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Smith D, Thomas C, Craig J, Brinkerhoff H, Abell S, Franzi M, Carrasco J, Hoshika S, Benner S, Gundlach J, Laszlo A. Nanopores map the acid-base properties of a single site in a single DNA molecule. Nucleic Acids Res 2024; 52:7429-7436. [PMID: 38884270 PMCID: PMC11260478 DOI: 10.1093/nar/gkae518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
Nanopores are increasingly powerful tools for single molecule sensing, in particular, for sequencing DNA, RNA and peptides. This success has spurred efforts to sequence non-canonical nucleic acid bases and amino acids. While canonical DNA and RNA bases have pKas far from neutral, certain non-canonical bases, natural RNA modifications, and amino acids are known to have pKas near neutral pHs at which nanopore sequencing is typically performed. Previous reports have suggested that the nanopore signal may be sensitive to the protonation state of an individual moiety. We sequenced ion currents with the MspA nanopore using a single stranded DNA containing a single non-canonical DNA base (Z) at various pH conditions. The Z-base has a near-neutral pKa ∼ 7.8. We find that the measured ion current is remarkably sensitive to the protonation state of the Z-base. We demonstrate how nanopores can be used to localize and determine the pKa of individual moieties along a polymer. More broadly, these experiments provide a path to mapping different protonation sites along polymers and give insight in how to optimize sequencing of polymers that contain moieties with near-neutral pKas.
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Affiliation(s)
- Drew C Smith
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, FL 32615, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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2
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Nardi AN, Olivieri A, D'Abramo M, Salvio R. Unveiling the Cleavage Mechanism of an RNA Model Compound on the whole pH Scale: Computations Meet Experiments in the Determination of Reaction Rates. Chemphyschem 2024; 25:e202300873. [PMID: 38526551 DOI: 10.1002/cphc.202300873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/29/2024] [Accepted: 03/24/2024] [Indexed: 03/26/2024]
Abstract
The knowledge of the mechanism of reactions occurring in solution is a primary research line both in the context of theoretical-computational chemistry and in the field of organic and bio-organic chemistry. Given the importance of the hydrolysis of nucleic acids in life-related phenomena, here we present a combined experimental and computational study on the cleavage of an RNA model compound. This phosphodiester features a cleavage rate strictly dependent on the pH with three different dependence domains. Such experimental evidence, highlighted by an in-depth kinetic investigation, unequivocally suggests a change in the reaction mechanism along the pH scale. In order to interpret the data and to explain the experimental behavior, we have applied a theoretical-computational procedure, involving a hybrid quantum/classical approach, able to model chemical reactions in complex environments, i. e. in solution. This study turns out to quantitatively reproduce the experimental data with accuracy and, in addition, provides useful mechanistic insight into the transesterification process of the investigated compound. The study indicates that the cleavage can occur through anA N D N ${A_N D_N }$ , anA N + D N ${A_N + D_N }$ , and aD N A N ${D_N A_N }$ mechanism depending on the pH values.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Riccardo Salvio
- Department of Chemical and Technological Sciences, University of Rome Tor Vergata, Rome, Italy
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3
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Yang Y, Nakayama K, Okada S, Sato K, Wada T, Sakaguchi Y, Murayama A, Suzuki T, Sakurai M. ICLAMP: a novel technique to explore adenosine deamination via inosine chemical labeling and affinity molecular purification. FEBS Lett 2024; 598:1080-1093. [PMID: 38523059 DOI: 10.1002/1873-3468.14854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine-to-inosine (A-to-I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore-conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin-conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A-to-I editing sites in RNA and DNA.
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Affiliation(s)
- Yuxi Yang
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Koki Nakayama
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, Izumo-shi, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda-shi, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Ayaka Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Japan
| | - Masayuki Sakurai
- Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
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4
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Xianyu B, Pan S, Gao S, Xu H, Li T. Selenium-Containing Nanocomplexes Achieve Dual Immune Checkpoint Blockade for NK Cell Reinvigoration. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306225. [PMID: 38072799 DOI: 10.1002/smll.202306225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 11/06/2023] [Indexed: 05/12/2024]
Abstract
The blockade of immune checkpoints has emerged as a promising strategy for cancer immunotherapy. However, most of the current approaches focus on T cells, leaving natural killer (NK) cell-mediated therapeutic strategies rarely explored. Here, a selenium-containing nanocomplex is developed that acts as a dual immune checkpoint inhibitor to reinvigorate NK cell-based cancer immunotherapy. The Se nanocomplex can deliver and release siRNA that targets programmed death ligand-1 (PD-L1) in tumor cells, thereby silencing the checkpoint receptor PD-L1. The intracellular reactive oxygen species generated by porphyrin derivatives in the nanocomplexes can oxidize the diselenide bond into seleninic acid, which blocks the expression of another checkpoint receptor, human leukocyte antigen E. The blockade of dual immune checkpoints shows synergistic effects on promoting NK cell-mediated antitumoral activity. This study provides a new strategy to reinvigorate NK cell immunity for the development of combined cancer immunotherapy.
