Metal ion binding to an RNA internal loop

Bártová, Simona; Alberti, Elena; Sigel, Roland K. O.; Donghi, Daniela

doi:10.1016/j.ica.2016.02.050

Cited by 9 publications

(3 citation statements)

References 39 publications

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“…Extensive efforts have been devoted to understand how metal ions influence RNA folding using various biophysical methods. − Due to the fluctuating nature of the ion atmosphere around the RNA, it is extremely difficult to study its influence on RNA folding using traditional techniques that probe structure, such as X-ray crystallography, NMR, or cryo-electron microscopy. These techniques only identify ions that specifically bind to a group of RNA atoms as part of their coordination shell and stabilize the RNA structure .…”

Section: Introductionmentioning

confidence: 99%

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Halder

Kumar

Valsson

et al. 2020

J. Chem. Theory Comput.

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RNA molecules selectively bind to specific metal ions to populate their functional active states making it important to understand their source of ion selectivity. In large RNA systems, metal ions interact with the RNA at multiple locations making it difficult to decipher the precise role of ions in folding. To overcome this complexity, we studied the role of different metal ions (Mg 2+ , Ca 2+ and K + ) in the folding of a small RNA hairpin motif (5 -ucCAAAga-3 ) using unbiased all-atom molecular dynamics simulations. The advantage in studying this small system is that it requires specific binding of a single metal ion to fold to its native state. We find that even for this small RNA, the folding free energy surface (FES) is multidimensional as different metal ions present in the solution can simultaneously facilitate folding. The FES shows that specific binding of a metal ion is indispensable for its folding. We further show that in addition to the negatively charged phosphate groups, spatial organization of electronegative nucleobase atoms drive the site specific binding of the metal ion. Even though the binding site cannot discriminate between different metal ions, RNA folds efficiently only in Mg 2+ solution. We show that the rigid network of Mg 2+ coordinated water molecules facilitate the formation of important interactions in the transition state. The other metal ions such as K + and Ca 2+ cannot facilitate the formation of such interactions. These results allow us to hypothesize possible metal sensing mechanisms in large metallo-riboswitches and they also provide useful insights for the design of appropriate collective variables for studying large RNA molecules using enhanced sampling methods.

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Section: Introductionmentioning

confidence: 99%

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Halder

Kumar

Valsson

et al. 2020

J. Chem. Theory Comput.

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“…Tb(III)) are currently used in RNA footprinting experiments to map secondary and tertiary structure as well as to identify metal ion binding sites [58,59]. Also, different transition metal ions, like Cd(II) and Mn(II), as well as cobalt(III)hexammine are used as Mg(II) mimics in NMR studies [60][61][62][63][64][65]. These aspects of metal ion-RNA interactions go beyond the scope of this review and will not be further discussed.…”

Section: Rna Structure and Its Intrinsic Need For Metal Ionsmentioning

confidence: 99%

Covalent and non-covalent binding of metal complexes to RNA

Alberti

Zampakou

Donghi

2016

Journal of Inorganic Biochemistry

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Targeting nucleic acids with metal complexes is an exciting and widely explored field of research. Following the discovery of the anticancer drug cisplatin, a number of metal complexes have been designed, synthesised, and tested for their DNA binding properties. On the contrary, the interaction of metal complexes with RNA has been much less investigated. RNA is an essential biomolecule, involved in a variety of crucial cellular functions, which offers a much wider structural diversity than DNA. As such, RNA represents an attractive target for the design and the development of structure-selective therapeutic and diagnostic agents. A few recent publications describe the ability of various metal complexes to interact with RNA, and the binding of cisplatin and derivatives to RNA is being currently investigated. This short review offers an overview of some recent advances on both covalent and non-covalent interactions of metal complexes with RNA and addresses the potential of targeting RNA non-duplex structures.

