title: Conformational studies of 10-23 DNAzyme in solution through pyrenyl-labeled 2'-deoxyadenosine derivatives.
abstract: 10-23 DNAzyme is a small catalytic DNA molecule. Studies on its conformation in solution are critical for understanding its catalytic mechanism and functional optimization. Based on our previous research, two fluorescent nucleoside analogues 1 and 2 were designed for the introduction of a pyrenyl group at one of the five dA residues in the catalytic core and the unpaired adenosine residue in its full-DNA substrate, respectively. Ten pyrenyl-pyrenyl pairs are formed in the DNAzyme-substrate complexes in solution for sensing the spacial positions of the five dA residues relative to the cleavage site using fluorescence spectra. The position-dependent quenching effect of pyrene emission fluorescence by nucleobases, especially the pyrenyl-pyrenyl interaction, was observed for some positions. The adenine residues in the 3'-part of the catalytic loop seem to be closer to the cleavage site than the adenine residues in the 5'-part, which is consistent with the molecular dynamics simulation result. The catalytic activities and Tmchanges also confirmed the effect of the pyrenyl-nucleobase and pyrenyl-pyrenyl pair interactions. Together with functional group mutations, catalytically relevant nucleobases will be identified for understanding the catalytic mechanism of 10-23 DNAzyme.
authors.affiliation: College of Life Science, Guizhou University, Guiyang 550025, China.
authors.forename: Zhiwen
authors.initials: Z
authors.lastname: Li
authors.affiliation: College of Life Science, Guizhou University, Guiyang 550025, China.
authors.forename: Junfei
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China. hejunlin@bmi.ac.cn.
authors.forename: Junlin
authors.initials: J
authors.lastname: He
mesh_terms: D055162:Biocatalysis; D021881:DNA, Catalytic / Q000737:chemistry* / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism*; D003839:Deoxyadenosines / Q000737:chemistry* / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011721:Pyrenes / Q000737:chemistry*; D012996:Solutions
chemical_list: D021881:DNA, Catalytic; D004277:DNA, Single-Stranded; D003839:Deoxyadenosines; D011721:Pyrenes; C402582:RNA-cleaving DNA 10-23; D012996:Solutions; C030984:pyrene; C058118:2'-deoxyadenosine