scholarly journals 2′-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP)

2018 ◽  
Vol 19 (12) ◽  
pp. 3883 ◽  
Author(s):  
Jasmin Aldag ◽  
Tina Persson ◽  
Roland Hartmann
Keyword(s):  
In Vitro Selection ◽  
Binding Protein ◽  
High Specificity ◽  
Rna Aptamers ◽  
Pyrimidine Nucleotides ◽  
Consensus Sequences ◽  
Structure Probing ◽  
Potential Applications ◽  
Nuclease Degradation

Lipopolysaccaride binding protein (LBP), a glycosylated acute phase protein, plays an important role in the pathophysiology of sepsis. LBP binds with high affinity to the lipid part of bacterial lipopolysaccaride (LPS). Inhibition of the LPS-LBP interaction or blockage of LBP-mediated transfer of LPS monomers to CD14 may be therapeutical strategies to prevent septic shock. LBP is also of interest as a biomarker to identify septic patients at high risk for death, as LBP levels are elevated during early stages of severe sepsis. As a first step toward such potential applications, we isolated aptamers specific for murine LBP (mLBP) by in vitro selection from a library containing a 60-nucleotide randomized region. Modified RNA pools were transcribed in the presence of 2′-fluoro-modified pyrimidine nucleotides to stabilize transcripts against nuclease degradation. As verified for one aptamer experimentally, the selected aptamers adopt a “three-helix junction” architecture, presenting single-stranded 7-nt (5′-YGCTTCY) or 6-nt (5′-RTTTCY) consensus sequences in their core. The best binder (aptamer A011; Kd of 270 nM for binding to mLBP), characterized in more detail by structure probing and boundary analysis, was demonstrated to bind with high specificity to murine LBP.

scholarly journals Potential applications of aptamers in veterinary science

2021 ◽  
Vol 52 (1) ◽  
Author(s):  
Solène Niederlender ◽  
Jean-Jacques Fontaine ◽  
Grégory Karadjian
Keyword(s):  
Veterinary Medicine ◽  
In Vitro Selection ◽  
Three Dimensional ◽  
Basic Research ◽  
High Specificity ◽  
Environmental Safety ◽  
Veterinary Science ◽  
Potential Market ◽  
Potential Applications

AbstractAptamers are small nucleic acids that fold in a three-dimensional conformation allowing them to bind specifically to a target. This target can be an organic molecule, free or carried in cells or tissues, or inorganic components, such as metal ions. Analogous to monoclonal antibodies, aptamers however have certain advantages over the latter: e.g., high specificity for their target, no to low immunogenicity and easy in vitro selection. Since their discovery more than 30 years ago, aptamers have led to various applications, although mainly restricted to basic research. This work reviews the applications of aptamers in veterinary science to date. First, we present aptamers, how they are selected and their properties, then we give examples of applications in food and environmental safety, as well as in diagnosis and medical treatment in the field of veterinary medicine. Because examples of applications in veterinary medicine are scarce, we explore the potential avenues for future applications based on discoveries made in human medicine. Aptamers may offer new possibilities for veterinarians to diagnose certain diseases—particularly infectious diseases—more rapidly or “at the patient’s bedside”. All the examples highlight the growing interest in aptamers and the premises of a potential market. Aptamers may benefit animals as well as their owners, breeders and even public health in a “One Health” approach.

scholarly journals RNA Aptamers for a tRNA-Binding Protein from Aeropyrum pernix with Homologous Counterparts Distributed Throughout Evolution

Life ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 11 ◽  
Author(s):  
Senri Ohmori ◽  
Marina Wani ◽  
Saki Kitabatake ◽  
Yuka Nakatsugawa ◽  
Tadashi Ando ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Binding Protein ◽  
Rna Aptamers ◽  
Rna Structures ◽  
Trna Synthetases ◽  
Aeropyrum Pernix ◽  
Trna Binding ◽  
Nucleotide Region

In the present in vitro selection study, we isolated and characterized RNA aptamers for a tRNA-binding protein (Trbp) from an extremophile archaeon Aeropyrum pernix. Trbp-like structures are frequently found not only in aminoacyl-tRNA synthetases but also in diverse types of proteins from different organisms. They likely arose early in evolution and have played important roles in evolution through interactions with key RNA structures. RNA aptamers specific for A. pernix Trbp were successfully selected from a pool of RNAs composed of 60 nucleotides, including a random 30-nucleotide region. From the secondary structures, we obtained a shortened sequence composed of 21 nucleotides, of which the 3′-terminal single stranded CA nucleotides are essential for binding. This may be related to the initial evolutionary role of the universal CCA-3′ terminus of tRNA in the interaction with Trbp-like structures.

scholarly journals Selection and Micropropagation of an Elite Melatonin Rich Tulsi (Ocimum sanctum L.) Germplasm Line

