Добірка наукової літератури з теми "Ion-RNA Interactions"
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Статті в журналах з теми "Ion-RNA Interactions"
Yu, Tao, Yuhong Zhu, Zhaojian He, and Shi-Jie Chen. "Predicting Molecular Crowding Effects in Ion–RNA Interactions." Journal of Physical Chemistry B 120, no. 34 (August 12, 2016): 8837–44. http://dx.doi.org/10.1021/acs.jpcb.6b05625.
Повний текст джерелаEdwards, Thomas E., and Snorri Th Sigurdsson. "EPR spectroscopic analysis of TAR RNA–metal ion interactions." Biochemical and Biophysical Research Communications 303, no. 2 (April 2003): 721–25. http://dx.doi.org/10.1016/s0006-291x(03)00411-x.
Повний текст джерелаFingerhut, Benjamin P., Eva M. Bruening, Jakob Schauss, Torsten Siebert, and Thomas Elsaesser. "Interactions of RNA and Water probed by 2D-IR Spectroscopy." EPJ Web of Conferences 205 (2019): 10003. http://dx.doi.org/10.1051/epjconf/201920510003.
Повний текст джерелаEdwards, Thomas E., Tamara M. Okonogi, and Snorri Th Sigurdsson. "Investigation of RNA-Protein and RNA-Metal Ion Interactions by Electron Paramagnetic Resonance Spectroscopy." Chemistry & Biology 9, no. 6 (June 2002): 699–706. http://dx.doi.org/10.1016/s1074-5521(02)00150-3.
Повний текст джерелаNguyen, Hung T., Naoto Hori, and D. Thirumalai. "Theory and simulations for RNA folding in mixtures of monovalent and divalent cations." Proceedings of the National Academy of Sciences 116, no. 42 (September 30, 2019): 21022–30. http://dx.doi.org/10.1073/pnas.1911632116.
Повний текст джерелаLe, Shu-Yun, Jih-H. Chen, N. Pattabiraman, and Jacob V. Maizel. "Ion-RNA Interactions in the RNA Pseudoknot of a Ribosomal Frameshifting Site: Molecular Modeling Studies." Journal of Biomolecular Structure and Dynamics 16, no. 1 (August 1998): 1–11. http://dx.doi.org/10.1080/07391102.1998.10508221.
Повний текст джерелаWu, Yuan-Yan, Zhong-Liang Zhang, Jin-Si Zhang, Xiao-Long Zhu, and Zhi-Jie Tan. "Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA." Nucleic Acids Research 43, no. 12 (May 27, 2015): 6156–65. http://dx.doi.org/10.1093/nar/gkv570.
Повний текст джерелаKhan, Mateen A. "Analysis of Ion and pH Effects on Iron Response Element (IRE) and mRNA-Iron Regulatory Protein (IRP1) Interactions." Current Chemical Biology 14, no. 2 (November 19, 2020): 88–99. http://dx.doi.org/10.2174/2212796814999200604121937.
Повний текст джерелаLemkul, Justin A. "Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes." Nucleic Acids Research 48, no. 2 (December 6, 2019): 561–75. http://dx.doi.org/10.1093/nar/gkz1154.
Повний текст джерелаKleiman, Diego E., Nawavi Naleem, and Serdal Kirmizialtin. "Exploring the Ion-Mediated RNA Interactions of a Helix-Junction-Helix RNA Model through Well-Tempered Metadynamics Simulations." Biophysical Journal 118, no. 3 (February 2020): 68a—69a. http://dx.doi.org/10.1016/j.bpj.2019.11.549.
Повний текст джерелаДисертації з теми "Ion-RNA Interactions"
Okafor, Chiamaka Denise. "Metallobiochemistry of RNA: Mg(II) and Fe(II) in divalent binding sites." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/53904.
Повний текст джерелаPiccolo, Stefano. "Biophysical characterization of aptamer-ligand interactions by native mass spectrometry." Thesis, Bordeaux, 2019. http://www.theses.fr/2019BORD0276.
