scholarly journals An Elegant Biosensor Molecular Beacon Probe: Challenges and Recent Solutions

Scientifica ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Dmitry M. Kolpashchikov
Keyword(s):  
Molecular Beacon ◽  
Signal To Noise Ratio ◽  
Probe Design ◽  
Rna Sequences ◽  
Molecular Sensing ◽  
Stem Loop ◽  
Nucleic Acid Analysis ◽  
Loop Shape ◽  
Folded Rna ◽  
Rna And Dna

Molecular beacon (MB) probes are fluorophore- and quencher-labeled short synthetic DNAs folded in a stem-loop shape. Since the first report by Tyagi and Kramer, it has become a widely accepted tool for nucleic acid analysis and triggered a cascade of related developments in the field of molecular sensing. The unprecedented success of MB probes stems from their ability to detect specific DNA or RNA sequences immediately after hybridization with no need to wash out the unbound probe (instantaneous format). Importantly, the hairpin structure of the probe is responsible for both the low fluorescent background and improved selectivity. Furthermore, the signal is generated in a reversible manner; thus, if the analyte is removed, the signal is reduced to the background. This paper highlights the advantages of MB probes and discusses the approaches that address the challenges in MB probe design. Variations of MB-based assays tackle the problem of stem invasion, improve SNP genotyping and signal-to-noise ratio, as well as address the challenges of detecting folded RNA and DNA.

scholarly journals Rationally Manipulating Aptamer Binding Affinities in a Stem-Loop Molecular Beacon

2014 ◽  
Vol 25 (10) ◽  
pp. 1769-1776 ◽  
Author(s):  
Rachel E. Armstrong ◽  
Geoffrey F. Strouse
Keyword(s):  
Molecular Beacon ◽  
Binding Affinities ◽  
Stem Loop

scholarly journals A Mathematical Analysis of HDV Genotypes: From Molecules to Cells

Mathematics ◽  
2021 ◽  
Vol 9 (17) ◽  
pp. 2063
Author(s):  
Rami Zakh ◽  
Alexander Churkin ◽  
Franziska Totzeck ◽  
Marina Parr ◽  
Tamir Tuller ◽  
...  
Keyword(s):  
Rna Editing ◽  
Virus Replication ◽  
Mathematical Analysis ◽  
Graph Representation ◽  
Genotype 3 ◽  
Mutational Robustness ◽  
Rna Sequences ◽  
Stem Loop ◽  
Hepatitis D ◽  
Hdv Genotype

Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.

scholarly journals A new entropy model for RNA: part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations

2013 ◽  
Vol 4 (1) ◽  
pp. 2 ◽  
Author(s):  
Wayne Dawson ◽  
Kenji Yamamoto ◽  
Kentaro Shimizu ◽  
Gota Kawai
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Degrees Of Freedom ◽  
Free Energy Calculations ◽  
Local Entropy ◽  
Entropy Model ◽  
Stem Loop ◽  
Entropy Correction ◽  
The Cross ◽  
Folded Rna

In previous work, we have shown that the entropy of a folded RNA molecule can be divided into local and global contributions using the cross-linking entropy (CLE) model, where, in the case of RNA, the cross- links are the base-pair stacking interactions. The local contribution to the CLE is revealed in the Kuhn length (a measure of the stiffness of the RNA). The Kuhn length acts as a scaling parameter. When the size of the system is rescaled, the relationship between local and global free energy must be renormalized to reflect this rescaling. In this renormalization process, the Kuhn length increases, the local entropy also increases due to freezing out of the local conformational degrees of freedom. At the same time, as the number of degrees of freedom decrease, there is a significant reduction in the global entropy. Here we present a method, based on the concepts of renormalization theory, to quantitatively estimate the size of the contribution from the local entropy as a function of the Kuhn length. The local entropy correction is used to predict the current empirically derived constant in the Jacobson-Stockmayer equation. The variation in the Kuhn length is shown to be largely influenced by the length of the double-stranded RNA stems formed in the secondary structure of folded RNA. This result is used to test the resulting entropy under a variable Kuhn length in stem-loop structures. Comparisons between a variable Kuhn length and a static Kuhn length on a short stem-loop of RNA are also examined. The model is quite general and is also directly applicable to protein structure and folding problems.