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 207
Author(s):  
Mukund R. Shukla ◽  
Annaliese Kibler ◽  
Christina E. Turi ◽  
Lauren A. E. Erland ◽  
J. Alan Sullivan ◽  
...  
Keyword(s):  
In Vitro Selection ◽  
Integrated Approach ◽  
Antioxidant Potential ◽  
Ocimum Sanctum ◽  
Natural Health Products ◽  
Seed Population ◽  
Health Products ◽  
Potential Applications ◽  
Medicinal Properties

Tulsi (Ocimum sanctum L.) is a sacred plant of medicinal and spiritual significance in many cultures. Medicinal properties of Tulsi are ascribed to its phytochemicals with antioxidant capabilities. The current study was undertaken to screen a large seed population of Tulsi to select germplasm lines with high antioxidant potential and to standardize protocols for micropropagation and biomass production to produce a phytochemically consistent crop. A total of 80 germplasm lines were established under in vitro conditions and screened for their antioxidant potential determined with the 2,2-diphenyl-1-picrylhydrazyl (DPPH) bioassay. The micropropagation of a selected line, named Vrinda, was established using nodal cultures grown on Murashige and Skoog medium containing benzylaminopurine (1.1 µM), gibberellic acid (0.3 µM), and activated charcoal (0.6%). The antioxidant phytohormones melatonin and serotonin were quantified in the field and greenhouse grown tissues of Vrinda and melatonin levels were found to be consistent in both conditions with higher serotonin levels under field conditions. This integrated approach combining the in vitro selection and propagation offers potential applications in the development of safe, effective, and novel natural health products of Tulsi, and many other medicinal plant species.

scholarly journals Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS)

Methods ◽  
2017 ◽  
Vol 118-119 ◽  
pp. 171-181 ◽  
Author(s):  
Tzu-Fang Lou ◽  
Chase A. Weidmann ◽  
Jordan Killingsworth ◽  
Traci M. Tanaka Hall ◽  
Aaron C. Goldstrohm ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
In Vitro Selection ◽  
Rna Binding ◽  
Protein Complexes ◽  
Binding Protein ◽  
Rna Binding Protein ◽  
Integrated Analysis ◽  
Sequence Specificity

scholarly journals In vitro selection of RNA aptamers that inhibit the activity of type A botulinum neurotoxin

2010 ◽  
Vol 396 (4) ◽  
pp. 854-860 ◽  
Author(s):  
Tzuu-Wang Chang ◽  
Michael Blank ◽  
Pavithra Janardhanan ◽  
Bal Ram Singh ◽  
Charlene Mello ◽  
...  
Keyword(s):  
Botulinum Neurotoxin ◽  
In Vitro Selection ◽  
Type A ◽  
Rna Aptamers ◽  
Selection Of

scholarly journals Presence of a Poly(A) Binding Protein and Two Proteins with Cell Cycle-Dependent Phosphorylation in Crithidia fasciculata mRNA Cycling Sequence Binding Protein II

2004 ◽  
Vol 3 (5) ◽  
pp. 1185-1197 ◽  
Author(s):  
Bidyottam Mittra ◽  
Dan S. Ray
Keyword(s):  
Cell Cycle ◽  
Binding Protein ◽  
High Specificity ◽  
Binding Activity ◽  
Mrna Levels ◽  
Crithidia Fasciculata ◽  
Target Mrna ◽  
Cycle Dependent

ABSTRACT Crithidia fasciculata cycling sequence binding proteins (CSBP) have been shown to bind with high specificity to sequence elements present in several mRNAs that accumulate periodically during the cell cycle. The first described CSBP has subunits of 35.6 (CSBPA) and 42 kDa (CSBPB). A second distinct binding protein termed CSBP II has been purified from CSBPA null mutant cells, lacking both CSBPA and CSBPB proteins, and contains three major polypeptides with predicted molecular masses of 63, 44.5, and 33 kDa. Polypeptides of identical size were radiolabeled in UV cross-linking assays performed with purified CSBP II and 32P-labeled RNA probes containing six copies of the cycling sequence. The CSBP II binding activity was found to cycle in parallel with target mRNA levels during progression through the cell cycle. We have cloned genes encoding these three CSBP II proteins, termed RBP63, RBP45, and RBP33, and characterized their binding properties. The RBP63 protein is a member of the poly(A) binding protein family. Homologs of RBP45 and RBP33 proteins were found only among the kinetoplastids. Both RBP45 and RBP33 proteins and their homologs have a conserved carboxy-terminal half that contains a PSP1-like domain. All three CSBP II proteins show specificity for binding the wild-type cycling sequence in vitro. RBP45 and RBP33 are phosphoproteins, and RBP45 has been found to bind in vivo specifically to target mRNA containing cycling sequences. The levels of phosphorylation of both RBP45 and RBP33 were found to cycle during the cell cycle.

In vitro selection of RNA aptamers that selectively bind danofloxacin

2014 ◽  
Vol 448 (4) ◽  
pp. 397-402 ◽  
Author(s):  
Seung Ryul Han ◽  
Jaehoon Yu ◽  
Seong-Wook Lee
Keyword(s):  
In Vitro Selection ◽  
Rna Aptamers ◽  
Selection Of
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