Повний текст джерелаAptamers are single-stranded nucleic acids capable to bind selectively to a ligand or to a family of molecules. Aptamers are the sensing part of riboswitches, which are regulatory segments of messenger RNA involved in gene expression. Aptamers are also promising artificial probes, sensors and stimuli-responsive elements. In the development of aptamer-based technology, it is crucial to understand how binding is occurring, to quantify affinities, and ligand-induced conformational changes. The objective of this thesis is to explore the applicability of native IM-MS to DNA and RNA aptamers to quantify binding and to detect conformational change upon binding.In the first part, we evaluated the quantitative determination of equilibrium dissociation constants (KD) by mass spectrometry (MS), and the necessity of including a correction for relative response factors of free and bound aptamers. We compared isothermal titration calorimetry and MS titrations to validate the quantifications. Two RNA aptamers were taken as models: the malachite green aptamer, extensively studied by ITC, and the riboflavin mononucleotide aptamer, a case of Mg2+-dependent ligand binding. We observed that typical volatile electrolytes ammonium acetate and trimethyl ammonium acetate are suitable to study RNA aptamer binding, and that comparable KD values are obtained from ITC and native MS. The neomycin and tobramycin RNA aptamers were chosen to test the limit of detection of native MS. We found that native MS is appropriate to determine KD values in the range from 50 nM to 30 µM. The relative response factor correction was relatively modest in all cases, suggesting that the ligand binding is not associated to a significant conformational difference upon ionization. For these aptamers, we conclude that assuming equal response factors is acceptable.In the second part, we evaluated whether the aptamers’ “adaptive binding” mechanism can be revealed by ion mobility spectrometry (IMS). To this aim, in addition to the systems listed above we studied the tetracycline RNA aptamer and a series of cocaine-binding DNA aptamers, for which the conformational change upon binding is reported in literature. For all aptamers except the tetracycline aptamer, we did not observe a significant difference in the shape of the gas-phase structure upon ligand or Mg2+ binding. However, a significant change was observed in tetracycline RNA aptamer’s ion mobilities, at biologically relevant concentration of Mg2+ (100 µM), and we found that Mg2+ is essential for ligand binding, in agreement with previous solution studies. For the cocaine-binding DNA aptamer series, although we observed similar compactness for the free and bound aptamers in soft pre-IMS conditions, a conformational extension occurs at high pre-IMS activation, best revealed by charge state 7-, suggesting gas-phase rearrangements. To better investigate whether the energetics of these rearrangements depend on pre-folding or on ligand binding, we modified the sequences with dA overhangs, to compare systems with similar numbers of degrees of freedom without altering the core structure. We also propose new ways of presenting the data, adapted to the cases where ligand dissociation, declustering and unfolding occur at similar voltages. The gradual increase of the pre-IMS collisional activation revealed that the unfolding energetics is correlated with the base pairs content, suggesting that base pairs are conserved in the gas-phase structures. We also found that ligand is lost at lower energies than unfolding.In summary, gas-phase compaction occur for both the free aptamers and bound aptamers, and memories of the solution-phase structures can only be revealed in some particular cases. However, the compaction towards similar shapes might constitute an advantage for the quantification, because molecular systems of similar shapes have similar electrospray responses. Consequently, native MS provides reliable estimations of KD values
Downey, Christopher Dale. "Metal ion dependence, thermodynamics, and kinetics of the GAAA tetraloop-receptor RNA tertiary interaction." Diss., Connect to online resource, 2006. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3239459.
Повний текст джерелаBrännvall, Mathias. "Metal ion cooperativity in Escherichia coli RNase P RNA." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2002. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-2056.
Повний текст джерелаYuan, Faqing. "RNA-metal ion interactions and metal ion- induced conformational change in the spliceosomal U2-U6 snRNA complex studied by lanthanide ion luminescence and resonance energy transfer techniques." 2008. http://etd.lib.fsu.edu/theses/available/etd-04122008-213549.
Повний текст джерелаAdvisors: Nancy L. Greenbaum [and] Geoffrey F. Strouse, Florida State University, College of Arts and Sciences, Dept. of Chemistry & Biochemistry. Title and description from dissertation home page (viewed June 20, 2008). Document formatted into pages; contains xv, 120 pages. Includes bibliographical references.
Mathews, Ryan. "Cleavage of an RNA analog by mononuclear zinc(II) macrocyclic complexes and metal ion and metallodrug interactions with deoxyribonucleic acids." 2008. http://proquest.umi.com/pqdweb?did=1594480911&sid=1&Fmt=2&clientId=39334&RQT=309&VName=PQD.