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“…It has been reported that the molecular size and affinity for cellulose significantly changed the dye absorption with cellulose paper 129 Da, assuming mRNA has an average length of 2200 nucleotide 131 ) or binding of molecules on Whatman paper/steel plates 132,133 . Both could potentially lead to a lower RNA recovery.…”

Section: Validation Of Using Thementioning

confidence: 99%

Advances of the skin microbiopsy for blood and skin sampling with streamlined handling and fabrication settings

Lei¹

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List of Figures List of Tables 1. Literature review, hypotheses and aims 1.1. Literature review 1.2. Hypotheses 1.3. Aims 2. Development of the absorbent microbiopsy for minimally invasive blood and skin sampling 2.1. Introduction 2.2. Materials and methods 2.3. Results 2.4. Conclusion 3. Fabrication scale-up with 3D printing technologies 3.1. Introduction 3.2. Materials and methods 3.3. Results 3.4. Conclusion 4. Plunger redesigning for improving inhouse fabrication capability 4.1. Introduction 4.2. Materials and methods 4.3. Results 4.4. Conclusion 5. Exploring approaches for improving the sample processing experience 5.1. Introduction 5.2. Materials and methods 5.3. Results 5.4. Conclusion 6. Conclusions, general discussion and future plans 6.1. Comparisons of current sampling approaches 6.2. Development of the absorbent microbiopsy for minimally invasive blood and skin sampling 6.3. Fabrication scale-up with 3D printing technologies 6.4. Plunger redesigning for improving inhouse fabrication capability 6.5. Exploring approaches for improving the user experience 6.6. General discussion and future directions 7. References 8. Appendices Appendix 1-Comparison of RNA recoveries between Whatman paper and the entire absorbent microbiopsy Appendix 2-Absorption capacity testing of Whatman paper Appendix 3-ELISA detection limit experiment Appendix 4-Modified skin microbiopsy permitted easier microscopic observation of sample after application Appendix 5-Plunger with removable handlebar improved handling experience Appendix 6-Combining skin and absorbent microbiopsies into one device permitted blood sampling, but the skin channel function required further optimization Appendix 7-Schematic illustration of the absorbent microbiopsy design for the pen applicator (chapter 2) Appendix 8-Schematic illustration of the absorbent microbiopsy array (chapter 3) Appendix 9-AutoCAD drawings of the pen applicator parts (chapter 3) Appendix 10-AutoCAD drawings of folding jig parts design 5 (chapter 3) Appendix 11-AutoCAD drawings of 3D-printed plunger design 2 (chapter 4) Appendix 12-Schematic illustration of the absorbent microbiopsy for acrylic sheet plunger design 8 (chapter 4) Appendix 13-Schematic illustration of acrylic sheet plunger design 8 Appendix 14-Accepted manuscript: Publication on Biomedical Microdevices Appendix 15-Accepted manuscript: Publication on Journal of Visual Experiment UV Ultraviolet VAMS Volumetric absorptive microsampling 2D Two-dimensional 3D Three-dimensional %CV Coefficients of variation Chapter 1: Literature review and hypotheses 1.1. Literature review The following literature review is modified from a published manuscript. A copy of the published version can be found in chapter 8.

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Metal ion binding to an RNA internal loop

Cited by 9 publications

References 39 publications

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Covalent and non-covalent binding of metal complexes to RNA

Advances of the skin microbiopsy for blood and skin sampling with streamlined handling and fabrication settings

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Metal ion binding to an RNA internal loop

Cited by 9 publications

References 39 publications

Mg2+ Sensing by an RNA Fragment: Role of Mg2+-Coordinated Water Molecules

Mg2+ Sensing by an RNA Fragment: Role of Mg2+-Coordinated Water Molecules

Covalent and non-covalent binding of metal complexes to RNA

Advances of the skin microbiopsy for blood and skin sampling with streamlined handling and fabrication settings

Contact Info

Product

Resources

About

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules

Mg²⁺ Sensing by an RNA Fragment: Role of Mg²⁺-Coordinated Water Molecules