The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K+, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. 1D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.

ARNA Laboratory Inserm U 1212 CNRS UMR5320 IECB Université de Bordeaux Pessac France; Institute of Biophysics of the CAS v v i Královopolská 135 612 65 Brno Czech Republic

Dalian National Laboratory of Clean Energy Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

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

State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China; Dalian National Laboratory of Clean Energy Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China

State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences Dalian 116023 China; University of Chinese Academy of Sciences No 19A Yuquan Road Beijing 100049 China

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Loop permutation affects the topology and stability of G-quadruplexes