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RNA folding
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Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. RNA modifications play a key role in RNA folding and function and their dysregulation in humans has been linked to several diseases such as cancer, metabolic diseases or neurological disorder
10p
viginny
23-12-2022
13
3
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Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes
General translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage.
24p
vielonmusk
30-01-2022
16
2
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Four-stranded G-quadruplexes (G4s) are DNA secondary structures in the human genome that are primarily found in active promoters associated with elevated transcription. Here, we explore the relationship between the folding of promoter G4s, transcription and chromatin state.
14p
viarchimedes
26-01-2022
10
0
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By definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis.
12p
visilicon2711
20-08-2021
10
1
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Physical forces, such as mechanical stress, are essential for tissue homeostasis and influence gene expression of cells. In particular, the fibroblast has demonstrated sensitivity to extracellular matrices with assumed adaptation upon various mechanical loads.
19p
visilicon2711
20-08-2021
8
1
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Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina.
13p
vijeeni2711
24-07-2021
9
0
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RNA sequencing analysis focus on the detection of differential gene expression changes that meet a two-fold minimum change between groups. This paper develops methods that apply variance and dispersion estimates to intra-group data to identify genes with expression values that diverge from the group envelope.
19p
vilichoo2711
23-06-2021
6
1
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Voice disorders are a worldwide problem impacting human health, particularly for occupational voice users. Avoidance of surface dehydration is commonly prescribed as a protective factor against the development of dysphonia.
13p
vilichoo2711
25-06-2021
17
1
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The temperature downshift results in (1) decrease in membrane fluidity (2) changes in nucleic acid structures (3) reduced ribosome function (4) inefficient protein folding. Bacteria respond to this low temperature change by producing cold-shock proteins (CSPs) that bind to single-stranded RNA and DNA thereby, maintaining cell physiology. CSPs have been widely studied in Escherichia coli and Bacillus subtilis. Here we discuss the cold adaptation by desaturase system, RNA chaperone, and transcription antitermination function of CspA homologues.
8p
cothumenhmong9
18-01-2021
15
2
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Dihydrouridine (D) is a modified base found in conserved positions in the D-loop of tRNA in Bacteria, Eukaryota, and some Archaea. Despite the abundant occurrence of D, little is known about its biochemical roles in mediating tRNA function. It is assumed that D may destabilize the structure of tRNA and thus enhance its conformational flexibility.
15p
viwyoming2711
16-12-2020
16
1
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RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: Given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The inverse problem of designing a sequence folding into a particular target structure has only more recently received notable interest.
12p
viwyoming2711
16-12-2020
15
0
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Perfectly formed duplex elements in RNA occur within folding units, often as a part of hairpin motifs which can be reliably predicted by various RNA folding algorithms. Double helices with consecutive Watson-Crick base-pairing may also be formed between distant RNA segments thereby facilitating long-range interactions of long-chain RNA that may be biologically functional.
8p
viwyoming2711
16-12-2020
10
1
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RNAalifold, a popular computational method for RNA consensus structure prediction, incorporates covarying mutations into a thermodynamic model to fold the aligned RNA sequences. When quantifying covariance, it evaluates conserved signals of two aligned columns with base-pairing rules.
10p
viwyoming2711
16-12-2020
10
1
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RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in the structure, as in the case of riboswitches, and thus the analysis of RNA folding kinetics is crucial for their study.
13p
vikentucky2711
26-11-2020
22
1
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Improving accuracy and efficiency of computational methods that predict pseudoknotted RNA secondary structures is an ongoing challenge. Existing methods based on free energy minimization tend to be very slow and are limited in the types of pseudoknots that they can predict.
17p
vikentucky2711
26-11-2020
12
3
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Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: The fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions.
12p
vikentucky2711
26-11-2020
9
1
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Identifying sequence-structure motifs common to two RNAs can speed up the comparison of structural RNAs substantially. The core algorithm of the existent approach ExpaRNA solves this problem for a priori known input structures.
14p
vikentucky2711
26-11-2020
8
1
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RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been done to align two known RNA secondary structures with pseudoknots taking into account both sequence and structure information of the two RNAs.
15p
vikentucky2711
26-11-2020
10
1
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RNA regulatory elements play a significant role in gene regulation. Riboswitches, a widespread group of regulatory RNAs, are vital components of many bacterial genomes. These regulatory elements generally function by forming a ligand-induced alternative fold that controls access to ribosome binding sites or other regulatory sites in RNA.
77p
vikentucky2711
24-11-2020
16
1
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Many functional RNA molecules fold into pseudoknot structures, which are often essential for the formation of an RNA’s 3D structure. Currently the design of RNA molecules, which fold into a specific structure (known as RNA inverse folding) within biotechnological applications, is lacking the feature of incorporating pseudoknot structures into the design.
7p
vioklahoma2711
19-11-2020
12
2
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