DNA and RNA Aptamers as Modulators of Protein Function

2005 ◽  
Vol 1 (2) ◽  
pp. 199-208 ◽  
Author(s):  
Henning Ulrich
Keyword(s):  
Protein Function ◽  
Rna Aptamers ◽  
Dna And Rna

DNA and RNA Aptamers: From Tools for Basic Research Towards Therapeutic Applications

2006 ◽  
Vol 9 (8) ◽  
pp. 619-632 ◽  
Author(s):  
Henning Ulrich ◽  
Cleber Trujillo ◽  
Arthur Nery ◽  
Janaina Alves ◽  
Paromita Majumder ◽  
...  
Keyword(s):  
Basic Research ◽  
Rna Aptamers ◽  
Therapeutic Applications ◽  
Dna And Rna

scholarly journals A Combined ELONA-(RT)qPCR Approach for Characterizing DNA and RNA Aptamers Selected against PCBP-2

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1213 ◽  
Author(s):  
Miguel Moreno ◽  
María Fernández-Algar ◽  
Javier Fernández-Chamorro ◽  
Jorge Ramajo ◽  
Encarnación Martínez-Salas ◽  
...  
Keyword(s):  
Binding Capacity ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
General Strategy ◽  
Label Free ◽  
Mobility Shift ◽  
Real Time Quantitative Pcr ◽  
High Affinity ◽  
Dna And Rna ◽  
Electrophoretic Mobility Shift Assays

Improvements in Systematic Evolution of Ligands by EXponential enrichment (SELEX) technology and DNA sequencing methods have led to the identification of a large number of active nucleic acid molecules after any aptamer selection experiment. As a result, the search for the fittest aptamers has become a laborious and time-consuming task. Herein, we present an optimized approach for the label-free characterization of DNA and RNA aptamers in parallel. The developed method consists in an Enzyme-Linked OligoNucleotide Assay (ELONA) coupled to either real-time quantitative PCR (qPCR, for DNA aptamers) or reverse transcription qPCR (RTqPCR, for RNA aptamers), which allows the detection of aptamer-target interactions in the high femtomolar range. We have applied this methodology to the affinity analysis of DNA and RNA aptamers selected against the poly(C)-binding protein 2 (PCBP-2). In addition, we have used ELONA-(RT)qPCR to quantify the dissociation constant (Kd) and maximum binding capacity (Bmax) of 16 high affinity DNA and RNA aptamers. The Kd values of the high affinity DNA aptamers were compared to those derived from colorimetric ELONA performed in parallel. Additionally, Electrophoretic Mobility Shift Assays (EMSA) were used to confirm the binding of representative PCBP-2-specific RNA aptamers in solution. We propose this ELONA-(RT)qPCR approach as a general strategy for aptamer characterization, with a broad applicability in biotechnology and biomedicine.

scholarly journals Oligonucleotide-based systems: DNA, microRNAs, DNA/RNA aptamers

2016 ◽  
Vol 60 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Pawan Jolly ◽  
Pedro Estrela ◽  
Michael Ladomery
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Rna Aptamers ◽  
Locked Nucleic Acid ◽  
Synthetic Analogue ◽  
Dna And Rna ◽  
Naturally Occurring ◽  
Wide Range ◽  
Synthetic Oligonucleotides ◽  
Shed Light

There are an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte is a strand of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) or a synthetic analogue of naturally occurring nucleic acids. This review will shed light on various types of nucleic acids such as DNA and RNA (particularly microRNAs), their role and their application in biosensing. It will also cover DNA/RNA aptamers, which can be used as bioreceptors for a wide range of targets such as proteins, small molecules, bacteria and even cells. It will also highlight how the invention of synthetic oligonucleotides such as peptide nucleic acid (PNA) or locked nucleic acid (LNA) has pushed the limits of molecular biology and biosensor development to new perspectives. These technologies are very promising albeit still in need of development in order to bridge the gap between the laboratory-based status and the reality of biomedical applications.

scholarly journals Selection of DNA aptamers with two modified bases

2017 ◽  
Vol 114 (11) ◽  
pp. 2898-2903 ◽  
Author(s):  
Bharat N. Gawande ◽  
John C. Rohloff ◽  
Jeffrey D. Carter ◽  
Ira von Carlowitz ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Chemical Diversity ◽  
Rna Aptamers ◽  
Dna Aptamers ◽  
Dramatic Improvement ◽  
Protein Targets ◽  
Dna And Rna ◽  
Modified Dna ◽  
Pyrimidine Bases ◽  
Representative Protein ◽  
Selection Of

