Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

Gong, Zhou; Yang, Shuai; Yang, Qingfen; Zhu, Yue-Ling; Jiang, Jie; Tang, Chun

doi:10.1007/s41048-019-00099-2

Cited by 4 publications

(3 citation statements)

References 55 publications

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“…Paramagnetic cosolutes, which have been used intensively for the study of proteins (section ), have also been used to study oligonucleotides by paramagnetic NMR spectroscopy. For example, the nitroxide radical TEMPOL (Figure ) and the Gd(III) complex of TTHA-TMA (Figure ) have been used to study the surface accessibility of RNA and refine its 3D structure. , …”

Section: General Overview Of Natural and Chemically Generated Paramag...mentioning

confidence: 99%

“…For example, the nitroxide radical TEMPOL (Figure 12) and the Gd(III) complex of TTHA-TMA (Figure 13) have been used to study the surface accessibility of RNA and refine its 3D structure. 396,397 To probe biomolecules more precisely, it is necessary to introduce the spin label at a defined position as rigidly as possible. In the case of proteins, this is usually achieved by siteselective mutation and subsequent covalent bond formation between probe and amino acid side chains (section 3.3).…”

Section: Paramagnetic Probes For Dna and Rnamentioning

confidence: 99%

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Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.

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Section: General Overview Of Natural and Chemically Generated Paramag...mentioning

confidence: 99%

Section: Paramagnetic Probes For Dna and Rnamentioning

confidence: 99%

Paramagnetic Chemical Probes for Studying Biological Macromolecules

et al. 2022

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“…The “RNA folding problem” mainly includes two problems: RNA structure prediction and folding mechanism. The former deals with the determination of secondary and tertiary structures of an RNA directly from its sequences and has been widely studied [ 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 ]. The latter studies how an RNA molecule folds into its secondary and tertiary structures and is still not well understood although there have been some experimental/theoretical studies on RNA folding pathway [ 16 , 17 ], like the hairpin formation [ 18 , 19 , 20 ].…”

Section: Introductionmentioning

confidence: 99%

Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search

Mao

Xiao

2021

Molecules

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RNA molecules participate in many important biological processes, and they need to fold into well-defined secondary and tertiary structures to realize their functions. Like the well-known protein folding problem, there is also an RNA folding problem. The folding problem includes two aspects: structure prediction and folding mechanism. Although the former has been widely studied, the latter is still not well understood. Here we present a deep reinforcement learning algorithms 2dRNA-Fold to study the fastest folding paths of RNA secondary structure. 2dRNA-Fold uses a neural network combined with Monte Carlo tree search to select residue pairing step by step according to a given RNA sequence until the final secondary structure is formed. We apply 2dRNA-Fold to several short RNA molecules and one longer RNA 1Y26 and find that their fastest folding paths show some interesting features. 2dRNA-Fold is further trained using a set of RNA molecules from the dataset bpRNA and is used to predict RNA secondary structure. Since in 2dRNA-Fold the scoring to determine next step is based on possible base pairings, the learned or predicted fastest folding path may not agree with the actual folding paths determined by free energy according to physical laws.

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Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

Tants

Schlundt

2023

ChemBioChem

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RNAs exhibit a plethora of functions far beyond transmitting genetic information. Often, RNA functions are entailed in their structure, be it as a regulatory switch, protein binding site, or providing catalytic activity. Structural information is a prerequisite for a full understanding of RNA‐regulatory mechanisms. Owing to the inherent dynamics, size, and instability of RNA, its structure determination remains challenging. Methods such as NMR spectroscopy, X‐ray crystallography, and cryo‐electron microscopy can provide high‐resolution structures; however, their limitations make structure determination, even for small RNAs, cumbersome, if at all possible. Although at a low resolution, small‐angle X‐ray scattering (SAXS) has proven valuable in advancing structure determination of RNAs as a complementary method, which is also applicable to large‐sized RNAs. Here, we review the technological and methodological advancements of RNA SAXS. We provide examples of the powerful inclusion of SAXS in structural biology and discuss possible future applications to large RNAs.

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Refining RNA solution structures with the integrative use of label-free paramagnetic relaxation enhancement NMR

Cited by 4 publications

References 55 publications

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Paramagnetic Chemical Probes for Studying Biological Macromolecules

Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search

Advances, Applications, and Perspectives in Small‐Angle X‐ray Scattering of RNA

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