Results 21 to 30 of about 1,213,585 (311)

Expanding the binding specificity for RNA recognition by a PUF domain

Nature Communications, 2021
The PUF RNAbinding domain has an eight-repeat structure with the ability to bind an eight-base RNA sequence. Here the authors generate a comprehensive library of variants of a PUF domain to find an RNA binding code and design PUF domains that recognize ...
Wei Zhou, Daniel Melamed, Gabor Banyai, Cindy Meyer, Thomas Tuschl, Marvin Wickens, Junyue Cao, Stanley Fields   +7 more
doaj   +1 more source

DMfold: A Novel Method to Predict RNA Secondary Structure With Pseudoknots Based on Deep Learning and Improved Base Pair Maximization Principle

Frontiers in Genetics, 2019
While predicting the secondary structure of RNA is vital for researching its function, determining RNA secondary structure is challenging, especially for that with pseudoknots. Typically, several excellent computational methods can be utilized to predict
Linyu Wang, Linyu Wang, Yuanning Liu, Yuanning Liu, Xiaodan Zhong, Xiaodan Zhong, Xiaodan Zhong, Haiming Liu, Haiming Liu, Chao Lu, Chao Lu, Cong Li, Cong Li, Hao Zhang, Hao Zhang   +14 more
doaj   +1 more source

NCResNet: Noncoding Ribonucleic Acid Prediction Based on a Deep Resident Network of Ribonucleic Acid Sequences

Frontiers in Genetics, 2020
Noncoding RNA (ncRNA) is a kind of RNA that plays an important role in many biological processes, diseases, and cancers, while cannot translate into proteins.
Sen Yang, Yan Wang, Yan Wang, Shuangquan Zhang, Xuemei Hu, Qin Ma, Yuan Tian   +6 more
doaj   +1 more source

Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing. [PDF]

PLoS ONE, 2014
Advances in sequencing technology have allowed for detailed analyses of the transcriptome at single-nucleotide resolution, facilitating the study of RNA editing or sequence differences between RNA and DNA genome-wide.
Jonathan M Toung, Nicholas Lahens, John B Hogenesch, Gregory Grant   +3 more
doaj   +1 more source

Cell-SELEX Identifies a “Sticky” RNA Aptamer Sequence

Journal of Nucleic Acids, 2017
Cell-SELEX is performed to select for cell binding aptamers. We employed an additional selection pressure by using RNAse to remove surface-binding aptamers and select for cell-internalizing aptamers.
Partha Ray, Rebekah R. White
doaj   +1 more source

The anti‐CRISPR protein AcrIE8.1 inhibits the type I‐E CRISPR‐Cas system by directly binding to the Cascade subunit Cas11

FEBS Letters, EarlyView.
In this study, we present the structure of AcrIE8.1, a previously uncharacterized anti‐CRISPR protein that inhibits the type I‐E CRISPR‐Cas system. Through a combination of structural and biochemical analyses, we demonstrate that AcrIE8.1 directly binds to the Cas11 subunit of the Cascade complex to inhibit the CRISPR‐Cas system.
Young Woo Kang, Hyun Ho Park
wiley   +1 more source

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE

BMC Research Notes, 2008
Background The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural level than on the sequence level. Understanding the function of
Dandekar Thomas, Müller Tobias, Seibel Philipp N, Wolf Matthias   +3 more
doaj   +1 more source

An intracellular transporter mitigates the CO2‐induced decline in iron content in Arabidopsis shoots

FEBS Letters, EarlyView.
This study identifies a gene encoding a transmembrane protein, MIC, which contributes to the reduction of shoot Fe content observed in plants under elevated CO2. MIC is a putative Fe transporter localized to the Golgi and endosomal compartments. Its post‐translational regulation in roots may represent a potential target for improving plant nutrition ...
Timothy Mozzanino, Meijie Li, Cécile Fizames, Mattia Adamo, Laurence Lejay, Christian Dubos, Matthieu Platre, Antoine Martin   +7 more
wiley   +1 more source

Sequence-structure relations of pseudoknot RNA

BMC Bioinformatics, 2009
Background The analysis of sequence-structure relations of RNA is based on a specific notion and folding of RNA structure. The notion of coarse grained structure employed here is that of canonical RNA pseudoknot contact-structures with at most two ...
Li Linda YM, Huang Fenix WD, Reidys Christian M   +2 more
doaj   +1 more source

RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.

PLoS Computational Biology, 2022
RNA molecules can adopt stable secondary and tertiary structures, which are essential in mediating physical interactions with other partners such as RNA binding proteins (RBPs) and in carrying out their cellular functions.
Hongli Ma, Han Wen, Zhiyuan Xue, Guojun Li, Zhaolei Zhang   +4 more
doaj   +1 more source