The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid–like modifications on both pyrimidine bases. Using proprotein convertase subtilisin/kexin type 9 as a representative protein target, we identify specific pairwise combinations of modifications that result in higher affinity, metabolic stability, and inhibitory potency compared with aptamers with single modifications. Such doubly modified aptamers are also more likely to be encoded in shorter sequences and occupy nonoverlapping epitopes more frequently than aptamers with single modifications. These highly modified DNA aptamers have broad utility in research, diagnostic, and therapeutic applications.

Why there is more to protein evolution than protein function: splicing, nucleosomes and dual-coding sequence

2009 ◽  
Vol 37 (4) ◽  
pp. 756-761 ◽  
Author(s):  
Tobias Warnecke ◽  
Claudia C. Weber ◽  
Laurence D. Hurst
Keyword(s):  
Amino Acid ◽  
Protein Evolution ◽  
Protein Function ◽  
Dual Coding ◽  
Splice Enhancer ◽  
Dna And Rna ◽  
Rates Of Evolution ◽  
Exonic Splice ◽  
Production History

There is considerable variation in the rate at which different proteins evolve. Why is this? Classically, it has been considered that the density of functionally important sites must predict rates of protein evolution. Likewise, amino acid choice is usually assumed to reflect optimal protein function. In the present article, we briefly review evidence suggesting that this protein function-centred view is too simplistic. In particular, we concentrate on how selection acting during the protein's production history can also affect protein evolutionary rates and amino acid choice. Exploring the role of selection at the DNA and RNA level, we specifically address how the need (i) to specify exonic splice enhancer motifs in pre-mRNA, and (ii) to ensure nucleosome positioning on DNA have an impact on amino acid choice and rates of evolution. For both, we review evidence that sequence affected by more than one coding demand is particularly constrained. Strikingly, in mammals, splicing-related constraints are quantitatively as important as expression parameters in predicting rates of protein evolution. These results indicate that there is substantially more to protein evolution than protein functional constraints.

scholarly journals Advances on Aptamers against Protozoan Parasites

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 584 ◽  
Author(s):  
Juan Ospina-Villa ◽  
César López-Camarillo ◽  
Carlos Castañón-Sánchez ◽  
Jacqueline Soto-Sánchez ◽  
Esther Ramírez-Moreno ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Drug Carriers ◽  
Rna Aptamers ◽  
Health Concern ◽  
Dimensional Structure ◽  
Parasitic Infections ◽  
Attractive Alternative ◽  
Protozoan Parasites ◽  
Rna Sequences ◽  
Dna And Rna

Aptamers are single-stranded DNA or RNA sequences with a unique three-dimensional structure that allows them to recognize a particular target with high affinity. Although their specific recognition activity could make them similar to monoclonal antibodies, their ability to bind to a large range of non-immunogenic targets greatly expands their potential as tools for diagnosis, therapeutic agents, detection of food risks, biosensors, detection of toxins, drug carriers, and nanoparticle markers, among others. One aptamer named Pegaptanib is currently used for treating macular degeneration associated with age, and many other aptamers are in different clinical stages of development of evaluation for various human diseases. In the area of parasitology, research on aptamers has been growing rapidly in the past few years. Here we describe the development of aptamers raised against the main protozoan parasites that affect hundreds of millions of people in underdeveloped and developing countries, remaining a major health concern worldwide, i.e. Trypanosoma spp., Plasmodium spp., Leishmania spp., Entamoeba histolytica, and Cryptosporidium parvuum. The latest progress made in this area confirmed that DNA and RNA aptamers represent attractive alternative molecules in the search for new tools to detect and treat these parasitic infections that affect human health worldwide.

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.

scholarly journals Therapeutic Applications of DNA and RNA Aptamers

2009 ◽  
Vol 19 (3) ◽  
pp. 209-222 ◽  
Author(s):  
Kristina W. Thiel ◽  
Paloma H. Giangrande
Keyword(s):  
Rna Aptamers ◽  
Therapeutic Applications ◽  
Dna And Rna
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