 (2013).
153.
E. Largy, W. Liu, A. Hasan, D. M. Perrin, A pyrimidopyrimidine janus-AT nucleoside with improved base-pairing properties to both a and T within a DNA duplex: The stabilizing effect of a second endocyclic ring nitrogen. Chem. – Eur. J. 20, 1495–1499 (2014).
154.
E. Largy, J.-L. Mergny, Shape matters: Size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Res. 42, e149–e149 (2014).
155.
E. Largy, A. Marchand, S. Amrane, V. Gabelica, J.-L. Mergny, Quadruplex turncoats: Cation-dependent folding and stability of quadruplex-DNA double switches. J. Am. Chem. Soc. 138, 2780–2792 (2016).
156.
E. Largy, J.-L. Mergny, V. Gabelica, “Role of alkali metal ions in g-quadruplex nucleic acid structure and stability” (Springer International Publishing, 2016), pp. 203–258.
157.
E. Largy, F. Cantais, G. Van Vyncht, A. Beck, A. Delobel, Orthogonal liquid chromatography–mass spectrometry methods for the comprehensive characterization of therapeutic glycoproteins, from released glycans to intact protein level. J. Chromatogr. A 1498, 128–146 (2017).
158.
E. Largy, V. Gabelica, Native hydrogen/deuterium exchange mass spectrometry of structured DNA oligonucleotides. Anal. Chem. 92, 4402–4410 (2020).
159.
E. Largy, A. König, A. Ghosh, D. Ghosh, S. Benabou, F. Rosu, V. Gabelica, Mass spectrometry of nucleic acid noncovalent complexes. Chem. Rev. 122, 7720–7839 (2022).
160.
E. Largy, B. Alies, G. Condesse, A. Gaubert, T. Livingston, K. Gaudin, Teaching with simulation tools to introduce the basics of analytical chemistry instrumentation. Anal. Bioanal. Chem. 414, 6709–6721 (2022).
161.
E. Largy, M. Ranz, OligoR: A native HDX/MS data processing application dedicated to oligonucleotides. Anal. Chem. 95, 9615–9622 (2023).
162.
E. Largy, M. Ranz, V. Gabelica, DNA-HDXMS_XchangeDB: A dataset of hydrogen-deuterium eXchange native mass spectrometry experiments on DNA oligonucleotides (2023). https://doi.org/10.5281/ZENODO.7713144.
163.
E. Largy, M. Ranz, V. Gabelica, A general framework to interpret hydrogen–deuterium exchange native mass spectrometry of G-quadruplex DNA. J. Am. Chem. Soc. 145, 26843–26857 (2023).
164.
E. Largy, A. Guédin, A. Kabbara, J.-L. Mergny, S. Amrane, Eps2Fold: A rapid method to characterize G-quadruplex DNA structures using single absorbance spectra. Nucleic Acids Res. 53, gkaf953 (2025).
165.
R. A. Laskowski, M. B. Swindells, LigPlot+: Multiple ligand–protein interaction diagrams for drug discovery. J. Chem. Inf. Model. 51, 2778–2786 (2011).
166.
A. M. C. Lau, Z. Ahdash, C. Martens, A. Politis, Deuteros: Software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry. Bioinformatics 35, 3171–3173 (2019).
167.
A. M. Lau, J. Claesen, K. Hansen, A. Politis, Deuteros 2.0: Peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry. Bioinformatics 37, 270–272 (2021).
168.
T. Le Doan, L. Perrouault, D. Praseuth, N. Habhoub, J.-L. Decout, N. T. Thuong, J. Lhomme, C. Héène, Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-(α]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 15, 7749–7760 (1987).
169.
S. Le Grand, A. W. Götz, R. C. Walker, SPFP: Speed without compromise—a mixed precision model for GPU accelerated molecular dynamics simulations. Comput. Phys. Commun. 184, 374–380 (2013).
170.
S. Lemieux, RNA canonical and non-canonical base pairing types: A recognition method and complete repertoire. Nucleic Acids Res. 30, 4250–4263 (2002).