scholarly journals Human Ribosomal RNA-Derived Resident MicroRNAs as the Transmitter of Information upon the Cytoplasmic Cancer Stress

2016 ◽  
Vol 2016 ◽  
pp. 1-14 ◽  
Author(s):  
Masaru Yoshikawa ◽  
Yoichi Robertus Fujii
Keyword(s):  
Gene Expression ◽  
Ribosomal Rna ◽  
Ribosome Biogenesis ◽  
Quantum Dynamic ◽  
Rna Sequences ◽  
Stem Loop ◽  
Important Regulator ◽  
Multiple Levels ◽  
Cellular Stresses ◽  
Nucleolar Rnas

Dysfunction of ribosome biogenesis induces divergent ribosome-related diseases including ribosomopathy and occasionally results in carcinogenesis. Although many defects in ribosome-related genes have been investigated, little is known about contribution of ribosomal RNA (rRNA) in ribosome-related disorders. Meanwhile, microRNA (miRNA), an important regulator of gene expression, is derived from both coding and noncoding region of the genome and is implicated in various diseases. Therefore, we performedin silicoanalyses using M-fold, TargetScan, GeneCoDia3, and so forth to investigate RNA relationships between rRNA and miRNA against cellular stresses. We have previously shown that miRNA synergism is significantly correlated with disease and the miRNA package is implicated in memory for diseases; therefore, quantum Dynamic Nexus Score (DNS) was also calculated using MESer program. As a result, seventeen RNA sequences identical with known miRNAs were detected in the human rRNA and termed as rRNA-hosted miRNA analogs (rmiRNAs). Eleven of them were predicted to form stem-loop structures as pre-miRNAs, and especially one stem-loop was completely identical withhsa-pre-miR-3678located in the non-rDNA region. Thus, these rmiRNAs showed significantly high DNS values, participation in regulation of cancer-related pathways, and interaction with nucleolar RNAs, suggesting that rmiRNAs may be stress-responsible resident miRNAs which transmit stress-tuning information in multiple levels.

scholarly journals RNA polymerase clamp movement aids dissociation from DNA but is not required for RNA release at intrinsic terminators

2018 ◽  
Author(s):  
Michael J Bellecourt ◽  
Ananya Ray-Soni ◽  
Alex Harwig ◽  
Rachel Anne Mooney ◽  
Robert Landick
Keyword(s):  
Nucleic Acid ◽  
Rna Polymerase ◽  
Conformational Changes ◽  
Transcription Initiation ◽  
Elongation Rate ◽  
List Type ◽  
Stem Loop ◽  
Dna Release ◽  
Transcription Complexes ◽  
Rna And Dna

ABSTRACTIn bacteria, disassembly of elongating transcription complexes (ECs) can occur at intrinsic terminators in a 2-3 nucleotide window after transcription of multiple kilobase pairs of DNA. Intrinsic terminators trigger pausing on weak RNA-DNA hybrids followed by formation of a strong, GC-rich stem-loop in the RNA exit channel of RNA polymerase (RNAP), inactivating nucleotide addition and inducing dissociation of RNA and RNAP from DNA. Although the movements of RNA and DNA during intrinsic termination have been studied extensively leading to multiple models, the effects of RNAP conformational changes remain less well-defined. RNAP contains a clamp domain that closes around the nucleic-acid scaffold during transcription initiation and can be displaced by either swiveling or opening motions. Clamp opening is proposed to promote termination by releasing RNAP-nucleic acid contacts. We developed a cysteine-crosslinking assay to constrain clamp movements and study effects on intrinsic termination. We found that biasing the clamp into different conformations perturbed termination efficiency, but that perturbations were due primarily to changes in elongation rate, not the competing rate at which ECs commit to termination. After commitment, however, inhibiting clamp movements slowed release of DNA but not of RNA from the EC. We also found that restricting trigger-loop movements with the RNAP inhibitor microcin J25 prior to commitment inhibits termination, in agreement with a recently proposed multistate-multipath model of intrinsic termination. Together our results support views that termination commitment and DNA release are separate steps and that RNAP may remain associated with DNA after termination.HighlightsDisulfide bond crosslinks probe the role of the RNAP clamp domain in terminationRNA but not DNA can release at terminators when the RNAP clamp is closedRestricting RNAP clamp movement affects elongation rate more than termination rateInhibiting TL conformational flexibility impairs both RNA and DNA release

