scholarly journals BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W243-W248 ◽  
Author(s):  
L. Wang ◽  
S. J. Brown
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Rna Binding ◽  
Amino Acid Sequences ◽  
Web Based ◽  
Dna And Rna ◽  
Efficient Prediction ◽  
Dna And Rna Binding ◽  
Rna Binding Sites

scholarly journals Novel cyanine dye as competitive ligand for probing the drug–nucleic acid interactions

2020 ◽  
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Binding Sites ◽  
Lanthanide Complexes ◽  
Rna Binding ◽  
Cyanine Dye ◽  
Dna And Rna ◽  
Dna And Rna Binding ◽  
Drug Displacement ◽  
Potential Antitumor

Background: During the past decades, increasing attention has been given to elucidating the molecular details of interactions between the pharmacological agents and nucleic acids since the drug–DNA complexation may lead to impairment of DNA replication, strand breaking and mutations. A variety of techniques have been developed to characterize the drug-nucleic acid binding, among which the fluorescence dye displacement assay is one of the most informative approaches. Recently, it was demonstrated that cyanine dyes can be successfully employed for the high throughput screening of the interactions between nucleic acids and drugs. To the best of our knowledge, so far, the potential application of cyanine dyes for the drug-displacement studies remains insufficiently evaluated. Objectives: The aim of the present study was to investigate the ability of a novel cyanine dye to serve as a competitor for the potential antitumor compounds, lanthanide complexes bearing europium (III) tris-β-diketonate (EC) for the DNA and RNA binding sites. Materials and methods: Calf thymus DNA, yeast RNA, trimethine cyanine dye and lanthanide complexes bearing europium (III) tris-β-diketonate were used for sample preparation. The fluorescence data were acquired using Perkin-Elmer LS-55 spectrofluorimeter. Results: Using the fluorescence spectroscopy technique we conducted the displacement reaction trimethine cyanine dye/europium coordination complexes in the presence of double stranded DNA and single-stranded RNA. An increase of the EC concentration in the systems AK3-5/DNA or AK3-5/RNA was followed by a gradual reduction in the AK3-5 fluorescence intensity, indicating that europium (III) tris-β-diketonate compounds can serve as competitors for the trimethine cyanine dye on the nucleic acids. Both the drug chemical structure and the type of nucleic acid proved to control the extent of EC-induced decrease of AK3-5 fluorescence in the presence of the DNA or RNA. Conclusion: By recruiting the potential antitumor agents europium chelate complexes as the competitive ligands for the cyanine dye for the DNA and RNA binding sites, we found that a novel trimethine compound can be effectively used in the fluorescence drug displacement assays.

scholarly journals Isolation and Analysis of Mutants of Double-Stranded-RNA Bacteriophage φ6 with Altered Packaging Specificity

2003 ◽  
Vol 185 (15) ◽  
pp. 4572-4577 ◽  
Author(s):  
Jian Qiao ◽  
Xueying Qiao ◽  
Yang Sun ◽  
Leonard Mindich
Keyword(s):  
Amino Acid ◽  
Conformational Changes ◽  
Binding Sites ◽  
Rna Binding ◽  
Structural Protein ◽  
Double Stranded Rna ◽  
Major Structural Protein ◽  
Nucleoside Triphosphates ◽  
Hydrolysis Of ◽  
Rna Binding Sites

ABSTRACT The genomes of bacteriophage φ6 and its relatives are packaged through a mechanism that involves the recognition and translocation of the three different plus strand transcripts of the segmented double-stranded RNA genomes into preformed polyhedral structures called procapsids or inner cores. This packaging requires hydrolysis of nucleoside triphosphates and takes place in the order S-M-L. Packaging is dependent on unique sequences of about 200 nucleotides near the 5′ ends of plus strand transcripts of the three genomic segments. Changes in the pac sequences lead to loss of packaging ability but can be suppressed by second-site changes in RNA or amino acid changes in protein P1, the major structural protein of the procapsid. It appears that P1 is the determinant of the RNA binding sites, and it is suggested that the binding sites overlap or are conformational changes of the same domains.

CSBPI_Site：Multi-Information Sources of Features to RNA Binding Sites Prediction

2021 ◽  
Vol 15 ◽  
Author(s):  
Lichao Zhang ◽  
Zihong Huang ◽  
Liang Kong
Keyword(s):  
Computational Model ◽  
Binding Sites ◽  
Noncoding Rna ◽  
Computational Models ◽  
Information Sources ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Gradient Boosting ◽  
Position Information ◽  
Rna Binding Sites

Background: RNA-binding proteins establish posttranscriptional gene regulation by coordinating the maturation, editing, transport, stability, and translation of cellular RNAs. The immunoprecipitation experiments could identify interaction between RNA and proteins, but they are limited due to the experimental environment and material. Therefore, it is essential to construct computational models to identify the function sites. Objective: Although some computational methods have been proposed to predict RNA binding sites, the accuracy could be further improved. Moreover, it is necessary to construct a dataset with more samples to design a reliable model. Here we present a computational model based on multi-information sources to identify RNA binding sites. Method: We construct an accurate computational model named CSBPI_Site, based on xtreme gradient boosting. The specifically designed 15-dimensional feature vector captures four types of information (chemical shift, chemical bond, chemical properties and position information). Results: The satisfied accuracy of 0.86 and AUC of 0.89 were obtained by leave-one-out cross validation. Meanwhile, the accuracies were slightly different (range from 0.83 to 0.85) among three classifiers algorithm, which showed the novel features are stable and fit to multiple classifiers. These results showed that the proposed method is effective and robust for noncoding RNA binding sites identification. Conclusion: Our method based on multi-information sources is effective to represent the binding sites information among ncRNAs. The satisfied prediction results of Diels-Alder riboz-yme based on CSBPI_Site indicates that our model is valuable to identify the function site.

Alteration of DNA and RNA Binding Activity of Human Telomere Binding Proteins Occurs during Cellular Senescence

1995 ◽  
Vol 218 (1) ◽  
pp. 241-247 ◽  
Author(s):  
Karen Hubbard ◽  
Sridevi N. Dhanaraj ◽  
Khalid A. Sethi ◽  
Janice Rhodes ◽  
Jeffrey Wilusz ◽  
...  
Keyword(s):  
Cellular Senescence ◽  
Binding Proteins ◽  
Rna Binding ◽  
Binding Activity ◽  
Dna And Rna ◽  
Human Telomere ◽  
Dna And Rna Binding
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