171.
N. B. Leontis, E. Westhof, Geometric nomenclature and classification of RNA base pairs. RNA 7, 499–512 (2001).
172.
H. L. Lightfoot, T. Hagen, N. J. Tatum, J. Hall, The diverse structural landscape of quadruplexes. FEBS Lett. 593, 2083–2102 (2019).
173.
K. W. Lim, S. Amrane, S. Bouaziz, W. Xu, Y. Mu, D. J. Patel, K. N. Luu, A. T. Phan, Structure of the human telomere in K+ solution: A stable basket-type G-quadruplex with only two G-tetrad layers. J. Am. Chem. Soc. 131, 4301–4309 (2009).
174.
R. Lindner, X. Lou, J. Reinstein, R. L. Shoeman, F. A. Hamprecht, A. Winkler, Hexicon 2: Automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. J. Am. Soc. Mass Spectrom. 25, 1018–1028 (2014).
175.
X. Liu, E. J. L. McInnes, C. A. Kilner, M. Thornton-Pett, M. A. Halcrow, Metal complexes of 4′-(3-phenylpropoxy)-2,2′:6′,2″-terpyridine and 4′-(3-propoxy)-2,2′:6′,2″-terpyridine. Polyhedron 20, 2889–2900 (2001).
176.
H. Liu, G. Ponniah, H.-M. Zhang, C. Nowak, A. Neill, N. Gonzalez-Lopez, R. Patel, G. Cheng, A. Z. Kita, B. Andrien, In vitro and in vivo modifications of recombinant and human IgG antibodies. mAbs 6, 1145–1154 (2014).
177.
C. Liu, B. Zhou, Y. Geng, D. Yan Tam, R. Feng, H. Miao, N. Xu, X. Shi, Y. You, Y. Hong, B. Z. Tang, P. Kwan Lo, V. Kuryavyi, G. Zhu, A chair-type G-quadruplex structure formed by a human telomeric variant DNA in K+ solution. Chem. Sci. 10, 218–226 (2019).
178.
W. Long, B.-X. Zheng, Y. Li, X.-H. Huang, D.-M. Lin, C.-C. Chen, J.-Q. Hou, T.-M. Ou, W.-L. Wong, K. Zhang, Y.-J. Lu, Rational design of small-molecules to recognize G-quadruplexes of c-MYC promoter and telomere and the evaluation of their in Vivo antitumor activity against breast cancer. Nucleic Acids Res. 50, 1829–1848 (2022).
179.
X. Lou, M. Kirchner, B. Y. Renard, U. Köthe, S. Boppel, C. Graf, C.-T. Lee, J. A. J. Steen, H. Steen, M. P. Mayer, F. A. Hamprecht, Deuteration distribution estimation with improved sequence coverage for HX/MS experiments. Bioinformatics 26, 1535–1541 (2010).
180.
X.-J. Lu, H. J. Bussemaker, W. K. Olson, DSSR: An integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res., gkv716 (2015).
181.
X. Lu, L. F. M. Passalacqua, M. Nodwell, K. Y. S. Kong, G. Caballero-García, E. V. Dolgosheina, A. R. Ferré-D’Amaré, R. Britton, P. J. Unrau, Symmetry breaking of fluorophore binding to a G-quadruplex generates an RNA aptamer with picomolar KD. Nucleic Acids Res. 52, 8039–8051 (2024).
182.
R. J. Lumpkin, E. A. Komives, DECA, a comprehensive, automatic post-processing program for HDX-MS data*. Mol. Cell. Proteomics 18, 2516–2523 (2019).
183.
K. E. Lundin, O. Gissberg, C. I. E. Smith, Oligonucleotide therapies: The past and the present. Hum. Gene Ther. 26, 475–485 (2015).
184.
I. D. Lutz, S. Wang, C. Norn, A. Courbet, A. J. Borst, Y. T. Zhao, A. Dosey, L. Cao, J. Xu, E. M. Leaf, C. Treichel, P. Litvicov, Z. Li, A. D. Goodson, P. Rivera-Sánchez, A.-M. Bratovianu, M. Baek, N. P. King, H. Ruohola-Baker, D. Baker, Top-down design of protein architectures with reinforcement learning. Science 380, 266–273 (2023).
