scholarly journals DNAmoreDB, a database of DNAzymes

2020 ◽  
Vol 49 (D1) ◽  
pp. D76-D81
Author(s):  
Almudena Ponce-Salvatierra ◽  
Pietro Boccaletto ◽  
Janusz M Bujnicki
Keyword(s):  
In Vitro Selection ◽  
Structural Information ◽  
Selection Procedure ◽  
Living Organisms ◽  
Catalyzed Reactions ◽  
Submission Form ◽  
Types Of Information ◽  
Machine Readable ◽  
Readable Format

Abstract Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates. DNAmoreDB is a comprehensive database resource for DNAzymes that collects and organizes the following types of information: sequences, conditions of the selection procedure, catalyzed reactions, kinetic parameters, substrates, cofactors, structural information whenever available, and literature references. Currently, DNAmoreDB contains information about DNAzymes that catalyze 20 different reactions. We included a submission form for new data, a REST-based API system that allows users to retrieve the database contents in a machine-readable format, and keyword and BLASTN search features. The database is publicly available at https://www.genesilico.pl/DNAmoreDB/.

scholarly journals Identification of Resistance Determinants for a Promising Antileishmanial Oxaborole Series

2021 ◽  
Vol 9 (7) ◽  
pp. 1408
Author(s):  
Magali Van den Kerkhof ◽  
Philippe Leprohon ◽  
Dorien Mabille ◽  
Sarah Hendrickx ◽  
Lindsay B. Tulloch ◽  
...  
Keyword(s):  
Drug Exposure ◽  
In Vitro Selection ◽  
Selection Procedure ◽  
Cosmid Library ◽  
Neglected Diseases ◽  
Chromosome 2 ◽  
Resistance Determinants ◽  
A Genome

Current treatment options for visceral leishmaniasis have several drawbacks, and clinicians are confronted with an increasing number of treatment failures. To overcome this, the Drugs for Neglected Diseases initiative (DNDi) has invested in the development of novel antileishmanial leads, including a very promising class of oxaboroles. The mode of action/resistance of this series to Leishmania is still unknown and may be important for its further development and implementation. Repeated in vivo drug exposure and an in vitro selection procedure on both extracellular promastigote and intracellular amastigote stages were both unable to select for resistance. The use of specific inhibitors for ABC-transporters could not demonstrate the putative involvement of efflux pumps. Selection experiments and inhibitor studies, therefore, suggest that resistance to oxaboroles may not emerge readily in the field. The selection of a genome-wide cosmid library coupled to next-generation sequencing (Cos-seq) was used to identify resistance determinants and putative targets. This resulted in the identification of a highly enriched cosmid, harboring genes of chromosome 2 that confer a subtly increased resistance to the oxaboroles tested. Moderately enriched cosmids encompassing a region of chromosome 34 contained the cleavage and polyadenylation specificity factor (cpsf) gene, encoding the molecular target of several related benzoxaboroles in other organisms.

scholarly journals High efficacy in vitro selection procedure for generating transgenic parasites of Plasmodium berghei using an antibiotic toxic to rodent hosts

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Akira Soga ◽  
Hironori Bando ◽  
Mami Ko-ketsu ◽  
Hirono Masuda-Suganuma ◽  
Shin-ichiro Kawazu ◽  
...  
Keyword(s):  
Plasmodium Berghei ◽  
In Vitro Selection ◽  
Selection Procedure ◽  
High Efficacy ◽  
Transgenic Parasites

Aptamer-based modulation of blood coagulation

2011 ◽  
Vol 31 (04) ◽  
pp. 258-263 ◽  
Author(s):  
F. Rohrbach ◽  
B. Pötzsch ◽  
J. Müller ◽  
G. Mayer
Keyword(s):  
Clinical Trials ◽  
Nucleic Acid ◽  
In Vitro Selection ◽  
Three Dimensional ◽  
Selection Procedure ◽  
Anticoagulant Drugs ◽  
Coagulation Proteins ◽  
Recent Developments ◽  
Target Molecules

SummaryNucleic acid based aptamers are singlestranded oligonucleotide ligands isolated from random libraries by an in-vitro selection procedure. Through the formation of unique three-dimensional structures, aptamers are able to selectively interact with a variety of target molecules and are therefore also promising candidates for the development of anticoagulant drugs. While thrombin represents the most prominent enzymatic target in this field, also aptamers directed against other coagulation proteins and proteases have been identified with some currently being tested in clinical trials.In this review, we summarize recent developments in the design and evaluation of aptamers for anticoagulant therapy and research.

scholarly journals Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

Pharmaceutics ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 646 ◽  
Author(s):  
Prabir Kumar Kulabhusan ◽  
Babar Hussain ◽  
Meral Yüce
Keyword(s):  
In Vitro Selection ◽  
Clinical Investigation ◽  
Environmental Pollutants ◽  
Selection Procedure ◽  
Iteration Process ◽  
High Specificity ◽  
Molecular Probes ◽  
Diagnostic Tools ◽  
Vast Number

Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.

scholarly journals A New Medicago truncatula Line with Superior in Vitro Regeneration, Transformation, and Symbiotic Properties Isolated Through Cell Culture Selection

