Genomic sequences susceptible to form G-quadruplexes (G4s) are always flanked by other nucleotides, but G4 formation in vitro is generally studied with short synthetic DNA or RNA oligonucleotides, for which bases adjacent to the G4 core are often omitted. Herein, we systematically studied the effects of flanking nucleotides on structural polymorphism of 371 different oligodeoxynucleotides that adopt intramolecular G4 structures. We found out that the addition of nucleotides favors the formation of a parallel fold, defined as the 'flanking effect' in this work. This 'flanking effect' was more pronounced when nucleotides were added at the 5'-end, and depended on loop arrangement. NMR experiments and molecular dynamics simulations revealed that flanking sequences at the 5'-end abolish a strong syn-specific hydrogen bond commonly found in non-parallel conformations, thus favoring a parallel topology. These analyses pave a new way for more accurate prediction of DNA G4 folding in a physiological context.

ARNA Laboratory Université de Bordeaux Inserm U1212 CNRS UMR5320 IECB Pessac33607 France

Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

Laboratoire d'Optique et Biosciences Ecole Polytechnique CNRS Inserm Institut Polytechnique de Paris 91128Palaiseau cedex France

Regional Centre of Advanced Technologies and Materials Czech Advanced Technology and Research Institute Palacky University Olomouc Šlechtitelů 241 27 783 71 Olomouc Holice Czech Republic

State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing210023 China

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Mergny J.-L., Sen D.. DNA quadruple helices in nanotechnology. Chem. Rev. 2019; 119:6290–6325. PubMed

Chaires J.B., Graves D.. Quadruplex Nucleic Acids. 2013; Springer.

Kwok C.K., Merrick C.J.. G-Quadruplexes: prediction, characterization, and biological application. Trends Biotechnol. 2017; 35:997–1013. PubMed

Tian T., Chen Y.-Q., Wang S.-R., Zhou X.. G-Quadruplex: a regulator of gene expression and its chemical targeting. Chem. 2018; 4:1314–1344.

Spiegel J., Adhikari S., Balasubramanian S.. The structure and function of DNA G-quadruplexes. Trends Chem. 2020; 2:123–136. PubMed PMC

Cheng M., Cheng Y., Hao J., Jia G., Zhou J., Mergny J.-L., Li C.. Loop permutation affects the topology and stability of G-quadruplexes. Nucleic Acids Res. 2018; 46:9264–9275. PubMed PMC

Risitano A., Fox K.R.. Influence of loop size on the stability of intramolecular DNA quadruplexes. Nucleic Acids Res. 2004; 32:2598–2606. PubMed PMC

Hazel P., Huppert J., Balasubramanian S., Neidle S.. Loop-length-dependent folding of G-quadruplexes. J. Am. Chem. Soc. 2004; 126:16405–16415. PubMed

Smargiasso N., Rosu F., Hsia W., Colson P., Baker E.S., Bowers M.T., De Pauw E., Gabelica V.. G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation. J. Am. Chem. Soc. 2008; 130:10208–10216. PubMed

Kettani A., Bouaziz S., Wang W., Jones R.A., Patel D.J.. Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads. Nat. Struct. Biol. 1997; 4:382–389. PubMed

Do N.Q., Phan A.T.. Monomer-dimer equilibrium for the 5′-5′ stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study. Chem. Eur. J. 2012; 18:14752–14759. PubMed

Pavc D., Wang B., Spindler L., Drevensek-Olenik I., Plavec J., Sket P.. GC ends control topology of DNA G-quadruplexes and their cation-dependent assembly. Nucleic Acids Res. 2020; 48:2749–2761. PubMed PMC

Hatzakis E., Okamoto K., Yang D.. Thermodynamic stability and folding kinetics of the major G-quadruplex and its loop isomers formed in the nuclease hypersensitive element in the human c-Myc promoter: effect of loops and flanking segments on the stability of parallel-stranded intramolecular G-quadruplexes. Biochemistry. 2010; 49:9152–9160. PubMed PMC

Zhang Z., Dai J., Veliath E., Jones R.A., Yang D.. 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. 2010; 38:1009–1021. PubMed PMC

Phan A.T.Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J. 2010; 277:1107–1117. PubMed

Dai J., Carver M., Yang D.. Polymorphism of human telomeric quadruplex structures. Biochimie. 2008; 90:1172–1183. PubMed PMC

Del Villar-Guerra R., Trent J.O., Chaires J.B.. G-Quadruplex secondary structure obtained from circular dichroism spectroscopy. Angew. Chem. Int. Ed. 2018; 57:7171–7175. PubMed PMC

Mergny J.-L., Phan A.T., Lacroix L.. Following G-quartet formation by UV-spectroscopy. FEBS Lett. 1998; 435:74–78. PubMed