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Affiliation(s)
- Banruo Xianyu
- Key Lab of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Shuojiong Pan
- Key Lab of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Shiqian Gao
- Key Laboratory of Polyoxometalate Science of the Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun, 130024, China
| | - Huaping Xu
- Key Lab of Organic Optoelectronics and Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Tianyu Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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5
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Peters-Clarke TM, Quan Q, Anderson BJ, McGee WM, Lohr E, Hebert AS, Westphall MS, Coon JJ. Phosphorothioate RNA Analysis by NETD Tandem Mass Spectrometry. Mol Cell Proteomics 2024; 23:100742. [PMID: 38401707 PMCID: PMC11047293 DOI: 10.1016/j.mcpro.2024.100742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/19/2024] [Indexed: 02/26/2024] Open
Abstract
Therapeutic RNAs are routinely modified during their synthesis to ensure proper drug uptake, stability, and efficacy. Phosphorothioate (PS) RNA, molecules in which one or more backbone phosphates are modified with a sulfur atom in place of standard nonbridging oxygen, is one of the most common modifications because of ease of synthesis and pharmacokinetic benefits. Quality assessment of RNA synthesis, including modification incorporation, is essential for drug selectivity and performance, and the synthetic nature of the PS linkage incorporation often reveals impurities. Here, we present a comprehensive analysis of PS RNA via tandem mass spectrometry (MS). We show that activated ion-negative electron transfer dissociation MS/MS is especially useful in diagnosing PS incorporation, producing diagnostic a- and z-type ions at PS linkage sites, beyond the standard d- and w-type ions. Analysis using resonant and beam-type collision-based activation reveals that, overall, more intense sequence ions and base-loss ions result when a PS modification is present. Furthermore, we report increased detection of b- and x-type product ions at sites of PS incorporation, in addition to the standard c- and y-type ions. This work reveals that the gas-phase chemical stability afforded by sulfur alters RNA dissociation and necessitates inclusion of additional product ions for MS/MS of PS RNA.
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Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Qiuwen Quan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benton J Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Emily Lohr
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander S Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Michael S Westphall
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
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6
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De Vos J, Morreel K, Alvarez P, Vanluchene H, Vankeirsbilck R, Sandra P, Sandra K. Evaluation of size-exclusion chromatography, multi-angle light scattering detection and mass photometry for the characterization of mRNA. J Chromatogr A 2024; 1719:464756. [PMID: 38402695 DOI: 10.1016/j.chroma.2024.464756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/16/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The recent approval of messenger ribonucleic acid (mRNA) as vaccine to combat the COVID-19 pandemic has been a scientific turning point. Today, the applicability of mRNA is being demonstrated beyond infectious diseases, for example in cancer immunotherapy, protein replacement therapy and gene editing. mRNA is produced by in vitro transcription (IVT) from a linear DNA template and modified at the 3' and 5' ends to improve translational efficiency and stability. Co-existing impurities such as RNA fragments and double-stranded RNA (dsRNA), amongst others, can drastically impact mRNA quality and efficacy. In this study, size-exclusion chromatography (SEC) is evaluated for the characterization of IVT-mRNA. The effect of mobile phase composition (ionic strength and organic modifier), pH, column temperature and pore size (300 Å, 1000 Å, and 2000 Å) on the separation performance and structural integrity of IVT-mRNA varying in size is described. Non-replicating, self-amplifying (saRNA), temperature degraded, and ribonuclease (RNase) digested mRNA, the latter to characterize the 3' poly(A) tail, were included in the study. Beyond ultraviolet (UV) detection, refractive index (RI) and multi-angle light scattering (MALS) detection were implemented to accurately determine molecular weight (MW) of mRNA. Finally, mass photometry is introduced as a complementary methodology to study mRNA under native conditions.
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Affiliation(s)
- Jelle De Vos
- RIC group, President Kennedypark 6, 8500 Kortrijk, Belgium
| | - Kris Morreel
- RIC group, President Kennedypark 6, 8500 Kortrijk, Belgium
| | - Piotr Alvarez
- RIC group, President Kennedypark 6, 8500 Kortrijk, Belgium
| | | | | | - Pat Sandra
- RIC group, President Kennedypark 6, 8500 Kortrijk, Belgium
| | - Koen Sandra
- RIC group, President Kennedypark 6, 8500 Kortrijk, Belgium.
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7
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Kaldis P, Zhao LN. Molecular basis of the reaction mechanism of the methyltransferase HENMT1. PLoS One 2024; 19:e0293243. [PMID: 38198468 PMCID: PMC10781085 DOI: 10.1371/journal.pone.0293243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 10/09/2023] [Indexed: 01/12/2024] Open
Abstract
PIWI-interacting RNAs (piRNAs) are important for ensuring the integrity of the germline. 3'-terminal 2'-O-methylation is essential for piRNA maturation and to protect them from degradation. HENMT1 (HEN Methyltransferase 1) carries out the 2'-O-methylation, which is of key importance for piRNA stability and functionality. However, neither the structure nor the catalytic mechanism of mammalian HENMT1 have been studied. We have constructed a catalytic-competent HENMT1 complex using computational approaches, in which Mg2+ is primarily coordinated by four evolutionary conserved residues, and is further auxiliary coordinated by the 3'-O and 2'-O on the 3'-terminal nucleotide of the piRNA. Our study suggests that metal has limited effects on substrate and cofactor binding but is essential for catalysis. The reaction consists of deprotonation of the 2'-OH to 2'-O and a methyl transfer from SAM to the 2'-O. The methyl transfer is spontaneous and fast. Our in-depth analysis suggests that the 2'-OH may be deprotonated before entering the active site or it may be partially deprotonated at the active site by His800 and Asp859, which are in a special alignment that facilitates the proton transfer out of the active site. Furthermore, we have developed a detailed potential reaction scenario indicating that HENMT1 is Mg2+ utilizing but is not a Mg2+ dependent enzyme.
