Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model

2011 ◽  
Vol 8 (6) ◽  
pp. 1468-1482 ◽  
Author(s):  
Markus E. Nebel ◽  
Anika Scheid
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Structure Model ◽  
Secondary Structure Model

scholarly journals A Structured RNA Motif Is Involved in Correct Placement of the tRNA3Lys Primer onto the Human Immunodeficiency Virus Genome

2000 ◽  
Vol 74 (5) ◽  
pp. 2227-2238 ◽  
Author(s):  
Nancy Beerens ◽  
Bep Klaver ◽  
Ben Berkhout
Keyword(s):  
Human Immunodeficiency Virus ◽  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Correct Placement ◽  
Immunodeficiency Virus ◽  
Trna Primer ◽  
Rna Motif ◽  
Hiv 1

ABSTRACT Human immunodeficiency virus type 1 (HIV-1) reverse transcription is primed by the cellular tRNA3 Lys molecule that binds with its 3′-terminal 18 nucleotides to the fully complementary primer-binding site (PBS) on the viral RNA genome. Besides this complementarity, annealing of the primer may be stimulated by additional base-pairing interactions between other parts of the tRNA molecule and viral sequences flanking the PBS. According to the RNA secondary structure model of the HIV-1 leader region, part of the PBS sequence is involved in base pairing to form a small stem-loop structure, termed the U5-PBS hairpin. This hairpin may be involved in the process of reverse transcription. To study the role of the U5-PBS hairpin in the viral replication cycle, we introduced mutations in the U5 region that affect the stability of this structured RNA motif. Stabilization and destabilization of the hairpin significantly inhibited virus replication. Upon prolonged culturing of the virus mutant with the stabilized hairpin, revertant viruses were obtained with additional mutations that restore the thermodynamic stability of the U5-PBS hairpin. The thermodynamic stability of the U5-PBS hairpin apparently has to stay within narrow limits for efficient HIV-1 replication. Transient transfection experiments demonstrated that transcription of the proviral genomes, translation of the viral mRNAs, and assembly of the virions with a normal RNA content is not affected by the mutations within the U5-PBS hairpin. We show that stabilization of the hairpin reduced the amount of tRNA primer that is annealed to the PBS. Destabilization of the hairpin did not affect tRNA annealing, but the viral RNA-tRNA complex was less stable. These results suggest that the U5-PBS hairpin is involved in correct placement of the tRNA primer on the viral genome. The analysis of virus mutants and revertants and the RNA structure probing experiments presented in this study are consistent with the existence of the U5-PBS hairpin as predicted in the RNA secondary structure model.

scholarly journals Secondary structure of subgenomic RNA M of SARS-CoV-2

2021 ◽  
Author(s):  
Marta Soszynska-Jozwiak ◽  
Ryszard Kierzek ◽  
Elzbieta Kierzek
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Structure Model ◽  
Genomic Rna ◽  
Secondary Structure Model ◽  
Subgenomic Rna ◽  
Positive Sense ◽  
Rna Genome ◽  
Virus Biology

SARS-CoV-2 belongs the Coronavirinae family. As other coronaviruses, SARS-CoV-2 is enveloped and possesses positive-sense, single-stranded RNA genome of ~30 kb. Genome RNA is used as the template for replication and transcription. During these processes, positive-sense genomic RNA (gRNA) and subgenomic RNAs (sgRNAs) are created. Several studies showed importance of genomic RNA secondary structure in SARS-CoV-2 replication. However, the structure of sgRNAs have remained largely unsolved so far. In this study, we performed probing of sgRNA M of SARS-CoV-2 in vitro. This is the first experimentally informed secondary structure model of sgRNA M, which presents features likely to be important in sgRNA M function. The knowledge about sgRNA M provides insights to better understand virus biology and could be used for designing new therapeutics.

Phylogeny of Criconematina Siddiqi, 1980 (Nematoda: Tylenchida) based on morphology and D2-D3 expansion segments of the 28S-rRNA gene sequences with application of a secondary structure model

Nematology ◽  
2005 ◽  
Vol 7 (6) ◽  
pp. 927-944 ◽  
Author(s):  
Renato Crozzoli ◽  
Franco Lamberti ◽  
Nicola Vovlas ◽  
James Baldwin ◽  
Sergei Subbotin ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Secondary Structure ◽  
Sequence Divergence ◽  
Complex Model ◽  
Rrna Gene ◽  
28S Rrna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Loop Region ◽  
Unidentified Species

AbstractThe suborder Criconematina is a large group of ecto- and endoparasitic nematodes, including several species of major agricultural importance. The D2-D3 expansion segments of the 28S nuclear ribosomal RNA gene were amplified and sequenced from 23 nominal and six unidentified species from the genera Mesocriconema, Criconemoides, Ogma, Criconema, Xenocriconemella, Hemicriconemoides, Hemicycliophora, Paratylenchus, Tylenchulus, Trophonema and Sphaeronema, together with outgroup taxa from Tylenchidae (Aglenchus) and Atylenchidae (Eutylenchus). A sequence alignment optimised using the secondary structure model was analysed using maximum parsimony, maximum likelihood and Bayesian inference approaches under two models. All analyses yielded a similar topology with differences primarily in the position of poorly supported clades. Although some molecular trees differ from the previous morphologically based hypotheses of criconematid phylogeny, maximum likelihood tests did not yield statistically significant differences between some of the tested classical morphological and molecular topologies. DNA data support monophyly for the genera Mesocriconema, Hemicriconemoides and Criconema and reject the hypothesis of a single origin of criconematids with a cuticular sheath or 'double cuticle'. Application of the complex model of rRNA evolution, considering paired nucleotides for the stem and unpaired nucleotides for the loop region, resulted in a majority rule consensus Bayesian tree with unresolved relationships between main clades. This lack of resolution is expected by the low number of independently evolving nucleotides. Sequence divergence in this DNA segment between populations of Mesocriconema xenoplax, M. sphaerocephalum and Hemicriconemoides cocophillus suggest the presence of several sibling species under these taxa names.

scholarly journals Secondary structure model for bacterial 16S ribosomal RNA: phylogenetic, enzymatic and chemical evidence

1980 ◽  
Vol 8 (10) ◽  
pp. 2275-2294 ◽  
Author(s):  
C.R. Woese ◽  
L.J. Magrum ◽  
R. Gupta ◽  
R.B. Siegel ◽  
D.A. Stahl ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Ribosomal Rna ◽  
16S Ribosomal Rna ◽  
Structure Model ◽  
Secondary Structure Model ◽  
Chemical Evidence

scholarly journals Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model

1982 ◽  
Vol 10 (15) ◽  
pp. 4679-4685 ◽  
Author(s):  
Bao-Ling Fang ◽  
Raymond De Baere ◽  
Antoon Vandenberghe ◽  
Rupert De Wachter
Keyword(s):  
Secondary Structure ◽  
Structure Model ◽  
Ribosomal Rnas ◽  
Secondary Structure Model
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