185.
K. N. Luu, A. T. Phan, V. Kuryavyi, L. Lacroix, D. J. Patel, Structure of the human telomere in K+ solution: An intramolecular (3 + 1) G-quadruplex scaffold. J. Am. Chem. Soc. 128, 9963–9970 (2006).
186.
M. R. Machado, S. Pantano, Split the charge difference in two! A rule of thumb for adding proper amounts of ions in MD simulations. J. Chem. Theory Comput. 16, 1367–1372 (2020).
187.
P. K. Mandal, B. Baptiste, B. Langlois d’Estaintot, B. Kauffmann, I. Huc, Multivalent interactions between an aromatic helical foldamer and a DNA G-quadruplex in the solid state. ChemBioChem 17, 1911–1914 (2016).
188.
A. Marchand, V. Gabelica, Native electrospray mass spectrometry of DNA G-quadruplexes in potassium solution. J. Am. Soc. Mass Spectrom. 25, 1146–1154 (2014).
189.
A. Marchand, V. Gabelica, Folding and misfolding pathways of G-quadruplex DNA. Nucleic Acids Res. 44, 10999–11012 (2016).
190.
G. R. Masson, J. E. Burke, N. G. Ahn, G. S. Anand, C. Borchers, S. Brier, G. M. Bou-Assaf, J. R. Engen, S. W. Englander, J. Faber, R. Garlish, P. R. Griffin, M. L. Gross, M. Guttman, Y. Hamuro, A. J. R. Heck, D. Houde, R. E. Iacob, T. J. D. Jørgensen, I. A. Kaltashov, J. P. Klinman, L. Konermann, P. Man, L. Mayne, B. D. Pascal, D. Reichmann, M. Skehel, J. Snijder, T. S. Strutzenberg, E. S. Underbakke, C. Wagner, T. E. Wales, B. T. Walters, D. D. Weis, D. J. Wilson, P. L. Wintrode, Z. Zhang, J. Zheng, D. C. Schriemer, K. D. Rand, Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat. Methods 16, 595–602 (2019).
191.
I. Maurizio, B. Tosoni, I. Gallina, E. Ruggiero, I. Zanin, S. N. Richter, “Production of the anti-G-quadruplex antibody BG4 for efficient genome-wide analyses: From plasmid quality control to antibody validation” (Elsevier, 2024), pp. 193–219.
192.
J.-L. Mergny, L. Lacroix, Analysis of thermal melting curves. Oligonucleotides 13, 515–537 (2003).
193.
J.-L. Mergny, Thermal difference spectra: A specific signature for nucleic acid structures. Nucleic Acids Res. 33, e138–e138 (2005).
194.
J.-L. Mergny, D. Sen, DNA quadruple helices in nanotechnology. Chem. Rev. 119, 6290–6325 (2019).
195.
E. Micheli, C. M. Lombardo, D. D’Ambrosio, M. Franceschin, S. Neidle, M. Savino, Selective G-quadruplex ligands: The significant role of side chain charge density in a series of perylene derivatives. Bioorg. Med. Chem. Lett. 19, 3903–3908 (2009).
196.
P. Mignon, Influence of the - interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucleic Acids Res. 33, 1779–1789 (2005).
197.
D. Monchaud, C. Allain, M.-P. Teulade-Fichou, Development of a fluorescent intercalator displacement assay (G4-FID) for establishing quadruplex-DNA affinity and selectivity of putative ligands. Bioorg. Med. Chem. Lett. 16, 4842–4845 (2006).
198.
D. Monchaud, M.-P. Teulade-Fichou, A hitchhiker’s guide to G-quadruplex ligands. Org, Biomol, Chem, 6, 627–636 (2008).
199.