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Affiliation(s)
- Philipp Kaldis
- Department of Clinical Sciences, Lund University, Malmö, Skåne, Sweden
- Lund University Diabetes Centre, Lund University, Malmö, Skåne, Sweden
| | - Li Na Zhao
- Department of Clinical Sciences, Lund University, Malmö, Skåne, Sweden
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8
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Sodnikar K, Kaegi R, Christl I, Schroth MH, Sander M. Transport of double-stranded ribonucleic acids (dsRNA) and deoxyribonucleic acids (DNA) in sand and iron oxide-coated sand columns under varying solution chemistries. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2023; 25:2067-2080. [PMID: 37870439 DOI: 10.1039/d3em00294b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
Assessing ecological risks associated with the use of genetically modified RNA interference crops demands an understanding of the fate of crop-released insecticidal double-stranded RNA (dsRNA) molecules in soils. We studied the adsorption of one dsRNA and two double-stranded DNA as model nucleic acids (NAs) during transport through sand- and iron oxide-coated sand (IOCS)-filled columns over a range of solution pH and ionic compositions. Consistent with NA-sand electrostatic repulsion, we observed only slight retention of NAs in sand columns. Conversely, pronounced NA retention in IOCS columns is consistent with strong and irreversible NA adsorption involving electrostatic attraction to and inner-sphere complex formation of NAs with iron oxide coatings. Adsorption of NAs to iron oxides revealed a fast and a slow kinetic adsorption regime, possibly caused by the excluded-area effect. Adsorption of NAs to sand and IOCS increased in the presence of dissolved Mg2+ and with increasing ionic strength, reflecting cation-bridging and screening of repulsive electrostatics, respectively. The co-solute phosphate and a pre-adsorbed dissolved organic matter isolate competitively suppressed dsRNA adsorption to IOCS. Similar adsorption characteristics of dsRNA and similarly sized DNA suggest that existing information on DNA adsorption to soil particles helps in predicting adsorption and fate of dsRNA molecules in soils.
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Affiliation(s)
- Katharina Sodnikar
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Ralf Kaegi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland
| | - Iso Christl
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Martin Herbert Schroth
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, 8092 Zurich, Switzerland.
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9
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Hayashida M, Suzuki R, Horie S, Masuda J, Yamaguchi T, Obika S. Applicability of supercritical fluid chromatography for oligonucleotide analysis: A proof-of-concept study. J Chromatogr A 2023; 1708:464333. [PMID: 37660558 DOI: 10.1016/j.chroma.2023.464333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/10/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
We evaluated the suitability of supercritical fluid chromatography (SFC) for oligonucleotide analysis using 4-mer oligonucleotides with various phosphorothioate (PS) contents as model compounds. Column screening showed that the diol-modified column was able to separate sequences with different PS contents. Optimization of the column body and additives allowed us to analyze polar oligonucleotides using SFC. Various sequences were also analyzed using the optimized method. A good peak shape was obtained when the guanine plus cytosine content of the analyte was two or less in the 4-mer oligonucleotides. Furthermore, we found that the retention times of the selected sequences were positively correlated with polar surface areas, indicating that oligonucleotides interact with polar stationary phases. In contrast, more hydrophobic full PS sequences were retained more strongly in the diol column than the full phosphodiester (PO) sequences. This suggests that the diol column has unique selectivity for PO and PS linkages. These results indicate that SFC is potentially applicable to oligonucleotide analysis with a separation mechanism that is different from that of ion-pair reversed-phase liquid chromatography.
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Affiliation(s)
- Momoka Hayashida
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Analytical Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Risa Suzuki
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinnosuke Horie
- Shimadzu Analytical Innovation Research Laboratories, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan; Shimadzu Europa GmbH, Albert-Hahn-Strasse 6-10, Duisburg 47269, Federal Republic of Germany
| | - Junichi Masuda
- Shimadzu Corporation, 1 Nishinokyo Kuwabara-cho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Takao Yamaguchi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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10
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Morais-Armas S, Medina-Suárez S, Machín F. Effect of carrier yeast RNAs in the detection of SARS-CoV-2 by RT-LAMP. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000979. [PMID: 37799204 PMCID: PMC10550381 DOI: 10.17912/micropub.biology.000979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has underscored the need for rapid and accurate diagnostic methods. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) has emerged as a promising molecular tool in least developed countries due to its simplicity, speed, and sensitivity. Nevertheless, reliable SARS-CoV-2 detection can be challenged by the chain custody of the samples. In this context, carrier RNA can act as a preservative. In this study, we explored the potential of yeast total and transference RNA (tRNA) in the SARS-CoV-2 RT-LAMP. We have found that most optimal conditions are reached with 1 μg/μL tRNA in the RT-LAMP reaction.
