scholarly journals Fitness of a Turnip Crinkle Virus Satellite RNA Correlates with a Sequence-Nonspecific Hairpin and Flanking Sequences That Enhance Replication and Repress the Accumulation of Virions

2003 ◽  
Vol 77 (14) ◽  
pp. 7880-7889 ◽  
Author(s):  
Xiaoping Sun ◽  
Anne E. Simon
Keyword(s):  
Systemic Infection ◽  
Turnip Crinkle Virus ◽  
Satellite Rna ◽  
Structural Requirements ◽  
Sense Orientation ◽  
Flanking Sequences ◽  
Satellite Rnas ◽  
Systematic Evolution ◽  
Base Replacement ◽  
Exponential Enrichment

ABSTRACT satC, a satellite RNA associated with Turnip crinkle virus (TCV), enhances the ability of the virus to colonize plants by interfering with stable virion accumulation (F. Zhang and A. E. Simon, unpublished data). Previous results suggested that the motif1-hairpin (M1H), a replication enhancer on minus strands, forms a plus-strand hairpin flanked by CA-rich sequence that may be involved in enhancing systemic infection (G. Zhang and A. E. Simon, J. Mol. Biol. 326:35-48, 2003). In this study, sequence and structural requirements of the M1H were further assayed by replacing the 28-base M1H with 10 random bases and then subjecting the pool of satellite RNA to functional selection in plants. Unlike previous results with 28-base replacement sequences (G. Zhang and A. E. Simon, J. Mol. Biol. 326:35-48, 2003), only a few of the 10-base SELEX (systematic evolution of ligands by exponential enrichment) assay winners contained short motifs in their minus-sense orientation that were similar to TCV replication elements. However, all second- and third-round winning replacement sequences folded into hairpins flanked by CA-rich sequence predicted to be more stable on plus strands than minus strands. Plus strands of several of the most fit satellite RNAs contained insertions of CA-rich sequence at the base of their hairpins whose presence correlated with enhanced replication and reduced detection of virions. Deletion of the M1H resulted in no detectable virions despite very low satellite accumulation. These results support the hypothesis that a sequence-nonspecific plus-strand hairpin brings together flanking CA-rich sequences in the M1H region that confers fitness to satC by reducing the accumulation of stable virions.

scholarly journals Satellite RNAs and Satellite Viruses

2016 ◽  
Vol 29 (3) ◽  
pp. 181-186 ◽  
Author(s):  
Peter Palukaitis
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Rna Silencing ◽  
Noncoding Rnas ◽  
Turnip Crinkle Virus ◽  
Satellite Rna ◽  
Satellite Rnas ◽  
Satellite Viruses

Satellite RNAs and satellite viruses are extraviral components that can affect either the pathogenicity, the accumulation, or both of their associated viruses while themselves being dependent on the associated viruses as helper viruses for their infection. Most of these satellite RNAs are noncoding RNAs, and in many cases, have been shown to alter the interaction of their helper viruses with their hosts. In only a few cases have the functions of these satellite RNAs in such interactions been studied in detail. In particular, work on the satellite RNAs of Cucumber mosaic virus and Turnip crinkle virus have provided novel insights into RNAs functioning as noncoding RNAs. These effects are described and potential roles for satellite RNAs in the processes involved in symptom intensification or attenuation are discussed. In most cases, models describing these roles involve some aspect of RNA silencing or its suppression, either directly or indirectly involving the particular satellite RNA.

FEATURES OF ORGANOPHOSPHATES IMMOBILIZATION VIA STREPTAVIDIN-BIOTIN SYSTEM FOR EXPERIMENTS ON SELECTION OF APTAMERS

2020 ◽  
pp. 12-20
Author(s):  
D. A. Belinskaya ◽  
Yu. V. Chelusnova ◽  
V. V. Abzianidze ◽  
N. V. Goncharov
Keyword(s):  
Polyethylene Glycol ◽  
Organophosphorus Compounds ◽  
Binding Energies ◽  
Rna Aptamers ◽  
Main Method ◽  
Modeling Methods ◽  
Molecular Dynamics Methods ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Selection Of

