Developing Community Resources for Nucleic Acid Structures

Berman, Helen M.; Lawson, Catherine L.; Schneider, Bohdan

doi:10.3390/life12040540

Cited by 9 publications

(5 citation statements)

References 79 publications

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“…The wide variety of flipon structures possible reflect alterations in DNA parameters like twist, writhe, pitch, and basepairing that affect the energetic cost of their formation with many defined by crystallographic and NMR studies [6] with dynamic changes now measurable with high-speed atomic force microscopy (Box 1, Figure 1). [7] The different types of outcomes are numbered in Figure 1 They also cause an overall change in twist reflecting the rotation of the DNA duplex around the nucleosome surface about an axis perpendicular to dyad axis of symmetry.…”

Section: Flipons and Dna Helical Parametersmentioning

confidence: 99%

“…A NoB database with analysis of different genomes is available at https://nonb‐abcc.ncifcrf.gov/apps/site/default. [ 25 ] The Nucleic Acid Database [ 6 ] ( http://ndbserver.rutgers.edu/) contains 12282 structures that can be easily searched to find examples of RNA and DNA flipon conformations (all sites accessed on September 23, 2022)(images in the figure arebased on PDB files1XAV,.1D3X, 4OCB, 1F66, 6HPJ,5F9R and rendered using NGL Viewer. [ 86 ] Helical parameters for A‐DNA, B‐DNA, and Z‐DNA are given in ref.…”

Section: Introductionmentioning

confidence: 99%

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Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate

Herbert

2022

BioEssays

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Alternative non‐B‐DNA conformations formed under physiological conditions by sequences called flipons include left‐handed Z‐DNA, three‐stranded triplexes, and four‐stranded i‐motifs and quadruplexes. These conformations accumulate and release energy to enable the local assembly of cellular machines in a context specific manner. In these transactions, nucleosomes store power, serving like rechargeable batteries, while flipons smooth energy flows from source to sink by acting as capacitors or resistors. Here, I review the known biological roles for flipons. I present recent and unequivocal findings showing how innate immune responses are regulated by Z‐flipons that identify endogenous RNAs as self. Evidence is also presented supporting important roles for other flipon classes. In these examples, the dynamic exchange of energy between flipons and nucleosomes enables rapid switching of genetic programs without altering flipon sequence. The increased phenotypic diversity enabled by flipons drives their natural selection, with adaptations evolving faster than is possible by codon mutation alone.

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Section: Flipons and Dna Helical Parametersmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate

Herbert

2022

BioEssays

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“…Cellular RNA appears as a single strand, which may adopt a variety of secondary structures. The most abundant of these secondary structures is a right-handed double helix known as the A-form, , which constitutes almost 40% of naked ribonucleotides in the Protein Data Bank (PDB, data taken from NDB , ). The similarity in chemical composition of DNA and RNA would suggest similar structural and physical properties for DNA duplex (DNA 2 ) and RNA duplex (RNA 2 ) helices, but in reality, they form duplexes that are notably different.…”

Section: Introductionmentioning

confidence: 99%

Sequence-Dependent Properties of the RNA Duplex

Battistini

Sala

Hospital

et al. 2023

J. Chem. Inf. Model.

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Sequence-dependent properties of the DNA duplex have been accurately described using extensive molecular dynamics simulations. The RNA duplex meanwhile�which is typically represented as a sequenceaveraged rigid rod�does not benefit from having equivalent molecular dynamics simulations. In this paper, we present a massive simulation effort using a set of ABC-optimized duplexes from which we derived tetramerresolution properties of the RNA duplex and a simple mesoscopic model that can represent elastic properties of long RNA duplexes. Despite the extreme chemical similarity between DNA and RNA, the local and global elastic properties of the duplexes are very different. DNA duplexes show a complex and nonelastic pattern of flexibility, for instance, while RNA duplexes behave as an elastic system whose deformations can be represented by simple harmonic potentials. In RNA duplexes (RNA 2 ), not only are intraand interbase pair parameters (equilibrium and mechanical) different from those in the equivalent DNA duplex sequences (DNA 2 ) but the correlations between movements also differ. Simple statements on the relative flexibility or stability of both polymers are meaningless and should be substituted by a more detailed description depending on the sequence and the type of deformation considered.

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“…The PDB database merely includes the bare minimum annotations for RNA chains, such as their names, lengths, and species. Downstream databases like NAKB (formerly known as NDB) [3], DNATCO [4], and BGSU RNA [5] offer more annotations for base pairing, backbone torsions, and 3D motifs, yet the annotation of the RNAs’ biological roles is still wanting. The MeRNA database [6] was probably the only database dedicated to function (in this case, metal ion binding sites) for experimental RNA structures, but it has long been defunct and was limited to 256 RNAs and their binding to metal ions.…”

Section: Introductionmentioning

confidence: 99%

FURNA: a database for function annotations of RNA structures

Zhang,

Freddolino

2023

Preprint

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Despite the increasing number of 3D RNA structures in the Protein Data Bank, the majority of experimental RNA structures lack thorough functional annotations. As the significance of the functional roles played by non-coding RNAs becomes increasingly apparent, comprehensive annotation of RNA function is becoming a pressing concern. In response to this need, we have developed FURNA (Functions ofRNAs), the first database for experimental RNA structures that aims to provide a comprehensive repository of high-quality functional annotations. These include Gene Ontology terms, Enzyme Commission numbers, ligand binding sites, RNA families, protein binding motifs, and cross-references to related databases. FURNA is available athttps://seq2fun.dcmb.med.umich.edu/furna/to enable quick discovery of RNA functions from their structures and sequences.

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Developing Community Resources for Nucleic Acid Structures

Cited by 9 publications

References 79 publications

Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate

Nucleosomes and flipons exchange energy to alter chromatin conformation, the readout of genomic information, and cell fate

Sequence-Dependent Properties of the RNA Duplex

FURNA: a database for function annotations of RNA structures

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