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Affiliation(s)
- Samantha Morais-Armas
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
| | - Sara Medina-Suárez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Canary Islands, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, San Cristóbal de La Laguna, Canary Islands, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Canary Islands, Spain
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11
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Faison EM, Nallathambi A, Zhang Q. Characterizing Protonation-Coupled Conformational Ensembles in RNA via pH-Differential Mutational Profiling with DMS Probing. J Am Chem Soc 2023; 145:18773-18777. [PMID: 37582279 DOI: 10.1021/jacs.3c07736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
RNA molecules undergo conformational transitions in response to cellular and environmental stimuli. Site-specific protonation, a fundamental chemical property, can alter the conformational landscape of RNA to regulate their functions. However, characterizing protonation-coupled RNA conformational ensembles on a large scale remains challenging. Here, we present pH-differential mutational profiling (PD-MaP) with dimethyl sulfate probing for high-throughput detection of protonation-coupled conformational ensembles in RNA. We demonstrated this approach on microRNA-21 precursor (pre-miR-21) and recapitulated a previously discovered A+-G-coupled conformational ensemble. Additionally, we identified a secondary protonation event involving an A+-C mismatch. We validated the occurrence of both protonation-coupled ensembles in pre-miR-21 using NMR relaxation dispersion spectroscopy. Furthermore, the application of PD-MaP on a library of well-annotated human primary microRNAs uncovered widespread protonation-coupled conformational ensembles, suggesting their potentially broad functions in biology.
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12
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Garrudo FFF, Linhardt RJ, Ferreira FC, Morgado J. Designing Electrical Stimulation Platforms for Neural Cell Cultivation Using Poly(aniline): Camphorsulfonic Acid. Polymers (Basel) 2023; 15:2674. [PMID: 37376320 DOI: 10.3390/polym15122674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Electrical stimulation is a powerful strategy to improve the differentiation of neural stem cells into neurons. Such an approach can be implemented, in association with biomaterials and nanotechnology, for the development of new therapies for neurological diseases, including direct cell transplantation and the development of platforms for drug screening and disease progression evaluation. Poly(aniline):camphorsulfonic acid (PANI:CSA) is one of the most well-studied electroconductive polymers, capable of directing an externally applied electrical field to neural cells in culture. There are several examples in the literature on the development of PANI:CSA-based scaffolds and platforms for electrical stimulation, but no review has examined the fundamentals and physico-chemical determinants of PANI:CSA for the design of platforms for electrical stimulation. This review evaluates the current literature regarding the application of electrical stimulation to neural cells, specifically reviewing: (1) the fundamentals of bioelectricity and electrical stimulation; (2) the use of PANI:CSA-based systems for electrical stimulation of cell cultures; and (3) the development of scaffolds and setups to support the electrical stimulation of cells. Throughout this work, we critically evaluate the revised literature and provide a steppingstone for the clinical application of the electrical stimulation of cells using electroconductive PANI:CSA platforms/scaffolds.
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Affiliation(s)
- Fábio F F Garrudo
- Instituto de Telecomunicações, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Robert J Linhardt
- Department of Chemical and Biological Engineering, Biology and Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
| | - Frederico Castelo Ferreira
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Jorge Morgado
- Instituto de Telecomunicações, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Avenida Rovisco Pais, 1049-001 Lisbon, Portugal
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13
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Sabei A, Caldas Baia TG, Saffar R, Martin J, Frezza E. Internal Normal Mode Analysis Applied to RNA Flexibility and Conformational Changes. J Chem Inf Model 2023; 63:2554-2572. [PMID: 36972178 DOI: 10.1021/acs.jcim.2c01509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
We investigated the capability of internal normal modes to reproduce RNA flexibility and predict observed RNA conformational changes and, notably, those induced by the formation of RNA-protein and RNA-ligand complexes. Here, we extended our iNMA approach developed for proteins to study RNA molecules using a simplified representation of the RNA structure and its potential energy. Three data sets were also created to investigate different aspects. Despite all the approximations, our study shows that iNMA is a suitable method to take into account RNA flexibility and describe its conformational changes opening the route to its applicability in any integrative approach where these properties are crucial.
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14
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Taylor SK, Kostic N, Stojanovic MN. Oligonucleotide-Blocked Streptavidin for Biotinylation Analysis. Bioconjug Chem 2023; 34:92-96. [PMID: 36006852 DOI: 10.1021/acs.bioconjchem.2c00255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Binding between streptavidin, or its homologues, to biotin is one of the most widely exploited biological interactions in the biomedical sciences. Controlling the extent of biotinylation is important for meeting the requirements of the intended design and to preserve the native function of the biotin recipient. Within the protein world, a"trial-and-error" optimization approach toward biotinylation reaction conditions is often necessary due to widely varying properties of proteins. Therefore, product analysis is important. We show here that a oligonucleotide-blocked streptavidin, effectively "monovalent streptavidin", can tag biotin moieties individually and the tagged products visualized via a polyacrylamide gel shift assay to reveal the product distribution, i.e., [protein-(biotin)n] products where n = 1, 2, 3, etc. This is in contrast, and complementary, to current commercially available analytical reagents for biotinylation characterization, which use an absorbance or fluorescence signal to yield the mean number of biotin moieties.