Poisoning with organophosphorus compounds occupy one of the leading places in exotoxicosis. At the first stage, the detoxification of organophosphates can be provided with the help of DNA or RNA aptamers that bind the poison in the bloodstream. Currently, the main method of searching for aptamers is the experimental method of systematic evolution of ligands by exponential enrichment (SELEX). In the process of aptamer selection, the target molecule must be immobilized via the streptavidin-biotin complex. Since the poison molecule is small in size, to increase its availability for binding to aptamer, it is necessary to use a spacer between organophosphorus compounds and biotin. The aim of this work was to optimize the selection of aptamers for organophosphorus compounds by increasing the availability of a poison molecule immobilized via the streptavidin-biotin complex on the example of paraoxon. For this purpose, three spacers between organophosphorus compounds and biotin were tested using molecular modeling methods: three links of polyethylene glycol (3-PEG), four links of polyethylene glycol (4-PEG) and aminohexyl. The conformation of the biotinylated paraoxon complex with streptavidin and the interaction of paraoxon with the binding fragment of the aptamer were modeled using molecular docking and molecular dynamics methods. The ability of biotinylated paraoxon to bind to the aptamer has been evaluated by analyzing the surface area of the paraoxon available to the solvent, as well as by calculating the free binding energies. It has been shown that only in the case of aminohexyl immobilized paraoxon can contact the aptamer. At the final stage, the synthesis of paraoxon bound to biotin via aminohexyl was carried out.

scholarly journals Corrigendum: Effect of temperature on the pathogenesis, accumulation of viral and satellite RNAs and on plant proteome in peanut stunt virus and satellite RNA-infected plants

2016 ◽  
Vol 7 ◽  
Author(s):  
Aleksandra Obrępalska-Stęplowska ◽  
Jenny Renaut ◽  
Sebastien Planchon ◽  
Arnika Przybylska ◽  
Przemysław Wieczorek ◽  
...  
Keyword(s):  
Effect Of Temperature ◽  
Satellite Rna ◽  
Satellite Rnas ◽  
Peanut Stunt Virus

scholarly journals Recombination between satellite RNAs of turnip crinkle virus.

1990 ◽  
Vol 9 (6) ◽  
pp. 1709-1715 ◽  
Author(s):  
P.J. Cascone ◽  
C.D. Carpenter ◽  
X.H. Li ◽  
A.E. Simon
Keyword(s):  
Turnip Crinkle Virus ◽  
Satellite Rnas

scholarly journals The interaction landscape between transcription factors and the nucleosome

2017 ◽  
Author(s):  
Fangjie Zhu ◽  
Lucas Farnung ◽  
Eevi Kaasinen ◽  
Biswajyoti Sahu ◽  
Yimeng Yin ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Affinity Purification ◽  
Rotational Symmetry ◽  
Free Dna ◽  
Nucleosomal Dna ◽  
Direct Gene ◽  
Systematic Evolution ◽  
Modes Of Interaction ◽  
Exponential Enrichment ◽  
Rich Interaction

Nucleosomes cover most of the genome and are thought to be displaced by transcription factors (TFs) in regions that direct gene expression. However, the modes of interaction between TFs and nucleosomal DNA remain largely unknown. Here, we use nucleosome consecutive affinity-purification systematic evolution of ligands by exponential enrichment (NCAP-SELEX) to systematically explore interactions between the nucleosome and 220 TFs representing diverse structural families. Consistently with earlier observations, we find that the vast majority of TFs have less access to nucleosomal DNA than to free DNA. The motifs recovered from TFs bound to nucleosomal and free DNA are generally similar; however, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many TFs preferentially bind close to the end of nucleosomal DNA, or to periodic positions at its solvent-exposed side. TFs often also bind nucleosomal DNA in a particular orientation, because the nucleosome breaks the local rotational symmetry of DNA. Some TFs also specifically interact with DNA located at the dyad position where only one DNA gyre is wound, whereas other TFs prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals striking differences in TF binding to free and nucleosomal DNA, and uncovers a rich interaction landscape between the TFs and the nucleosome.

Pattern recognition of enrichment levels of SELEX-based candidate aptamers for human C-reactive protein

2017 ◽  
Vol 62 (3) ◽  
Author(s):  
Xinliang Yu ◽  
Ruqin Yu ◽  
Xiaohai Yang
Keyword(s):  
Pattern Recognition ◽  
Latent Variables ◽  
Molecular Descriptors ◽  
Principal Component ◽  
Support Vector ◽  
C Reactive Protein ◽  
Reactive Protein ◽  
Systematic Evolution ◽  
Model C ◽  
Exponential Enrichment

