Cargando…

Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes

For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson–Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dawson, Wayne K., Shino, Amiu, Kawai, Gota, Morishita, Ella Czarina
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	MDPI 2021
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8467000/ https://www.ncbi.nlm.nih.gov/pubmed/34575896 http://dx.doi.org/10.3390/ijms22189708

Ejemplares similares

Free energy estimation of short DNA duplex hybridizations
por: Tulpan, Dan, et al.
Publicado: (2010)

Prediction of RNA Pseudoknots Using Heuristic Modeling with Mapping and Sequential Folding
por: Dawson, Wayne K., et al.
Publicado: (2007)

Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase
por: Yamamoto, Norifumi, et al.
Publicado: (2022)

Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules
por: Juan, Ella Czarina Magat, et al.
Publicado: (2007)

Structures of DNA duplexes containing O(6)-carboxymethylguanine, a lesion associated with gastrointestinal cancer, reveal a mechanism for inducing pyrimidine transition mutations
por: Zhang, Fang, et al.
Publicado: (2013)

Improved Model to Predict the Free Energy Contribution of Trinucleotide Bulges to RNA Duplex Stability
por: Murray, Meghan H., et al.
Publicado: (2014)

Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs
por: Yildirim, Ilyas, et al.
Publicado: (2011)

Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study
por: Vergara, Fredd, et al.
Publicado: (2016)

Free energy of DNA duplex formation on short oligonucleotide microarrays
por: Zhang, Li, et al.
Publicado: (2007)

Chemical Profiling of Jatropha Tissues under Different Torrefaction Conditions: Application to Biomass Waste Recovery
por: Watanabe, Taiji, et al.
Publicado: (2014)

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
por: Alkan, Ferhat, et al.
Publicado: (2018)

Multi-Spectroscopic Analysis of Seed Quality and (13)C-Stable-Iotopologue Monitoring in Initial Growth Metabolism of Jatropha curcas L.
por: Komatsu, Takanori, et al.
Publicado: (2014)

Solid-, Solution-, and Gas-state NMR Monitoring of (13)C-Cellulose Degradation in an Anaerobic Microbial Ecosystem
por: Yamazawa, Akira, et al.
Publicado: (2013)

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA
por: Yang, Changwon, et al.
Publicado: (2015)

Nearest-neighbor parameters for 7-deaza-adenosine·uridine base pairs in RNA duplexes
por: Richardson, Katherine E., et al.
Publicado: (2016)

Thermodynamic characterization and nearest neighbor parameters for RNA duplexes under molecular crowding conditions
por: Adams, Miranda S, et al.
Publicado: (2019)

Compaction of RNA Duplexes in the Cell
por: Collauto, Alberto, et al.
Publicado: (2020)

Joint Full-Duplex/Half-Duplex Transmission-Switching Scheduling and Transmission-Energy Allocation in Cognitive Radio Networks with Energy Harvesting
por: Nhut Khai Hoan, Tran, et al.
Publicado: (2018)

Cellulose Digestion and Metabolism Induced Biocatalytic Transitions in Anaerobic Microbial Ecosystems
por: Yamazawa, Akira, et al.
Publicado: (2013)

Pyrene is highly emissive when attached to the RNA duplex but not to the DNA duplex: the structural basis of this difference
por: Nakamura, Mitsunobu, et al.
Publicado: (2005)

Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions
por: Ghosh, Saptarshi, et al.
Publicado: (2023)

Superimposed signaling inspired channel estimation in full-duplex systems
por: Koohian, Abbas, et al.
Publicado: (2018)

Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one
por: Magat Juan, Ella Czarina, et al.
Publicado: (2010)

ISRES+: an improved evolutionary strategy for function minimization to estimate the free parameters of systems biology models
por: Bandodkar, Prasad, et al.
Publicado: (2023)

Equivalence in Color-coded Duplex Sonography Parameters before Complex Microsurgery
por: Rendón-Medina, Marco Aurelio, et al.
Publicado: (2023)

Energy Landscapes for Base-Flipping in a Model DNA Duplex
por: Nicy,, et al.
Publicado: (2022)

Optimal Transport for Free Energy Estimation
por: Decherchi, S., et al.
Publicado: (2023)

Estimating uncertainty in predicted folding free energy changes of RNA secondary structures
por: Zuber, Jeffrey, et al.
Publicado: (2019)

Parameter-free rendering of single-molecule localization microscopy data for parameter-free resolution estimation
por: Descloux, Adrien C., et al.
Publicado: (2021)

Genes and models for estimating genetic parameters for heat tolerance in dairy cattle
por: Habimana, Vincent, et al.
Publicado: (2023)

Improved siRNA/shRNA Functionality by Mismatched Duplex
por: Wu, Haoquan, et al.
Publicado: (2011)

Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
por: Doshi, Kishore J, et al.
Publicado: (2004)

Preoperative duplex ultrasound parameters predicting male fertility after successful varicocelectomy
por: Alshehri, Fahad M., et al.
Publicado: (2015)

Influence of two bulge loops on the stability of RNA duplexes
por: Crowther, Claire V., et al.
Publicado: (2017)

Stability of RNA duplexes containing inosine·cytosine pairs
por: Wright, Daniel J, et al.
Publicado: (2018)

Transposase-assisted tagmentation of RNA/DNA hybrid duplexes
por: Lu, Bo, et al.
Publicado: (2020)

Microwave duplexers
por: Smullin, Louis D, et al.
Publicado: (1948)

Duplex Obturator
por: Rhone, J. W.
Publicado: (1894)

Influence of the 5′-terminal sequences on the 5′-UTR structure of HIV-1 genomic RNA
por: Obayashi, Camille Michiko, et al.
Publicado: (2021)

T-hairpin structure found in the RNA element involved in piRNA biogenesis
por: Takase, Naomi, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_p9n2h5bgd4ocg3d9vn1sil89oe