scholarly journals An evaluation of the accelerometer output as a motion artifact signal during photoplethysmograph signal processing control

2020 ◽  
Vol 20 (1) ◽  
pp. 125
Author(s):  
Muhideen Abbas Hasan ◽  
Munther Naif Thiyab ◽  
Settar S. Keream ◽  
Uzba H, Salaman ◽  
Kaleid W. Abid
Keyword(s):  
Adaptive Filters ◽  
Signal To Noise Ratio ◽  
Motion Artifact ◽  
Probe Design ◽  
Real Motion ◽  
Cardiovascular Assessment ◽  
Health Related ◽  
Processing Control ◽  
Adaptive Noise ◽  
Better Than

<span>Photoplethysmography (PPG) sensors are widely used in medical applications due to their attractive properties such as non-invasiveness, inexpensive, and easy setup. However, they are still inefficient in non-stationary states of important measurements related to cardiovascular assessment.  Adaptive noise cancellation (ANC) has existed as a kind of technique to address this issue. Unfortunately, the traditional 3-Axis Accelerometer (ACC) in ANC implementation has failed to provide the real motion artifact (MA) as the main factor for efficient adaptive filtering. In this work, the performance of ACC will be investigated and compared with a new twin photodiodes PPG probe design (TPs-PPD) that has been proven in previous work. The TPs-PPD contained an added covered photodiode (CPD) customized to obtain the MA instead of classic use of ACC. During different motions, PPG data were recorded and processed at the same time by the same two units of adaptive filters using ACC and CPD as noise references. The results indicated a clear failure of the ACC compared to the CPD in determining important features of PPG signal, in addition to the accuracy of signal to noise ratio (SNR) and mean square error (MSE). The CPD was better than ACC as it reduced the MSE by 14 times while the SNR was multiplied 10 times. Without any doubt, it has been proven with evidence that the ACC is not suitable for the processing of human health-related signals while PPG can be used for such purposes.</span>

scholarly journals DNA Detection ofToxoplasma gondiiwith a Magnetic Molecular Beacon Probe via CdTe@Ni Quantum Dots as Energy Donor

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Shichao Xu ◽  
Chen Zhang ◽  
Lei He ◽  
Tongyao Wang ◽  
Liusong Ni ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Toxoplasma Gondii ◽  
Molecular Beacon ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Xrd Analysis ◽  
Stem Loop ◽  
Current Sensing ◽  
Energy Donor ◽  
Base Pair Mismatch

A new method for detection ofToxoplasma gondiivia DNA sensing technology was developed in this study. It was based on the mechanism of fluorescence resonance energy transfer (FRET) in which multifunctional and magnetic-fluorescent CdTe@Ni quantum dots (mQDs) were utilized as energy donor and a commercial BHQ2as acceptor. The sensing probe was fabricated by labeling a stem-loopToxoplasma gondiiDNA oligonucleotide with CdTe@Ni mQDs at the 5′ end and BHQ2at 3′ end, respectively. The surface assembly of CdTe on Ni core and the formation of CdTe@Ni were confirmed by XRD analysis. The sizes of CdTe, Ni nanoparticles, and CdTe@Ni were measured via TEM and XRD methods and estimated to be~3 nm,~15 nm, and~20 nm, respectively. The sensing ability was investigated by the fluorescence spectrum (FS). An obvious fluorescence recovery was observed when the complete complimentary targetToxoplasma gondiiDNA was introduced, which did not happen in the case of the target DNA with one-base pair mismatch. Our research indicates that the current sensing probe is sensitive and specific in detection ofToxoplasma gondiiDNA and has great potential in Toxoplasmosis diagnosis.

