2015
DOI: 10.1007/s00239-015-9712-x
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Sequence Mutation and Structural Alteration Transform a Noncatalytic DNA Sequence into an Efficient RNA-Cleaving DNAzyme

Abstract: We have previously shown that through test-tube molecular evolution, an arbitrarily chosen noncatalytic DNA sequence can be evolved into a catalytic DNA (DNAzyme) with significant RNA-cleaving activity. In this study, we aim to address the question of whether the catalytic activity of such a DNAzyme can be further optimized using in vitro selection. Several cycles of selective enrichment starting with a partially randomized DNA library have resulted in the isolation of many sequence variations that show notabl… Show more

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Cited by 12 publications
(8 citation statements)
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“…By round 16, the DNA pool showed a significant improvement in geniposide-dependent elution: geniposide was able to elude ~25% of column-bound DNA while the mixture of genipin and glucose produced about 3% elution. The pool from round 16 was then subjected to deep sequencing followed a previously published protocol [ 39 , 40 , 41 ]. Top 6 sequence classes are listed in Table 2 (see details of deep sequencing result in Supplementary Materials Table S1 ).…”
Section: Resultsmentioning
confidence: 99%
“…By round 16, the DNA pool showed a significant improvement in geniposide-dependent elution: geniposide was able to elude ~25% of column-bound DNA while the mixture of genipin and glucose produced about 3% elution. The pool from round 16 was then subjected to deep sequencing followed a previously published protocol [ 39 , 40 , 41 ]. Top 6 sequence classes are listed in Table 2 (see details of deep sequencing result in Supplementary Materials Table S1 ).…”
Section: Resultsmentioning
confidence: 99%
“…This is especially useful for DNAzymes, as studies have shown that just a few nucleotide changes can make a difference in the DNAzyme activity under different conditions . Reselection has been used to improve the activity of DNAzymes by more than 500-fold …”
Section: Advantages Of Dnazymes As Activity-based Sensorsmentioning
confidence: 99%
“…For example, the Spinach2 aptamer [5] regulates the fluorescence of a fluorophore via binding, providing an interesting alternative to GFP tagging. In vitro selection has been applied to discover a variety of ribozymes [6], deoxyribozymes [7], aptazymes [8], and riboswitches [9]. With appropriate polymerase enzymes, selection experiments can even be done with non-natural nucleic acids, as shown for a series of xeno-nucleic acids (XNAs).…”
Section: In Vitro Evolution and Fitness Landscapes Of Nucleic Acidsmentioning
confidence: 99%