Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method

Recently, aptamers get the attention of many scientist, because they have all advantages of antibodies which found in human body. They also have unique merits like thermal stability, low cost, and many more. Aptamers are the short sequence nucleic acid with a high affinity and specificity. It is globally adopted as a one of the advance and promising drug delivery technique. These aptamers are produced by in vitro selection method using SELEX technique. This review contains the discussion on the aspect of design, unique properties, applications of aptamers to aid in cancer diagnosis, prevention and treatment under fine condition. Finally, several medical and analytical applications are presented.

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Analysis of the P7 region within the catalytic core of the Tetrahymena ribozyme by employing in vitro selection

Nucleic Acids Symposium Series ◽

10.1093/nass/44.1.197 ◽

2000 ◽

Vol 44 (1) ◽

pp. 197-198 ◽

Cited By ~ 2

Author(s):

Y. Oe ◽

Y. Ikawa ◽

H. Shiraishi ◽

T. Inoue

Keyword(s):

In Vitro Selection ◽

Catalytic Core

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Zn2+-dependent DNAzymes that cleave all combinations of ribonucleotides

Communications Biology ◽

10.1038/s42003-021-01738-6 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Rika Inomata ◽

Jing Zhao ◽

Makoto Miyagishi

Keyword(s):

In Vitro Selection ◽

Sequence Similarity ◽

Sequencing Analysis ◽

Sequence Specificity ◽

Rna Sequences ◽

Catalytic Core ◽

Highly Active ◽

Target Rna ◽

Deep Sequencing Analysis

AbstractAlthough several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each DNAzyme showed different Zn2+-concentration and pH-dependent reaction profiles, and cleaved the target RNA sequences at different sites. Using various substrate RNA sequences, we found that the cleavage sequence specificity of ZincDz2 and its highly active mutant ZincDz2-v2 to be 5′-rN↓rNrPu-3′. Furthermore, we demonstrated that the designed ZincDz2 could cut microRNA miR-155 at three different sites. These DNAzymes could be useful in a broad range of applications in the fields of medicine and biotechnology.

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In vitro selections with RNAs of variable length converge on a robust catalytic core

Nucleic Acids Research ◽

10.1093/nar/gkaa1238 ◽

2020 ◽

Author(s):

Milena Popović ◽

Alexander Q Ellingson ◽

Theresa P Chu ◽

Chenyu Wei ◽

Andrew Pohorille ◽

...

Keyword(s):

In Vitro Selection ◽

Point Mutations ◽

Rna Structures ◽

Catalytic Core ◽

Basic Principles ◽

Rna Ligase ◽

Rna Evolution ◽

Conserved Core ◽

Functional Rnas

Abstract In vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.

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