Повний текст джерелаTitle from PDF title page (viewed on Jan. 22, 2009) Available through UMI ProQuest Digital Dissertations. Thesis adviser: Morrow, Janet R. Includes bibliographical references.
Kumar, Sunil. "Metal Ion Mediated Riboswitch Folding and Cognate Ligand Sensing." Thesis, 2022. https://etd.iisc.ac.in/handle/2005/6007.
Повний текст джерелаChiu, Wen-Chieh, та 邱玟潔. "Effect of Side Chain Length on Ion Pairing Interaction in β-Hairpin and Arginine Di-Methylation on RNA Recognition and Cellular Uptake". Thesis, 2013. http://ndltd.ncl.edu.tw/handle/06565281535238628465.
Повний текст джерела國立臺灣大學
化學研究所
101
Ion pairing interactions play important roles in protein stability and RNA recognition. Ion pairs are formed between a pair of oppositely charged amino acids. Interestingly, natural charged amino acids have different number of hydrophobic methylenes on their side chains. For negatively charged residues, Asp has one methylene and Glu has two methylenes. The analogous non-encoded negatively charged amino acid, Aad, contains three methylenes. To study the effect of negatively charged amino acid side chain length on cross strand ion pairs in β-sheets stability, a basic β-hairpin model HPTZbbArg was designed. Zbb denotes the negatively charged residues. The hairpin structure for peptides HPTAspArg, HPTGluArg, and HPTAadArg were confirmed by NMR methods. The fraction folded of the peptides was determined using chemical shift data involving the fully unfolded and the fully folded reference peptides. The interaction free energy followed the trend: Aad-Arg > Glu-Arg ≈ AspArg. Apparently, the longer the negatively charged residue side chain length, the stronger the ion pairing interaction. HIV-1 Tat protein contains an arginine-rich sequence (Tat49-57), which binds specifically to the trans-activating responsive (TAR) element and plays an important role in nuclear localization. The binding of HIV-1 Tat protein and TAR RNA is essential for HIV-1 virus genome replication. To study the effect of arginine dimethylation on RNA recognition and cellular uptake, each arginine residue in Tat49-57 was replaced with a dimethylated arginine including ADMA and SDMA, the asymmetric and symmetric dimethylated forms, respectively. The dissociation constant for the Tat derived peptide-TAR RNA complexes was determined by gel shift assay. The cellular uptake efficiency of these Tat derived peptides into Jurkat cells was assessed by flow cytometry.
Cieplak-Rotowska, Maja. "Biophysical and molecular biology studies of proteins involved in gene silencing." Doctoral thesis, 2017. https://depotuw.ceon.pl/handle/item/2368.
Повний текст джерелаNiniejsza praca doktorska dotyczy biofizycznych podstaw oddziaływania między białkami zaangażowanymi w wyciszanie ekspresji genów przez mikro-RNA (miRNA), a mianowicie pomiędzy białkiem CNOT1 a domeną wyciszającą białka GW182. W procesie wyciszania ekspresji genów przez miRNA, cząsteczki te wiążą się z białkiem Argonaute i naprowadzają je na cząsteczkę mRNA, która ma ulec wyciszeniu. Z białkiem Argonaute oddziałuje białko GW182, które z kolei wiąże się z kompleksem deadenylaz CCR4-NOT. Kompleks ten deadenyluje mRNA oraz może także blokować jego translację, co łącznie prowadzi do wyciszenia ekspresji danego genu. Z kolei w wyciszaniu mRNA zawierających sekwencje bogate w adeninę i urydynę, rolę miRNA wraz z Argonaute i GW182 pełni białko o nazwie tristetraprolina, które odgrywa kluczową rolę w procesach odpowiedzi na stany zapalne. Oddziaływania pomiędzy składnikami tego skomplikowanego układu białek o wielkich masach cząsteczkowych są jeszcze stosunkowo słabo poznane. W szczególności, nieznane były miejsca odpowiedzialne za tworzenie kompleksu pomiędzy GW182 a CCR4-NOT. Doświadczenia z zakresu biologii molekularnej