Abstract
When not constrained to long double-helical arrangements, DNA is capable of forming structural arrangements that enable specific sequences to perform functions such as binding and catalysis under defined conditions. Through a process called in vitro selection, numerous catalytic DNAs, known as deoxyribozymes or DNAzymes, have been isolated. Many of these molecules have the potential to act as therapeutic agents and diagnostic tools. As such, a better understanding of the structural arrangements present in these functional DNAs will aid further efforts in the development and optimization of these useful molecules. Structural characterization of several deoxyribozymes through mutagenesis, in vitro re-selection, chemical probing and circular dichroism has revealed many distinct and elaborate structural classes. Deoxyribozymes have been found to contain diverse structural elements including helical junctions, pseudoknots, triplexes, and guanine quadruplexes. Some of these studies have further shown the repeated isolation of similar structural motifs in independent selection experiments for the same type of chemical reaction, suggesting that some structural motifs are well suited for catalyzing a specific chemical reaction. To investigate the extent of structural diversity possible in deoxyribozymes, a group of kinase deoxyribozymes have been extensively characterized. Such studies have discovered some interesting structural features of these DNAzymes while revealing some novel DNA structures.
Highlights
Nucleic acids were once thought to be used solely for the storage and transfer of genetic information in living cells, with proteins performing other cellular functions such as catalysis
High-resolution study of these deoxyribozymes will be of particular value as it can reveal the exact nature of these interactions and show which structural folds are preferable to DNAzymes that function at low pH
The revelation that deoxyribozymes adopt various complex structural arrangements to carry out catalysis on nucleic acid-based substrates or nucleic acid-containing substrates suggests that DNA may be capable of “creating” more complex structures needed to perform more difficult or more diverse reactions that involve non-nucleic acid substrates
Summary
Nucleic acids were once thought to be used solely for the storage and transfer of genetic information in living cells, with proteins performing other cellular functions such as catalysis. Several more catalytic DNA molecules, called deoxyribozymes or DNAzymes, have been isolated to catalyze other biologically relevant chemical reactions (reviewed in [11,12,13]), such as DNA ligation [14,15], RNA ligation and branching [16,17,18], DNA phosphorylation [19,20], DNA adenylation [21], DNA cleavage [22], DNA hydrolysis [23], porphyrin metalation [24], thymine dimer repair [25], nucleopeptide bond formation [26], and carbon-carbon bond formation [27] Despite these many examples of DNA-mediated catalysis, it is noteworthy that most of the DNAzymes isolated to date bind and process nucleic acid-containing substrates. Deoxyribozymes isolated through in vitro selection have been shown to use many different arrangements in their active structures, such as Watson-Crick helices and higher-order structures containing guanine quadruplex and triple helix motifs
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
