To understand the role of ribose G-quartets and how they affect the properties of G-quadruplex structures, we studied three systems in which one, two, three, or four deoxyribose G-quartets were substituted with ribose G-quartets. These systems were a parallel DNA intramolecular G-quadruplex, d(TTGGGTGGGTTGGGTGGGTT), and two tetramolecular G-quadruplexes, d(TGGGT) and d(TGGGGT). Thermal denaturation experiments revealed that ribose G-quartets have position-dependent and cumulative effects on G-quadruplex stability. An unexpected destabilization was observed when rG quartets were presented at the 5'-end of the G stack. This observation challenges the general belief that RNA residues stabilize G-quadruplexes. Furthermore, in contrast to past proposals, hydration is not the main factor determining the stability of our RNA/DNA chimeric G-quadruplexes. Interestingly, the presence of rG residues in a central G-quartet facilitated the formation of additional tetramolecular G-quadruplex topologies showing positive circular dichroism signals at 295 nm. 2D NMR analysis of the tetramolecular TGgGGT (lowercase letter indicates ribose) indicates that Gs in the 5'-most G-quartet adopt the syn conformation. These analyses highlight several new aspects of the role of ribose G-quartets on G-quadruplex structure and stability, and demonstrate that the positions of ribose residues are critical for tuning G-quadruplex properties.

Collaborative Innovation Center of Advanced Microstructures and Department of Physics Nanjing University Nanjing 210093 China

Frontier Institute for Biomolecular Engineering Research Konan University 7 1 20 Minatojima minamimachi Chuo ku Kobe 650 0047 Japan

Institute of Biophysics of the CAS v v i Královopolská 135 612 65 Brno Czech Republic

Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics Institute of Biophysics Dezhou University Dezhou 253023 China

State Key Laboratory of Analytical Chemistry for Life Science School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 China

Université de Bordeaux CNRS UMS 3033 INSERM US001 IECB F 33600 Pessac France

Université de Bordeaux INSERM U1212 CNRS UMR 5320 ARNA Laboratory IECB F 33600 Pessac France

References provided by Crossref.org

Diversity of Parallel Guanine Quadruplexes Induced by Guanine Substitutions