pozwoliły na identyfikację miejsc wiążących CCR4-NOT w sekwencji domeny wyciszającej białka GW182. Jedno z nich ma kluczowy wpływ na deadenylację, a drugie - kluczowy wpływ na oddziaływanie z kompleksem CCR4-NOT za pośrednictwem jego centralnej podjednostki CNOT1. Badania biofizyczne metodą wymiany wodór-deuter sprzężoną ze spektrometrią mas pozwoliły z kolei na identyfikację miejsca oddziaływania GW182 na białku CNOT1 (we fragmencie 800-999), które, niespodziewanie, okazało się bardzo dobrze pokrywać z miejscem oddziaływania CNOT1(800-999) z tristetraproliną. Eksperymenty biochemiczne wykazały, że białka te konkurują o miejsce oddziaływania na CNOT1(800-999). Białka GW182 i tristetraprolina oddziałują z CNOT1 wykorzystując ten sam motyw sekwencji, RLPXφ, w bardzo podobny, jednak nie identyczny sposób. Sekwencja ta prawdopodobnie działa jako tzw. krótki motyw liniowy (z ang. short linear motif, SLiM). Zatem te dwa szlaki kontroli nad ekspresją genów krzyżują się. W pracy zbadano także dynamikę strukturalną białka CNOT1(800-999) oraz domeny wyciszającej białka GW182. Wykazano eksperymentalnie, że białko GW182 ma nieustrukturyzowany charakter, oprócz domeny wiążącej RNA (RRM), która ma strukturę bardzo dynamiczną. Natomiast białko CNOT1(800-999) charakteryzuje się stabilną, ściśle upakowaną strukturą. Przeprowadzone badania doprowadziły do odkrycia miejsc oddziaływania pomiędzy natywnie nieustrukturyzowaną domeną wyciszającą GW182, a helikalnym fragmentem białka CNOT1(800 999), przyczyniając się do zrozumienia molekularnych mechanizmów rozpoznawania w kompleksach białkowych odpowiedzialnych za regulację ekspresji genów w różnych procesach komórkowych.
Книги з теми "Ion-RNA Interactions"
Benarroch, Eduardo E. Neuroscience for Clinicians. Oxford University Press, 2021. http://dx.doi.org/10.1093/med/9780190948894.001.0001.
Повний текст джерелаЧастини книг з теми "Ion-RNA Interactions"
Donghi, Daniela, and Roland K. O. Sigel. "Metal Ion–RNA Interactions Studied via Multinuclear NMR." In Methods in Molecular Biology, 253–73. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-545-9_16.
Повний текст джерелаHarris, Michael E. "Identification and Characterization of Metal Ion Coordination Interactions with RNA by Quantitative Analysis of Thiophilic Metal Ion Rescue of Site-Specific Phosphorothioate Modifications." In Handbook of RNA Biochemistry, 285–300. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2014. http://dx.doi.org/10.1002/9783527647064.ch14.
Повний текст джерелаLeipply, Desirae, Dominic Lambert, and David E. Draper. "Ion–RNA Interactions." In Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B, 433–63. Elsevier, 2009. http://dx.doi.org/10.1016/s0076-6879(09)69021-2.
Повний текст джерелаDeRose, Victoria J., and Matthew V. Yglesias. "Metal Ion Interactions With DNA, RNA, and Nucleic Acid Enzymes." In Comprehensive Coordination Chemistry III, 968–93. Elsevier, 2021. http://dx.doi.org/10.1016/b978-0-08-102688-5.00112-4.
Повний текст джерелаGoodenough, Ursula. "How Life Works." In The Sacred Depths of Nature, 41–62. 2nd ed. Oxford University PressNew York, 2023. http://dx.doi.org/10.1093/oso/9780197662069.003.0005.
Повний текст джерелаGreenfeld, Max, and Daniel Herschlag. "Probing Nucleic Acid–Ion Interactions with Buffer Exchange-Atomic Emission Spectroscopy." In Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B, 375–89. Elsevier, 2009. http://dx.doi.org/10.1016/s0076-6879(09)69018-2.
Повний текст джерелаPabit, Suzette A., Kenneth D. Finkelstein, and Lois Pollack. "Using Anomalous Small Angle X-Ray Scattering to Probe the Ion Atmosphere Around Nucleic Acids." In Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B, 391–410. Elsevier, 2009. http://dx.doi.org/10.1016/s0076-6879(09)69019-4.
Повний текст джерела