D. Monchaud, C. Allain, H. Bertrand, N. Smargiasso, F. Rosu, V. Gabelica, A. De Cian, J.-L. Mergny, M.-P. Teulade-Fichou, Ligands playing musical chairs with G-quadruplex DNA: A rapid and simple displacement assay for identifying selective G-quadruplex binders. Biochimie 90, 1207–1223 (2008).
200.
D. Monchaud, M.-P. Teulade-Fichou, “G4-FID: A fluorescent DNA probe displacement assay for rapid evaluation of quadruplex ligands” (Humana Press, 2009), pp. 257–271.
201.
M. J. B. Moore, C. M. Schultes, J. Cuesta, F. Cuenca, M. Gunaratnam, F. A. Tanious, W. D. Wilson, S. Neidle, Trisubstituted acridines as G-quadruplex telomere targeting agents. Effects of extensions of the 3,6- and 9-side chains on quadruplex binding, telomerase activity, and cell proliferation. J. Med. Chem. 49, 582–599 (2006).
202.
M. J. Morris, S. Basu, An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry 48, 5313–5319 (2009).
203.
S. Müller, K. Laxmi-Reddy, P. V. Jena, B. Baptiste, Z. Dong, F. Godde, T. Ha, R. Rodriguez, S. Balasubramanian, I. Huc, Targeting DNA G-quadruplexes with helical small molecules. ChemBioChem 15, 2563–2570 (2014).
204.
C. C. Mundorff, S. Hadley, L. M. Tuttle, Y. Shi, G. C. McAlister, R. Viner, R. E. Klevit, M. Guttman, Mapping hydrogen migration thresholds for site-specific HDX-MS. Mol. Cell. Proteomics 24, 101075 (2025).
205.
P. Murat, Y. Singh, E. Defrancq, Methods for investigating G-quadruplex DNA/ligand interactions. Chem. Soc. Rev. 40, 5293 (2011).
206.
S. Na, J.-J. Lee, J. W. J. Joo, K.-J. Lee, E. Paek, deMix: Decoding deuterated distributions from heterogeneous protein states via HDX-MS. Sci. Rep. 9, 3176 (2019).
207.
M. Nadai, S. N. Richter, “G-quadruplex visualization in cells via antibody and fluorescence probe” (Springer New York, 2019), pp. 383–395.
208.
N. Nakatsuka, K.-A. Yang, J. M. Abendroth, K. M. Cheung, X. Xu, H. Yang, C. Zhao, B. Zhu, Y. S. Rim, Y. Yang, P. S. Weiss, M. N. Stojanović, A. M. Andrews, Aptamer–field-effect transistors overcome debye length limitations for small-molecule sensing. Science 362, 319–324 (2018).
209.
S. Neidle, M. A. Read, G-quadruplexes as therapeutic targets. Biopolymers 56, 195–208 (2000).
210.
S. Neidle, Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J. 277, 1118–1125 (2010).
211.
S. Neidle, Beyond the double helix: DNA structural diversity and the PDB. J. Biol. Chem. 296, 100553 (2021).
212.
G. N. Parkinson, M. P. H. Lee, S. Neidle, Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417, 876–880 (2002).
213.
M. Petenzi, D. Verga, E. Largy, F. Hamon, F. Doria, M.-P. Teulade-Fichou, A. Guédin, J.-L. Mergny, M. Mella, M. Freccero, Cationic pentaheteroaryls as selective G-quadruplex ligands by solvent-free microwave-assisted synthesis. Chem. – Eur. J. 18, 14487–14496 (2012).
214.
A. T. Phan, V. Kuryavyi, J.-B. Ma, A. Faure, M.-L. Andréola, D. J. Patel, An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase. Proc. Natl. Acad. Sci. 102, 634–639 (2005).
215.
A. T. Phan, V. Kuryavyi, D. J. Patel, DNA architecture: From G to Z. Curr. Opin. Struct. Biol. 16, 288–298 (2006).
216.
A. T. Phan, V. Kuryavyi, K. N. Luu, D. J. Patel, Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K + solution . Nucleic Acids Res. 35, 6517–6525 (2007).
217.
