scholarly journals In Vitro Selection of an ATP-Binding TNA Aptamer

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4194
Author(s):  
Li Zhang ◽  
John C. Chaput
Keyword(s):  
In Vitro Selection ◽  
Hydrolytic Enzymes ◽  
Atp Binding ◽  
Biological Stability ◽  
Protein Targets ◽  
Dna And Rna ◽  
Nuclease Digestion ◽  
Polymerase Engineering ◽  
Threose Nucleic Acid

Recent advances in polymerase engineering have made it possible to isolate aptamers from libraries of synthetic genetic polymers (XNAs) with backbone structures that are distinct from those found in nature. However, nearly all of the XNA aptamers produced thus far have been generated against protein targets, raising significant questions about the ability of XNA aptamers to recognize small molecule targets. Here, we report the evolution of an ATP-binding aptamer composed entirely of α-L-threose nucleic acid (TNA). A chemically synthesized version of the best aptamer sequence shows high affinity to ATP and strong specificity against other naturally occurring ribonucleotide triphosphates. Unlike its DNA and RNA counterparts that are susceptible to nuclease digestion, the ATP-binding TNA aptamer exhibits high biological stability against hydrolytic enzymes that rapidly degrade DNA and RNA. Based on these findings, we suggest that TNA aptamers could find widespread use as molecular recognition elements in diagnostic and therapeutic applications that require high biological stability.

scholarly journals In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule

2020 ◽  
Vol 48 (4) ◽  
pp. 1669-1680 ◽  
Author(s):  
Sougata Dey ◽  
Jonathan T Sczepanski
Keyword(s):  
In Vitro Selection ◽  
Rna Binding ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
Binding Properties ◽  
Rna Molecules ◽  
Dna And Rna ◽  
Selection Of

Abstract The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.

In Vitro Selection of ATP-Binding Receptors Using a Ribonucleopeptide Complex

2002 ◽  
Vol 124 (17) ◽  
pp. 4617-4622 ◽  
Author(s):  
Takashi Morii ◽  
Masaki Hagihara ◽  
Shin-ichi Sato ◽  
Keisuke Makino
Keyword(s):  
In Vitro Selection ◽  
Atp Binding ◽  
Selection Of

In Vitro Selection Procedures for Identifying DNA and RNA Aptamers Targeted to Nucleic Acids and Proteins

2004 ◽  
pp. 391-410
Author(s):  
Eric Dausse ◽  
Christian Cazenave ◽  
Bernard Rayner ◽  
Jean-Jacques Toulmé
Keyword(s):  
Nucleic Acids ◽  
In Vitro Selection ◽  
Rna Aptamers ◽  
Selection Procedures ◽  
Dna And Rna

scholarly journals Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders

2020 ◽  
Author(s):  
SIDDIK SARKAR ◽  
TARUN SHARMA ◽  
DEBLEENA BASU ◽  
SOURABRATA CHAKRABORTY ◽  
RIDDHI PAL
Keyword(s):  
First Generation ◽  
In Vitro Selection ◽  
Fungal Infections ◽  
In Vitro System ◽  
Nuclease Digestion ◽  
History Of ◽  
Novel Biomarkers ◽  
Exponential Enrichment ◽  
Selection Of

Aptamer is short sequence of synthetic oligonucleotides which bind to their cognate target specifically while maintaining similar or higher sensitivity as antibody. Small size, chemical synthesis, low batch variation, cost effectiveness, long shelf life and above all low immunogenicity provide advantages over antibody. The in-vitro selection of aptamer applying a conjoining approach of chemistry and molecular biology is referred as Systematic Evolution of Ligands by Exponential enrichment (SELEX). These initial products of SELEX are considered as first generation aptamers, further modified chemically in an attempt to make it stable in biofluid avoiding nuclease digestion and renal clearance. These types of aptamers are called second generation aptamers. While modification is incorporated, enough care should be taken to maintain its sensitivity and specificity. These modifications and several improvisations have widened the window frame of aptamer application that is currently not only restricted to in-vitro system, but have been used in molecular imaging for disease pathology and treatment. In food industry it is used as sensor for detection of different diseases or fungal infections. In this review we have discussed a brief history of its journey, process of synthesis, different types of modifications to improve its characters. We have also focused on its applications and highlighted its role as therapeutic plus diagnostic; theranostic tools. Finally, the review is concluded with a brief discussion on future prospective in immunotherapy, as well as in identification of novel biomarkers in stem cell, and also in single cell proteomics (scProteomics) to study intra or intertumor heterogeneity at protein level.

scholarly journals Identification and Engineering of Aptamers for Theranostic Application in Human Health and Disorders

2021 ◽  
Vol 22 (18) ◽  
pp. 9661
Author(s):  
Debleena Basu ◽  
Sourabrata Chakraborty ◽  
Riddhi Pal ◽  
Tarun Kumar Sharma ◽  
Siddik Sarkar
Keyword(s):  
Human Health ◽  
In Vitro Selection ◽  
Fungal Infections ◽  
Chemical Properties ◽  
Nuclease Digestion ◽  
History Of ◽  
In Vitro Systems ◽  
Novel Biomarkers ◽  
Physical And Chemical

An aptamer is a short sequence of synthetic oligonucleotides which bind to their cognate target, specifically while maintaining similar or higher sensitivity compared to an antibody. The in-vitro selection of an aptamer, applying a conjoining approach of chemistry and molecular biology, is referred as Systematic Evolution of Ligands by Exponential enrichment (SELEX). These initial products of SELEX are further modified chemically in an attempt to make them stable in biofluid, avoiding nuclease digestion and renal clearance. While the modification is incorporated, enough care should be taken to maintain its sensitivity and specificity. These modifications and several improvisations have widened the window frame of aptamer applications that are currently not only restricted to in-vitro systems, but have also been used in molecular imaging for disease pathology and treatment. In the food industry, it has been used as sensor for detection of different diseases and fungal infections. In this review, we have discussed a brief history of its journey, along with applications where its role as a therapeutic plus diagnostic (theranostic) tool has been demonstrated. We have also highlighted the potential aptamer-mediated strategies for molecular targeting of COVID-19. Finally, the review focused on its future prospective in immunotherapy, as well as in identification of novel biomarkers in stem cells and also in single cell proteomics (scProteomics) to study intra or inter-tumor heterogeneity at the protein level. Small size, chemical synthesis, low batch variation, cost effectiveness, long shelf life and low immunogenicity provide advantages to the aptamer over the antibody. These physical and chemical properties of aptamers render them as a strong biomedical tool for theranostic purposes over the existing ones. The significance of aptamers in human health was the key finding of this review.

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