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15
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Vlasova N, Markitan O. Nucleotide Interaction with Nanocrystalline Ceria Surface. CHEMISTRY & CHEMICAL TECHNOLOGY 2022. [DOI: 10.23939/chcht16.04.581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The adsorption of nucleotides on the surface of nanocrystalline cerium dioxide (pHpzc = 6.3) in NaCl solutions was investigated using multi-batch adsorption experiments over a wide range of pH. The obtained results were interpreted as a formation of outer and inner sphere surface complexes with the participation of phosphate moieties. The Basic Stern surface complexation model was applied to obtain quantitative equilibrium reaction constants.
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16
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Gong X, Cho SY, Kuo S, Ogunlade B, Tso K, Salem DP, Strano MS. Divalent Metal Cation Optical Sensing Using Single-Walled Carbon Nanotube Corona Phase Molecular Recognition. Anal Chem 2022; 94:16393-16401. [DOI: 10.1021/acs.analchem.2c03648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Soo-Yeon Cho
- School of Chemical Engineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sydney Kuo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Babatunde Ogunlade
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kathryn Tso
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel P. Salem
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Jung WH, Park JH, Kim S, Cui C, Ahn DJ. Molecular doping of nucleic acids into light emitting crystals driven by multisite-intermolecular interaction. Nat Commun 2022; 13:6193. [PMID: 36261659 PMCID: PMC9581973 DOI: 10.1038/s41467-022-33999-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
We reveal the fundamental understanding of molecular doping of DNAs into organic semiconducting tris (8-hydroxyquinoline) aluminum (Alq3) crystals by varying types and numbers of purines and pyrimidines constituting DNA. Electrostatic, hydrogen bonding, and π-π stacking interactions between Alq3 and DNAs are the major factors affecting the molecular doping. Longer DNAs induce a higher degree of doping due to electrostatic interactions between phosphate backbone and Alq3. Among four bases, single thymine bases induce the multisite interactions of π-π stacking and hydrogen bonding with single Alq3, occurring within a probability of 4.37%. In contrast, single adenine bases form multisite interactions, within lower probability (1.93%), with two-neighboring Alq3. These multisite interactions facilitate the molecular doping into Alq3 particles compared to cytosines or guanines only forming π-π stacking. Thus, photoluminescence and optical waveguide phenomena of crystals were successfully tailored. This discovery should deepen our fundamental understanding of incorporating DNAs into organic semiconducting crystals.
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Affiliation(s)
- Woo Hyuk Jung
- grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, 02841 Korea
| | - Jin Hyuk Park
- grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, 02841 Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841 Korea
| | - Seokho Kim
- grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, 02841 Korea
| | - Chunzhi Cui
- grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, 02841 Korea ,grid.440752.00000 0001 1581 2747Department of Chemistry, National Demonstration Centre for Experimental Chemistry Education, Yanbian University, Yanji, 133002 China
| | - Dong June Ahn
- grid.222754.40000 0001 0840 2678Department of Chemical and Biological Engineering, Korea University, Seoul, 02841 Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841 Korea
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18
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Liu Y, Munsayac A, Hall I, Keane SC. Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA. J Mol Biol 2022; 434:167688. [PMID: 35717998 PMCID: PMC9474619 DOI: 10.1016/j.jmb.2022.167688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/22/2022]
Abstract
The miR-17 ∼ 92a polycistron, also known as oncomiR-1, is commonly overexpressed in multiple cancers and has several oncogenic properties. OncomiR-1 encodes six constituent microRNAs (miRs), each enzymatically processed with different efficiencies. However, the structural mechanism that regulates this differential processing remains unclear. Chemical probing of oncomiR-1 revealed that the Drosha cleavage sites of pri-miR-92a are sequestered in a four-way junction. NPSL2, an independent stem loop element, is positioned just upstream of pri-miR-92a and sequesters a crucial part of the sequence that constitutes the basal helix of pri-miR-92a. Disruption of the NPSL2 hairpin structure could promote the formation of a pri-miR-92a structure that is primed for processing by Drosha. Thus, NPSL2 is predicted to function as a structural switch, regulating pri-miR-92a processing. Here, we determined the solution structure of NPSL2 using solution NMR spectroscopy. This is the first high-resolution structure of an oncomiR-1 element. NPSL2 adopts a hairpin structure with a large, but highly structured, apical and internal loops. The 10-bp apical loop contains a pH-sensitive A+·C mismatch. Additionally, several adenosines within the apical and internal loops have elevated pKa values. The protonation of these adenosines can stabilize the NPSL2 structure through electrostatic interactions. Our study provides fundamental insights into the secondary and tertiary structure of an important RNA hairpin proposed to regulate miR biogenesis.
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Affiliation(s)
- Yaping Liu
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/YapingLiu5
| | - Aldrex Munsayac
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA
| | - Ian Hall
- Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA. https://twitter.com/ihallu14
| | - Sarah C Keane
- Biophysics Program, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA; Department of Chemistry, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109, USA.