A. Piazza, J.-B. Boulé, J. Lopes, K. Mingo, E. Largy, M.-P. Teulade-Fichou, A. Nicolas, Genetic instability triggered by G-quadruplex interacting phen-DC compounds in saccharomyces cerevisiae. Nucleic Acids Res. 38, 4337–4348 (2010).
218.
B. Prasad, M. Doimo, M. Andréasson, V. L’Hôte, E. Chorell, S. Wanrooij, A complementary chemical probe approach towards customized studies of G-quadruplex DNA structures in live cells. Chem. Sci. 13, 2347–2354 (2022).
219.
A. Delobel, F. Dusserre-Bresson, E. Largy, C. Lepers, C. Mantini, C. Plennevaux, F. Vandermeers, “Analytical approaches for the evaluation of ADCC activity of mAbs” (Quality Assitance, Donstiennes, Belgique, 2017).
220.
W. Puchała, M. Burdukiewicz, M. Kistowski, K. A. Dąbrowska, A. E. Badaczewska-Dawid, D. Cysewski, M. Dadlez, HaDeX: An R package and web-server for analysis of data from hydrogen–deuterium exchange mass spectrometry experiments. Bioinformatics 36, 4516–4518 (2020).
221.
G. Qin, Z. Liu, J. Yang, X. Liao, C. Zhao, J. Ren, X. Qu, Targeting specific DNA G-quadruplexes with CRISPR-guided G-quadruplex-binding proteins and ligands. Nat. Cell Biol. 26, 1212–1224 (2024).
222.
E.-A. Raiber, R. Kranaster, E. Lam, M. Nikan, S. Balasubramanian, A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. Nucleic Acids Res. 40, 1499–1508 (2012).
223.
K. D. Rand, M. Zehl, T. J. D. Jørgensen, Measuring the hydrogen/deuterium exchange of proteins at high spatial resolution by mass spectrometry: Overcoming gas-phase hydrogen/deuterium scrambling. Acc. Chem. Res. 47, 3018–3027 (2014).
224.
M. Read, R. J. Harrison, B. Romagnoli, F. A. Tanious, S. H. Gowan, A. P. Reszka, W. D. Wilson, L. R. Kelland, S. Neidle, Structure-based design of selective and potent G quadruplex-mediated telomerase inhibitors. Proc. Natl. Acad. Sci. 98, 4844–4849 (2001).
225.
J. E. Reed, A. J. P. White, S. Neidle, R. Vilar, Effect of metal coordination on the interaction of substituted phenanthroline and pyridine ligands with quadruplex DNA. Dalton Trans., 2558 (2009).
226.
J. Ren, J. B. Chaires, Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 38, 16067–16075 (1999).
227.
A. Renaud De La Faverie, F. Hamon, C. Di Primo, E. Largy, E. Dausse, L. Delaurière, C. Landras-Guetta, J.-J. Toulmé, M.-P. Teulade-Fichou, J.-L. Mergny, Nucleic acids targeted to drugs: SELEX against a quadruplex ligand. Biochimie 93, 1357–1367 (2011).
228.
M. Renders, S. Dumbre, M. Abramov, D. Kestemont, L. Margamuljana, E. Largy, C. Cozens, J. Vandenameele, V. B. Pinheiro, D. Toye, J.-M. Frère, P. Herdewijn, Kinetic analysis of N -alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases. Nucleic Acids Res. 47, 2160–2168 (2019).
229.
D. Rhodes, H. J. Lipps, G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627–8637 (2015).
230.
R. Rigo, W. L. Dean, R. D. Gray, J. B. Chaires, C. Sissi, Conformational profiling of a G-rich sequence within the c-KIT promoter. Nucleic Acids Res. 45, 13056–13067 (2017).
231.
D. R. Roe, B. R. Brooks, A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. J. Chem. Phys. 153, 54123 (2020).
232.
L. Rossetti, M. Franceschin, A. Bianco, G. Ortaggi, M. Savino, Perylene diimides with different side chains are selective in inducing different G-quadruplex DNA structures and in inhibiting telomerase. Bioorg. Med. Chem. Lett. 12, 2527–2533 (2002).