1997 ◽  
Vol 10 (3) ◽  
pp. 307-315 ◽  
Author(s):  
Beate Hoffmann ◽  
Toan Hanh Trinh ◽  
Jeffrey Leung ◽  
Adam Kondorosi ◽  
Eva Kondorosi
Keyword(s):  
Medicago Truncatula ◽  
In Vitro Selection ◽  
Rhizobium Meliloti ◽  
In Vitro Regeneration ◽  
Selection Procedure ◽  
Genetic System ◽  
Strain Specificity ◽  
Meliloti Strain ◽  
Symbiotic Properties

The understanding of how leguminous plants establish symbiosis with rhizobia is limited by the lack of genetic system in most legume plants. Here we propose a Medicago truncatula line suitable for genetic analysis of Medicago-Rhizobium meliloti symbiosis because of its high regeneration capacity and broad R. meliloti strain specificity. This line has been isolated by extensive in vitro screening of explants from several ecotypes of M. truncatula that are known to be autogamous and have small diploid genomes. One such derivative identified from ecotype 108-1 has gained the capacity to be readily regenerated in vitro. The derivative, called R108-1, like its parent, can establish effective symbiosis with several widely studied R. meliloti strains (Rm41, Rm2011, Rm1021, F51, and GR4). Importantly, the nodulation characteristics of the R108-1 line were not compromised by the in vitro selection procedure. We have further established the conditions for efficient transformation of R108-1 by co-cultivation with Agrobacterium tumefaciens. Thus, this in vitro-derived plant line has most of the favorable attributes, otherwise rare among legumes, of a complementary model plant system for investigating symbiosis at the genetic and the molecular levels.

scholarly journals Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons

2021 ◽  
Author(s):  
Philip L. Tzou ◽  
Kaiming Tao ◽  
Sergei L. Kosakovsky Pond ◽  
Robert W. Shafer
Keyword(s):  
Monoclonal Antibodies ◽  
Mutation Detection ◽  
Published Data ◽  
Experimental Conditions ◽  
Susceptibility Data ◽  
Machine Readable ◽  
Different Levels ◽  
Readable Format ◽  
Machine Readable Format

As novel SARS-CoV-2 variants with different patterns of spike mutations have emerged, the susceptibility of these variants to neutralization by antibodies has been rapidly assessed. However, neutralization data are generated using different approaches and are scattered across different publications making it difficult for these data to be located and synthesized. The Stanford Coronavirus Resistance Database (CoV-RDB; https://covdb.stanford.edu ) is designed to house comprehensively curated published data on the neutralizing susceptibility of SARS-CoV-2 variants and spike mutations to monoclonal antibodies (mAbs), convalescent plasma (CP), and vaccinee plasma (VP). As of October 2021, CoV-RDB contains 186 publications including 64 (34%) containing 7,328 neutralizing mAb susceptibility results, 96 (52%) containing 11,390 neutralizing CP susceptibility results, and 125 (68%) containing 20,872 neutralizing VP results. The database also records which spike mutations are selected during in vitro passage of SARS-CoV-2 in the presence of mAbs and which emerge in persons receiving mAbs as treatment. The CoV-RDB interface interactively displays neutralizing susceptibility data at different levels of granularity by filtering and/or aggregating query results according to one or more experimental conditions. The CoV-RDB website provides a companion sequence analysis program that outputs information about mutations present in a submitted sequence and that also assists users in determining the appropriate mutation-detection thresholds for identifying non-consensus amino acids. The most recent data underlying the CoV-RDB can be downloaded in its entirety from a Github repository in a documented machine-readable format.

scholarly journals Novel Approach to Analyzing RNA Aptamer-Protein Interactions: Toward Further Applications of Aptamers

2006 ◽  
Vol 11 (6) ◽  
pp. 599-605 ◽  
Author(s):  
Joonsung Hwang ◽  
Satoshi Nishikawa
Keyword(s):  
Protein Interactions ◽  
In Vitro Selection ◽  
Selection Procedure ◽  
Rna Aptamers ◽  
Sensor Chip ◽  
Rna Aptamer ◽  
Surface Plasmon Resonance Analysis ◽  
Resonance Analysis ◽  
Novel Approach

Surface plasmon-resonance analysis using a Biacore biosensor is a powerful tool for the detailed study of biomolecular interactions. The authors examined the methods of immobilizing proteins on the surface of NTA, SA, and CM5 sensor chips to study RNA aptamer-protein interactions. RNA aptamers and their deletion variants were loaded onto a protein-immobilized sensor chip, and their binding affinities were analyzed. Immobilizing the protein on a CM5 sensor chip via an anti-His-tag antibody was the only strategy that clearly detected the kinetic parameters of the interactions. ΔNEO-III-14U, one of the deletion variants of the NS3 aptamer, had the highest binding affinity for the ΔNS3 protein in this study (KD = 4 × 10-8). Moreover, the 29-amino-acid spacer fragment was essential for protein immobilization using this strategy. This novel method will be useful in comparing the affinity of various RNA aptamers and selecting the most suitable candidates for a given target, as well as facilitating the in vitro selection procedure itself.

Sign in / Sign up

Export Citation Format

Share Document