scholarly journals QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable

2019 ◽  
Author(s):  
Michele Berselli ◽  
Enrico Lavezzo ◽  
Stefano Toppo
Keyword(s):  
Human Gene ◽  
State Of The Art ◽  
Comprehensive Analysis ◽  
Supplementary Information ◽  
Gene Promoters ◽  
Supplementary Data ◽  
Stem Loop ◽  
Hiv 1 ◽  
Rna And Dna ◽  
The Web

Abstract Motivation G-quadruplexes (G4s) are non-canonical nucleic acid conformations that are widespread in all kingdoms of life and are emerging as important regulators both in RNA and DNA. Recently, two new higher-order architectures have been reported: adjacent interacting G4s, and G4s with stable long loops forming stem-loop structures. As there are no specialized tools to identify these conformations, we developed QPARSE. Results QPARSE can exhaustively search for degenerate potential quadruplex-forming sequences (PQSs) containing bulges and/or mismatches at genomic level, as well as either multimeric or long-looped PQS (MPQS and LLPQS respectively). While its assessment vs. known reference datasets is comparable with the state-of-the-art, what is more interesting is its performance in the identification of MPQS and LLPQS that present algorithms are not designed to search for. We report a comprehensive analysis of MPQS in human gene promoters and the analysis of LLPQS on three experimentally validated case studies from HIV-1, BCL2, and hTERT. Availability QPARSE is freely accessible on the web at http://www.medcomp.medicina.unipd.it/qparse/index or downloadable from github as a python 2.7 program https://github.com/B3rse/qparse Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Identification of a cis-Acting Replication Element within the Poliovirus Coding Region

2000 ◽  
Vol 74 (10) ◽  
pp. 4590-4600 ◽  
Author(s):  
Ian Goodfellow ◽  
Yasmin Chaudhry ◽  
Andrew Richardson ◽  
Janet Meredith ◽  
Jeffrey W. Almond ◽  
...  
Keyword(s):  
Rna Virus ◽  
Site Directed Mutagenesis ◽  
Evolutionary Significance ◽  
Rna Structures ◽  
Coding Region ◽  
Rna Sequences ◽  
Stem Loop ◽  
Cis Acting ◽  
Function Recovery ◽  
Positive Sense

ABSTRACT The replication of poliovirus, a positive-stranded RNA virus, requires translation of the infecting genome followed by virus-encoded VPg and 3D polymerase-primed synthesis of a negative-stranded template. RNA sequences involved in the latter process are poorly defined. Since many sequences involved in picornavirus replication form RNA structures, we searched the genome, other than the untranslated regions, for predicted local secondary structural elements and identified a 61-nucleotide (nt) stem-loop in the region encoding the 2C protein. Covariance analysis suggested the structure was well conserved in the Enterovirus genus of the Picornaviridae. Site-directed mutagenesis, disrupting the structure without affecting the 2C product, destroyed genome viability and suggested that the structure was required in the positive sense for function. Recovery of revertant viruses suggested that integrity of the structure was critical for function, and analysis of replication demonstrated that nonviable mutants did not synthesize negative strands. Our conclusion, that this RNA secondary structure constitutes a novel polioviruscis-acting replication element (CRE), is supported by the demonstration that subgenomic replicons bearing lethal mutations in the native structure can be restored to replication competence by the addition of a second copy of the 61-nt wild-type sequence at another location within the genome. This poliovirus CRE functionally resembles an element identified in rhinovirus type 14 (K. L. McKnight and S. M. Lemon, RNA 4:1569–1584, 1998) and the cardioviruses (P. E. Lobert, N. Escriou, J. Ruelle, and T. Michiels, Proc. Natl. Acad. Sci. USA 96:11560–11565, 1999) but differs in sequence, structure, and location. The functional role and evolutionary significance of CREs in the replication of positive-sense RNA viruses is discussed.

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