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19
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Vlasova N, Markitan O. Phosphate–nucleotide–nucleic acid: Adsorption onto nanocrystalline ceria surface. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Kshirsagar PG, Seshacharyulu P, Muniyan S, Rachagani S, Smith LM, Thompson C, Shah A, Mallya K, Kumar S, Jain M, Batra SK. DNA-gold nanoprobe-based integrated biosensing technology for non-invasive liquid biopsy of serum miRNA: A new frontier in prostate cancer diagnosis. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2022; 43:102566. [PMID: 35569810 PMCID: PMC9942096 DOI: 10.1016/j.nano.2022.102566] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/22/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
The low specificity of prostate-specific antigen contributes to overdiagnosis and ov ertreatment of prostate cancer (PCa) patients. Hence, there is an urgent need for inclusive diagnostic platforms that could improve the diagnostic accuracy of PCa. Dysregulated miRNAs are closely associated with the progression and recurrence and have emerged as promising diagnostic and prognostic biomarkers for PCa. Nevertheless, simple, rapid, and ultrasensitive quantification of serum miRNAs is highly challenging. This study designed, synthesized, and demonstrated the practicability of DNA-linked gold nanoprobes (DNA-AuNPs) for the single-step quantification of miR-21/miR-141/miR-375. In preclinical study, the assay differented PCa Pten conditional knockout (PtencKO) mice compared to their age-matched Pten wild-type (PtenWT) control mice. In human sera, receiver operating characteristic (ROC) curve-based correlation analyses revealed clear discrimination between PCa patients from normal healthy controls using training and validation sets. Overall, we established integrated nano-biosensing technology for the PCR-free, non-invasive liquid biopsies of multiple miRNAs for PCa diagnosis.
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Affiliation(s)
- Prakash G. Kshirsagar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Parthasarathy Seshacharyulu
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sakthivel Muniyan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Satyanarayan Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lynette M. Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Christopher Thompson
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ashu Shah
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kavita Mallya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Sushil Kumar
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA; Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Fred and Pamela Buffett Cancer Center, Omaha, Nebraska, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Corresponding authors: Surinder K. Batra, Ph.D., , Phone: 402-559-5455; Maneesh Jain, Ph.D., , Phone: 402-559-7667
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21
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Improvement of chemo- and stereoselectivity for phosphorothioate oligonucleotides in capillary electrophoresis by addition of cyclodextrins. J Chromatogr A 2022; 1676:463270. [PMID: 35763948 DOI: 10.1016/j.chroma.2022.463270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 11/21/2022]
Abstract
Phosphorothioate (PS) modification is one of the most widely used oligonucleotide chemical alterations in the oligonucleotide backbone. It has proven to be crucial in the field of therapeutic oligonucleotides regarding the optimization of their physicochemical and biological properties. In this study, a capillary electrophoresis (CE) method with an acidic background electrolyte (BGE) containing a combination of β- and γ-cyclodextrins derivatives as chiral selectors is proposed for the diastereomeric separation of 5-mer oligonucleotides containing 0, 1, 2, or 3 phosphorothioate linkages (5´-TCGTG-3´). The effects of the BGE pH, organic modifier addition, and type of cyclodextrin (CD) on chemo- and stereoselectivity and resolution were studied. A mixture of 25 mM (2-hydroxy-3-N,N,N-trimethylamino)propyl-γ-CD and 10 mM carboxymethyl-β-cyclodextrin in a pH 3 buffer was found to be the most appropriate system for the qualitative evaluation of the short oligonucleotides investigated. These phosphorothioate oligonucleotides were separated with high efficiency in less than 11 min with no capillary treatment. The suggested approach can be the basis for purity testing of this new generation of therapeutics.
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22
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Dayie TK, Olenginski LT, Taiwo KM. Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs. Chem Rev 2022; 122:9357-9394. [PMID: 35442658 PMCID: PMC9136934 DOI: 10.1021/acs.chemrev.1c00845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Indexed: 02/07/2023]
Abstract
RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.
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Affiliation(s)
- Theodore K. Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Lukasz T. Olenginski
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Kehinde M. Taiwo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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23
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Tikunov AP, Tipton JD, Garrett TJ, Shinde SV, Kim HJ, Gerber DA, Herring LE, Graves LM, Macdonald JM. Green Chemistry Preservation and Extraction of Biospecimens for Multi-omic Analyses. Methods Mol Biol 2022; 2394:267-298. [PMID: 35094334 DOI: 10.1007/978-1-0716-1811-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The Environmental Protection Agency's definition of "Green Chemistry" is "the design of chemical products and processes that reduces or eliminates the use or generation of hazardous substances. Green chemistry applies across the life cycle of a chemical product, including its design, manufacture, use, and ultimate disposal." Conventional omic tissue extraction procedures use solvents that are toxic and carcinogenic, such as chloroform and methyl-tert-butyl ether for lipidomics, or caustic chaotropic solutions for genomics and transcriptomics, such as guanidine or urea. A common preservation solution for pathology is formaldehyde, which is a carcinogen. Use of acetonitrile as a universal biospecimen preservation and extraction solvent will reduce these hazardous wastes, because it is less toxic and more environmentally friendly than the conventional solvents used in biorepository and biospecimen research. A new extraction method never applied to multi-omic, system biology research, called cold-induced phase separation (CIPS), uses freezing point temperatures to induce a phase separation of acetonitrile-water mixtures. Also, the CO2 exposure during CIPS will acidify the water precipitating DNA out of aqueous phase. The resulting phase separation brings hydrophobic lipids to the top acetonitrile fraction that is easily decanted from the bottom aqueous fraction, especially when the water is frozen. This CIPS acetonitrile extract contains the lipidome (lipids), the bottom aqueous fraction is sampled to obtain the transcriptome (RNA) fraction, and the remaining water and pellet is extracted with 60% acetonitrile to isolate the metabolome (<1 kD polar molecules). Finally, steps 4 and 5 use a TRIzol™ liquid-liquid extraction SOP of the pellet to isolate the genome (DNA) and proteome (proteins). This chapter details the multi-omic sequential extraction SOP and potential problems associated with each of the 5 steps, with steps 2, 4, and 5 still requiring validation. The metabolomic and lipidomic extraction efficiencies using the CIPS SOP is compared to conventional solvent extraction SOPs and is analyzed by nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS), respectively. Acetonitrile biospecimen preservation combined with the CIPS multi-omic extraction SOP is green chemistry technology that will eliminate the generation of the hazardous substances associated with biospecimen processing and permits separation and safe disposal of acetonitrile avoiding environmental contamination.