AbstractSelecting aptamers for human C-reactive protein (CRP) would be of critical importance in predicting the risk for cardiovascular disease. The enrichment level of DNA aptamers is an important parameter for selecting candidate aptamers for further affinity and specificity determination. This paper is the first report on pattern recognition used for CRP aptamer enrichment levels in the systematic evolution of ligands by exponential enrichment (SELEX) process, by applying structure-activity relationship models. After generating 10 rounds of graphene oxide (GO)-SELEX and 1670 molecular descriptors, eight molecular descriptors were selected and five latent variables were then obtained with principal component analysis (PCA), to develop a support vector classification (SVC) model. The SVC model (C=8.1728 and

Differentiating breast cancer molecular subtypes using a DNA aptamer selected against MCF-7 cells

2018 ◽  
Vol 6 (12) ◽  
pp. 3152-3159 ◽  
Author(s):  
Mei Liu ◽  
Tong Yang ◽  
Zhongsi Chen ◽  
Zhifei Wang ◽  
Nongyue He
Keyword(s):  
Breast Cancer ◽  
Molecular Subtypes ◽  
Personalized Therapy ◽  
Dna Aptamer ◽  
Single Stranded Dna ◽  
Systematic Evolution ◽  
Exponential Enrichment ◽  
Mcf 7

Aptamers are single-stranded DNA or RNA oligonucleotides selected by systematic evolution of ligands by exponential enrichment (SELEX), which show great potential in the diagnosis and personalized therapy of cancers, due to their specific advantages over antibodies.

scholarly journals G-Quadruplex-Forming Aptamers—Characteristics, Applications, and Perspectives

Molecules ◽  
2019 ◽  
Vol 24 (20) ◽  
pp. 3781 ◽  
Author(s):  
Carolina Roxo ◽  
Weronika Kotkowiak ◽  
Anna Pasternak
Keyword(s):  
Nucleic Acid ◽  
Production Costs ◽  
Biological Processes ◽  
Disease Treatment ◽  
Diagnostic Potential ◽  
G Quadruplex ◽  
Fast Development ◽  
Systematic Evolution ◽  
Nucleic Acid Structures ◽  
Exponential Enrichment

G-quadruplexes constitute a unique class of nucleic acid structures formed by G-rich oligonucleotides of DNA- or RNA-type. Depending on their chemical nature, loops length, and localization in the sequence or structure molecularity, G-quadruplexes are highly polymorphic structures showing various folding topologies. They may be formed in the human genome where they are believed to play a pivotal role in the regulation of multiple biological processes such as replication, transcription, and translation. Thus, natural G-quadruplex structures became prospective targets for disease treatment. The fast development of systematic evolution of ligands by exponential enrichment (SELEX) technologies provided a number of G-rich aptamers revealing the potential of G-quadruplex structures as a promising molecular tool targeted toward various biologically important ligands. Because of their high stability, increased cellular uptake, ease of chemical modification, minor production costs, and convenient storage, G-rich aptamers became interesting therapeutic and diagnostic alternatives to antibodies. In this review, we describe the recent advances in the development of G-quadruplex based aptamers by focusing on the therapeutic and diagnostic potential of this exceptional class of nucleic acid structures.

scholarly journals Aptamers, the Nucleic Acid Antibodies, in Cancer Therapy

2020 ◽  
Vol 21 (8) ◽  
pp. 2793 ◽  
Author(s):  
Zhaoying Fu ◽  
Jim Xiang
Keyword(s):  
Monoclonal Antibody ◽  
Clinical Trials ◽  
Cancer Therapy ◽  
Specific Binding ◽  
High Specificity ◽  
Medical Community ◽  
Therapeutic Uses ◽  
Repeated Use ◽  
Systematic Evolution ◽  
Exponential Enrichment

The arrival of the monoclonal antibody (mAb) technology in the 1970s brought with it the hope of conquering cancers to the medical community. However, mAbs, on the whole, did not achieve the expected wonder in cancer therapy although they do have demonstrated successfulness in the treatment of a few types of cancers. In 1990, another technology of making biomolecules capable of specific binding appeared. This technique, systematic evolution of ligands by exponential enrichment (SELEX), can make aptamers, single-stranded DNAs or RNAs that bind targets with high specificity and affinity. Aptamers have some advantages over mAbs in therapeutic uses particularly because they have little or no immunogenicity, which means the feasibility of repeated use and fewer side effects. In this review, the general properties of the aptamer, the advantages and limitations of aptamers, the principle and procedure of aptamer production with SELEX, particularly the undergoing studies in aptamers for cancer therapy, and selected anticancer aptamers that have entered clinical trials or are under active investigations are summarized.

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