233.
S. Rottenberg, C. Disler, P. Perego, The rediscovery of platinum-based cancer therapy. Nat. Rev. Cancer 21, 37–50 (2021).
234.
C. Roxo, W. Kotkowiak, A. Pasternak, G-quadruplex-forming aptamers—characteristics, applications, and perspectives. Molecules 24, 3781 (2019).
235.
R. G. Sadygov, Poisson model to generate isotope distribution for biomolecules. J. Proteome Res. 17, 751–758 (2018).
236.
W. Saenger, Principles of Nucleic Acid Structure (Springer New York, 1984).
237.
J. Sági, A. Szemzõ, J. Szécsi, L. Ötvös, Biochemical properties of oligo[(+)]-carbocyclic-thymidylates] and their complexes. Nucleic Acids Res. 18, 2133–2140 (1990).
238.
J. P. Salisbury, Q. Liu, J. N. Agar, QUDeX-MS: Hydrogen/deuterium exchange calculation for mass spectra with resolved isotopic fine structure. BMC Bioinf. 15, 403 (2014).
239.
R. Salomon-Ferrer, A. W. Götz, D. Poole, S. Le Grand, R. C. Walker, Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh ewald. J. Chem. Theory Comput. 9, 3878–3888 (2013).
240.
J. D. Schmit, N. L. Kariyawasam, V. Needham, P. E. Smith, SLTCAP: A simple method for calculating the number of ions needed for MD simulation. J. Chem. Theory Comput. 14, 1823–1827 (2018).
241.
J. Keirstead, Scholar: Analyse citation data from Google scholar. (2016).
242.
N. Seetaloo, M. Kish, J. J. Phillips, HDfleX : Software for flexible high structural resolution of hydrogen/deuterium-exchange mass spectrometry data. Anal. Chem. 94, 4557–4564 (2022).
243.
D. Sehnal, S. Bittrich, M. Deshpande, R. Svobodová, K. Berka, V. Bazgier, S. Velankar, S. K. Burley, J. Koča, A. S. Rose, Mol* viewer: Modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49, W431–W437 (2021).
244.
D. Sen, W. Gilbert, The structure of telomeric DNA: DNA quadriplex formation. Curr. Opin. Struct. Biol. 1, 435–438 (1991).
245.
X. Shen, B. Gu, S. A. Che, F. S. Zhang, Solvent effects on the conformation of DNA dodecamer segment: A simulation study. J. Chem. Phys. 135, 34509 (2011).
246.
A. Sidibe, F. Hamon, E. Largy, D. Gomez, M.-P. Teulade-Fichou, C. Trentesaux, J.-F. Riou, Effects of a halogenated G-quadruplex ligand from the pyridine dicarboxamide series on the terminal sequence of XpYp telomere in HT1080 cells. Biochimie 94, 2559–2568 (2012).
247.
J. H. Smit, S. Krishnamurthy, B. Y. Srinivasu, R. Parakra, S. Karamanou, A. Economou, Probing universal protein dynamics using hydrogen–deuterium exchange mass spectrometry-derived residue-level gibbs free energy. Anal. Chem. 93, 12840–12847 (2021).
248.
E. Largy, A. Delobel, “Stress testing of humira (adalimumab) monitored by hydrogen-deuterium exchange mass spectrometry (HDX-MS)” (Quality Assitance, Donstiennes, Belgique, 2017).
249.
A. V. Tataurov, Y. You, R. Owczarzy, Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys. Chem. 133, 66–70 (2008).
250.
V. Voynov, J. A. Caravella, Eds., Therapeutic Proteins (Humana Press, 2012).
251.
V. A. Traag, P. Van Dooren, Y. Nesterov, Narrow scope for resolution-limit-free community detection. Phys. Rev. E 84, 16114 (2011).
252.
M. Trajkovski, M. Webba Da Silva, J. Plavec, Unique structural features of interconverting monomeric and dimeric G-quadruplexes adopted by a sequence from the intron of the N-myc gene. J. Am. Chem. Soc. 134, 4132–4141 (2012).