Mergny J.-L., Li J., Lacroix L., Amrane S., Chaires J.B.. Thermal difference spectra: a specific signature for nucleic acid structures. Nucleic Acids Res. 2005; 33:e138. PubMed PMC

Phan A.T.Long-range imino proton-13C J-couplings and the through-bond correlation of imino and non-exchangeable protons in unlabeled DNA. J. Biomol. NMR. 2000; 16:175–178. PubMed

Clark G.R., Pytel P.D., Squire C.J.. The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages. Nucleic Acids Res. 2012; 40:5731–5738. PubMed PMC

Wang Y., Patel D.J.. Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure. 1993; 1:263–282. PubMed

Luu K.N., Phan A.T., Kuryavyi V., Lacroix L., Patel D.J.. Structure of the human telomere in K+ solution: an intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc. 2006; 128:9963–9970. PubMed PMC

Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W.et al. .. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000; 33:889–897. PubMed

Islam B., Stadlbauer P., Neidle S., Haider S., Sponer J.. Can we execute reliable MM-PBSA free energy computations of relative stabilities of different guanine quadruplex folds. J. Phys. Chem. B. 2016; 120:2899–2912. PubMed

Case D., Ben-Shalom I., Brozell S., Cerutti D., Cheatham T. III, Cruzeiro V., Darden T., Duke R., Ghoreishi D., Gilson M.K.et al. .. 2018; San Francisco. AMBER 2018.

Zgarbova M., Šponer J., Otyepka M., Cheatham T.E. 3rd, Galindo-Murillo R., Jurecka P.. Refinement of the sugar-phosphate backbone torsion beta for AMBER force fields improves the description of Z- and B-DNA. J. Chem. Theory Comput. 2015; 11:5723–5736. PubMed

Largy E., Marchand A., Amrane S., Gabelica V., Mergny J.-L.. Quadruplex turncoats: cation-dependent folding and stability of quadruplex-DNA double switches. J. Am. Chem. Soc. 2016; 138:2780–2792. PubMed

Dvorkin S.A., Karsisiotis A.I., Webba da Silva M.. Encoding canonical DNA quadruplex structure. Sci. Adv. 2018; 4:eaat3007. PubMed PMC

Largy E., Mergny J.-L.. Shape matters: size-exclusion HPLC for the study of nucleic acid structural polymorphism. Nucleic Acids Res. 2014; 42:e149. PubMed PMC

Cang X., Šponer J., Cheatham T.E. 3rd. Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res. 2011; 39:4499–4512. PubMed PMC

Šponer J., Mladek A., Spackova N., Cang X.H., Cheatham T.E., Grimme S.. Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations. J. Am. Chem. Soc. 2013; 135:9785–9796. PubMed PMC

Travascio P., Li Y., Sen D.. DNA-enhanced peroxidase activity of a DNA-aptamer-hemin complex. Chem. Biol. 1998; 5:505–517. PubMed

Puig Lombardi E., Londono-Vallejo A.. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res. 2020; 48:1–15. PubMed PMC

Rodriguez R., Miller K.M., Forment J.V., Bradshaw C.R., Nikan M., Britton S., Oelschlaegel T., Xhemalce B., Balasubramanian S., Jackson S.P.. Small-molecule-induced DNA damage identifies alternative DNA structures in human genes. Nat. Chem. Biol. 2012; 8:301–310. PubMed PMC

Chambers V.S., Marsico G., Boutell J.M., Di Antonio M., Smith G.P., Balasubramanian S.. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat. Biotechnol. 2015; 33:877–881. PubMed

Gray R.D., Trent J.O., Chaires J.B.. Folding and unfolding pathways of the human telomeric G-quadruplex. J. Mol. Biol. 2014; 426:1629–1650. PubMed PMC

Li X.M., Zheng K.W., Zhang J.Y., Liu H.H., Yuan B.F., Hao Y.H., Tan Z.. Guanine-vacancy–bearing G-quadruplexes responsive to guanine derivatives. Proc. Natl. Acad. Sci. U.S.A. 2015; 112:14581–14586. PubMed PMC

Winnerdy F.R., Das P., Heddi B., Phan A.T.. Solution structures of a G-quadruplex bound to linear-and cyclic-dinucleotides. J. Am. Chem. Soc. 2019; 141:18038–18047. PubMed

Mukundan V.T., Phan A.T.. Bulges in G-quadruplexes: broadening the definition of G-quadruplex-forming sequences. J. Am. Chem. Soc. 2013; 135:5017–5028. PubMed

RNA G-quadruplex formation in biologically important transcribed regions: can two-tetrad intramolecular RNA quadruplexes be formed?

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations

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