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Affiliation(s)
- Andrey P Tikunov
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeremiah D Tipton
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, College of Medicine, Gainesville, FL, USA
| | - Sachi V Shinde
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Hong Jin Kim
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - David A Gerber
- Departments of Surgery, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Laura E Herring
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Lee M Graves
- Departments of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Jeffrey M Macdonald
- Departments of Biomedical Engineering, University of North Carolina School of Medicine, Chapel Hill, NC, USA.
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24
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Jones EL, Mlotkowski AJ, Hebert SP, Schlegel HB, Chow CS. Calculations of p Ka Values for a Series of Naturally Occurring Modified Nucleobases. J Phys Chem A 2022; 126:1518-1529. [PMID: 35201779 DOI: 10.1021/acs.jpca.1c10905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Modified nucleobases are found in functionally important regions of RNA and are often responsible for essential structural roles. Many of these nucleobase modifications are dynamically regulated in nature, with each modification having a different biological role in RNA. Despite the high abundance of modifications, many of their characteristics are still poorly understood. One important property of a nucleobase is its pKa value, which has been widely studied for unmodified nucleobases, but not for the modified versions. In this study, the pKa values of modified nucleobases were determined by performing ab initio quantum mechanical calculations using a B3LYP density functional with the 6-31+G(d,p) basis set and a combination of implicit-explicit solvation systems. This method, which was previously employed to determine the pKa values of unmodified nucleobases, is applicable to a variety of modified nucleobases. Comparisons of the pKa values of modified nucleobases give insight into their structural and energetic impacts within nucleic acids.
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Affiliation(s)
- Evan L Jones
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Alan J Mlotkowski
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Sebastien P Hebert
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - H Bernhard Schlegel
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Christine S Chow
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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25
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Guo YJ, Liu YJ. QM/MM study on enzymatic mechanism in sinigrin biosynthesis. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2111250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
As the major and abundant type of glucosinolates (GL) in plants, sinigrin has potential functions in promoting health and insect defense. The final step in the biosynthesis of sinigrin core structure is highly representative in GL compounds, which corresponds to the process from 3-methylthiopropyl ds-GL to 3-methylthiopropyl GL catalyzed by sulfotransferase (SOT). However, due to the lack of the crystallographic structure of SOT complexed with the 3-methylthiopropyl GL, little is known about this sulfonation process. Fortunately, the crystal structure of SOT 18 from Arabidopsis thaliana (AtSOT18) containing the substance (sinigrin) similar to 3-methylthiopropyl GL has been determined. To understand the enzymatic mechanism, we employed molecular dynamics (MD) simulation and quantum mechanics combined with molecular mechanics (QM/MM) methods to study the conversion from ds-sinigrin to sinigrin catalyzed by AtSOT18. The calculated results demonstrate that the reaction occurs through a concerted dissociative mechanism. Moreover, Lys93, Thr96, Thr97, Tyr130, His155, and two enzyme peptide chains (Pro92-Lys93 and Gln95-Thr96-Thr97) play a role in positioning the substrates and promoting the catalytic reaction by stabilizing the transition state geometry. Particularly, His155 acts as a catalytic base while Lys93 acts as a catalytic acid in the reaction process. The presently proposed concerted dissociative mechanism explains the role of AtSOT18 in sinigrin biosynthesis, and could be instructive for the study of GL biosynthesis catalyzed by other SOTs.
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Affiliation(s)
- Ya-Jie Guo
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
- Center for Advanced Materials Research, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai 519087, China
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26
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Abstract
More than 55 distinct classes of riboswitches that respond to small metabolites or elemental ions have been experimentally validated to date. The ligands sensed by these riboswitches are biased in favor of fundamental compounds or ions that are likely to have been relevant to ancient forms of life, including those that might have populated the "RNA World", which is a proposed biochemical era that predates the evolutionary emergence of DNA and proteins. In the following text, I discuss the various types of ligands sensed by some of the most common riboswitches present in modern bacterial cells and consider implications for ancient biological processes centered on the proven capabilities of these RNA-based sensors. Although most major biochemical aspects of metabolism are represented by known riboswitch classes, there are striking sensory gaps in some key areas. These gaps could reveal weaknesses in the performance capabilities of RNA that might have hampered RNA World evolution, or these could highlight opportunities to discover additional riboswitch classes that sense essential metabolites.