253.
P. L. T. Tran, E. Largy, F. Hamon, M.-P. Teulade-Fichou, J.-L. Mergny, Fluorescence intercalator displacement assay for screening G4 ligands towards a variety of G-quadruplex structures. Biochimie 93, 1288–1296 (2011).
254.
A. Tsalmpouris, E. Largy, D. Guillarme, Systematic evaluation of phenyl stationary phases for oligonucleotide analysis without ion-pairing reagents. J. Chromatogr. A 1762, 466395 (2025).
255.
T. G. Uil, Therapeutic modulation of endogenous gene function by agents with designed DNA-sequence specificities. Nucleic Acids Res. 31, 6064–6078 (2003).
256.
E. Largy, A. Catrain, G. Van Vyncht, A. Delobel, 2D-LC–MS for the analysis of monoclonal antibodies and antibody–drug conjugates in a regulated environment. LCGC: Spec. Issues 14, 29–35 (2016).
257.
D. Varshney, J. Spiegel, K. Zyner, D. Tannahill, S. Balasubramanian, The regulation and functions of DNA and RNA G-quadruplexes. Nat. Rev. Mol. Cell Biol. 21, 459–474 (2020).
258.
P. H. Von Hippel, N. P. Johnson, A. H. Marcus, Fifty years of DNA “breathing”: Reflections on old and new approaches. Biopolymers 99, 923–954 (2013).
259.
A. H. J. Wang, G. Ughetto, G. J. Quigley, A. Rich, Interactions between an anthracycline antibiotic and DNA: Molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1.2-.ANG. resolution. Biochemistry 26, 1152–1163 (1987).
260.
Y. Wang, D. J. Patel, Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure 1, 263–282 (1993).
261.
J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case, Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).
262.
Z. Wang, H. Sun, X. Yao, D. Li, L. Xu, Y. Li, S. Tian, T. Hou, Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: The prediction accuracy of sampling power and scoring power. Phys. Chem. Chem. Phys. 18, 12964–12975 (2016).
263.
Q. Wang, N. B. Borotto, K. Håkansson, Gas-phase hydrogen/deuterium scrambling in negative-ion mode tandem mass spectrometry. J. Am. Soc. Mass Spectrom. 30, 855–863 (2019).
264.
R. Wang, M.-H. Hu, Development of a fluorescent ligand that specifically binds to the c-MYC G-quadruplex by migrating the benzene group on a carbazole-benzothiazolium scaffold. Bioorg. Chem. 151, 107690 (2024).
265.
D. D. Weis, J. R. Engen, I. J. Kass, Semi-automated data processing of hydrogen exchange mass spectra using HX-express. J. Am. Soc. Mass Spectrom. 17, 1700–1703 (2006).
266.
D. D. Weis, T. E. Wales, J. R. Engen, M. Hotchko, L. F. Ten Eyck, Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Am. Soc. Mass Spectrom. 17, 1498–1509 (2006).
267.
M. Wieland, J. S. Hartig, RNA quadruplex-based modulation of gene expression. Chem. Biol. 14, 757–763 (2007).
268.
C. Williams, D. Richardson, J. Richardson, High quality protein residues: Top2018 mainchain-filtered residues (2021). https://doi.org/10.5281/ZENODO.5777651.
269.
C. J. Williams, D. C. Richardson, J. S. Richardson, The importance of residue-level filtering and the Top2018 best-parts dataset of high-quality protein residues. Protein Sci. 31, 290–300 (2022).
270.
J. R. Williamson, M. K. Raghuraman, T. R. Cech, Monovalent cation-induced structure of telomeric DNA: The G-quartet model. Cell 59, 871–880 (1989).
271.
D. T. W. Wollenberg, S. Pengelley, J. C. Mouritsen, D. Suckau, C. I. Jørgensen, T. J. D. Jørgensen, Avoiding H/D scrambling with minimal ion transmission loss for HDX-MS/MS-ETD analysis on a high-resolution Q-TOF mass spectrometer. Anal. Chem. 92, 7453–7461 (2020).
