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Does RNA easily make secondary structure than DNA?

Nucleic acid secondary structure

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RNA tends to form secondary structures more readily than DNA. RNA sequences fold into secondary structures where bases pair with each other, creating intricate patterns . This folding is crucial as the three-dimensional structure of RNA determines its cellular functions . Computational prediction of RNA structures is increasingly important due to the vast number of RNA sequences being discovered, with RNA folding models like Vfold2D-MC and VfoldMCPX enhancing structure predictions . In contrast, DNA typically forms a double-helix structure, which is more stable and less prone to secondary structure formation compared to RNA . The differences in structural stability and folding behavior between RNA and DNA highlight the unique functional roles and properties of these two nucleic acids.

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Book Chapter•DOI RNA Secondary Structures: Combinatorial Models and Folding Algorithms Qijun He, Matthew S. Macauley, Robin Davies - Show less +2 more 01 Jan 2015 1 Citations	RNA easily forms secondary structures compared to DNA due to its single-stranded nature, which allows it to fold and bond to itself, influencing cellular function and biological processes.
Open access•Posted Content Designing RNA Secondary Structures is Hard Édouard Bonnet, Paweł Rzążewski, Paweł Rzążewski, Florian Sikora - Show less +3 more 31 Oct 2017-arXiv: Data Structures and Algorithms 2 Citations	Designing RNA secondary structures is NP-complete, indicating it is not easier than DNA. Both RNA and DNA have complexities in forming secondary structures.
Open access•Book•DOI Designing RNA Secondary Structures is Hard Édouard Bonnet, Paweł Rzążewski, Paweł Rzążewski, Florian Sikora - Show less +3 more 21 Apr 2018 17 Citations	Designing RNA secondary structures is NP-complete, indicating it is not easy. The complexity remains unsettled, contrasting with DNA secondary structure formation.
Open access•Journal Article•DOI Designing RNA Secondary Structures Is Hard. Édouard Bonnet, Paweł Rzążewski, Paweł Rzążewski, Florian Sikora - Show less +3 more 11 Mar 2020-Journal of Computational Biology 11 Citations	Designing RNA secondary structures is challenging, indicating that RNA does not easily form secondary structures compared to DNA. The process is complex due to base pairing constraints.
Dissertation•DOI Predicting RNA secondary structures using physics-based modeling and evolutionary inferences Tiziano Dorandi 07 Feb 2023	RNA easily forms secondary structures due to its single-stranded nature, allowing for base pairing interactions, unlike DNA, which is typically double-stranded and less prone to secondary structure formation.

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What are the different approaches to predicting RNA secondary structures?4 answersThere are several approaches to predicting RNA secondary structures. Traditional energy-based algorithms have been used, but they lack precision for non-nested sequences. Machine learning algorithms, such as deep learning and shallow learning, have also been employed, but their performance varies depending on the data distribution and the RNA families being predicted. Another approach is using gate-based quantum algorithms, which have shown promise in accurately predicting RNA folding. Physics-based models, such as the Vfold2D-MC and VfoldMCPX models, have been developed to compute loop free energy parameters and predict the folding of multi-RNA complexes. Additionally, a deep learning model called RNA-par has been proposed, which partitions an RNA sequence into fragments and assembles them to acquire the complete secondary structure.

Why RNA extraction is tougher than DNA extraction?3 answersRNA extraction is tougher than DNA extraction due to several factors. RNA is a fragile molecule that requires clean conditions and careful handling, compared to the more rugged DNA. RNA is also transient and easily degraded by RNase enzymes, which are present for biological cellular function. Additionally, the extraction of high-quality RNA requires the removal of proteins and inhibitor enzymes that can interfere with downstream processes. Furthermore, the long-term survival of RNA in postmortem tissues is challenging, with high rates of null/inconclusive PCR-based results observed in aged/forensic specimens. Despite these challenges, RNA extraction is crucial for understanding the various types and functions of RNA, which play important roles in cellular processes and disease development.

What is not a difference between DNA and RNA?5 answersDNA and RNA have several differences, but one thing that is not a difference between them is the presence of adenine, guanine, and cytosine in both DNA and RNA.

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