272.
H. M. Wong, O. Stegle, S. Rodgers, J. L. Huppert, A toolbox for predicting G-quadruplex formation and stability. J. Nucleic Acids 2010, 564946 (2010).
273.
X. Xie, B. Choi, E. Largy, R. Guillot, A. Granzhan, M.-P. Teulade-Fichou, Asymmetric distyrylpyridinium dyes as red-emitting fluorescent probes for quadruplex DNA. Chem. – Eur. J. 19, 1214–1226 (2013).
274.
T. Yamamoto, T. Yamagaki, H. Satake, Development of software for the In-depth analysis of protein dynamics as determined by MALDI mass spectrometry-based hydrogen/deuterium exchange. Mass Spectrom. 8, S0082–S0082 (2020).
275.
Q.-Z. Yang, L.-Z. Wu, Z.-X. Wu, L.-P. Zhang, C.-H. Tung, Long-lived emission from platinum(II) terpyridyl acetylide complexes. Inorg. Chem. 41, 5653–5655 (2002).
276.
P. Yang, A. De Cian, M.-P. Teulade-Fichou, J.-L. Mergny, D. Monchaud, Engineering bisquinolinium/thiazole orange conjugates for fluorescent sensing of G-quadruplex DNA. Angew. Chem. Int. Ed. 48, 2188–2191 (2009).
277.
B. K. S. Yeung, W. C. Tse, D. L. Boger, Determination of binding affinities of triplex forming oligonucleotides using a fluorescent intercalator displacement (FID) assay. Bioorg. Med. Chem. Lett. 13, 3801–3804 (2003).
278.
L. C. Young, J. B. Hays, V. A. Tron, S. E. Andrew, DNA mismatch repair proteins: Potential guardians against genomic instability and tumorigenesis induced by ultraviolet photoproducts. J. Invest. Dermatol. 121, 435–440 (2003).
279.
A. Zaid, J.-S. Sun, C.-H. Nguyen, E. Bisagni, T. Garestier, D. S. Grierson, R. Zain, Triple-helix directed cleavage of double-stranded DNA by benzoquinoquinoxaline-1,10-phenanthroline conjugates. ChemBioChem 5, 1550–1557 (2004).
280.
Y. Zeng, Y. Pratumyot, X. Piao, D. Bong, Discrete assembly of synthetic peptide–DNA triplex structures from polyvalent melamine–thymine bifacial recognition. J. Am. Chem. Soc. 134, 832–835 (2012).
281.
W. Zhang, C. Bensimon, R. J. Crutchley, (Terpyridine)palladium(II) complexes of phenylcyanamide ligands. Inorg. Chem. 32, 5808–5812 (1993).
282.
Z. Zhang, J. Dai, E. Veliath, R. A. Jones, D. Yang, Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: Insights into the interconversion of human telomeric G-quadruplex structures. Nucleic Acids Res. 38, 1009–1021 (2010).
283.
N. Zhang, X. Yu, X. Zhang, S. D’Arcy, HD-eXplosion: Visualization of hydrogen–deuterium exchange data as chiclet and volcano plots with statistical filtering. Bioinformatics 37, 1926–1927 (2021).
284.
J. Zhou, S. Amrane, F. Rosu, G. F. Salgado, Y. Bian, H. Tateishi-Karimata, E. Largy, D. N. Korkut, A. Bourdoncle, D. Miyoshi, J. Zhang, H. Ju, W. Wang, N. Sugimoto, V. Gabelica, J.-L. Mergny, Unexpected position-dependent effects of ribose G-quartets in G-quadruplexes. J. Am. Chem. Soc. 139, 7768–7779 (2017).
285.
M. Zuffo, A. Guédin, E.-D. Leriche, F. Doria, V. Pirota, V. Gabelica, J.-L. Mergny, M. Freccero, More is not always better: Finding the right trade-off between affinity and selectivity of a G-quadruplex ligand. Nucleic Acids Res. 46, e115–e115 (2018).