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Affiliation(s)
- Ronald R. Breaker
- Corresponding Author: Ronald R. Breaker - Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103, United States; Phone: 203-432-9389; , Twitter: @RonBreaker
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27
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Kotar A, Ma S, Keane SC. pH dependence of C•A, G•A and A•A mismatches in the stem of precursor microRNA-31. Biophys Chem 2022; 283:106763. [DOI: 10.1016/j.bpc.2022.106763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 12/22/2022]
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28
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Leucine-Responsive Regulatory Protein in Acetic Acid Bacteria Is Stable and Functions at a Wide Range of Intracellular pH Levels. J Bacteriol 2021; 203:e0016221. [PMID: 34228496 DOI: 10.1128/jb.00162-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acetic acid bacteria grow while producing acetic acid, resulting in acidification of the culture. Limited reports elucidate the effect of changes in intracellular pH on transcriptional factors. In the present study, the intracellular pH of Komagataeibacter europaeus was monitored with a pH-sensitive green fluorescent protein, showing that the intracellular pH decreased from 6.3 to 4.7 accompanied by acetic acid production during cell growth. The leucine-responsive regulatory protein of K. europaeus (KeLrp) was used as a model to examine pH-dependent effects, and its properties were compared with those of the Escherichia coli ortholog (EcLrp) at different pH levels. The DNA-binding activities of EcLrp and KeLrp with the target DNA (Ec-ilvI and Ke-ilvI) were examined by gel mobility shift assays under various pH conditions. EcLrp showed the highest affinity with the target at pH 8.0 (Kd [dissociation constant], 0.7 μM), decreasing to a minimum of 3.4 μM at pH 4.0. Conversely, KeLrp did not show significant differences in binding affinity between pH 4 and 7 (Kd, 1.0 to 1.5 μM), and the highest affinity was at pH 5.0 (Kd, 1.0 μM). Circular dichroism spectroscopy revealed that the α-helical content of KeLrp was the highest at pH 5.0 (49%) and was almost unchanged while being maintained at >45% over a range of pH levels examined, while that of EcLrp decreased from its maximum (49% at pH 7.0) to its minimum (36% at pH 4.0). These data indicate that KeLrp is stable and functions over a wide range of intracellular pH levels. IMPORTANCE Lrp is a highly conserved transcriptional regulator found in bacteria and archaea and regulates transcriptions of various genes. The intracellular pH of acetic acid bacteria (AAB) changes accompanied by acetic acid production during cell growth. The Lrp of AAB K. europaeus (KeLrp) was structurally stable over a wide range of pH and maintained DNA-binding activity even at low pH compared with Lrp from E. coli living in a neutral environment. An in vitro experiment showed DNA-binding activity of KeLrp to the target varied with changes in pH. In AAB, change of the intracellular pH during a cell growth would be an important trigger in controlling the activity of Lrp in vivo.
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29
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Markitan OV, Vlasova NN. Adsorption of Deoxyribonucleic Acid on Nanocrystalline Titanium and Cerium Dioxide Surfaces. COLLOID JOURNAL 2021. [DOI: 10.1134/s1061933x21040050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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30
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Araki H, Hagiwara S, Shinomiya R, Momotake A, Kotani H, Kojima T, Ochiai T, Shimada N, Maruyama A, Yamamoto Y. A cationic copolymer as a cocatalyst for a peroxidase-mimicking heme-DNAzyme. Biomater Sci 2021; 9:6142-6152. [PMID: 34346413 DOI: 10.1039/d1bm00949d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heme binds to a parallel-stranded G-quadruplex DNA to form a peroxidase-mimicking heme-DNAzyme. An interpolyelectrolyte complex between the heme-DNAzyme and a cationic copolymer possessing protonated amino groups was characterized and the peroxidase activity of the complex was evaluated to elucidate the effect of the polymer on the catalytic activity of the heme-DNAzyme. We found that the catalytic activity of the heme-DNAzyme is enhanced through the formation of the interpolyelectrolyte complex due to the general acid catalysis of protonated amino groups of the polymer, enhancing the formation of the iron(iv)oxo porphyrin π-cation radical intermediate known as Compound I. This finding indicates that the polymer with protonated amino groups can act as a cocatalyst for the heme-DNAzyme in the oxidation catalysis. We also found that the enhancement of the activity of the heme-DNAzyme by the polymer depends on the local heme environment such as the negative charge density in the proximity of the heme and substrate accessibility to the heme. These findings provide novel insights as to molecular design of the heme-DNAzyme for enhancing its catalytic activity.
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Affiliation(s)
- Haruka Araki
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Shota Hagiwara
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Ryosuke Shinomiya
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hiroaki Kotani
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takahiko Kojima
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Takuro Ochiai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Naohiko Shimada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Atsushi Maruyama
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan and Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba 305-8571, Japan
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31
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Bereiter R, Himmelstoß M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R. Impact of 3-deazapurine nucleobases on RNA properties. Nucleic Acids Res 2021; 49:4281-4293. [PMID: 33856457 PMCID: PMC8096147 DOI: 10.1093/nar/gkab256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Deazapurine nucleosides such as 3-deazaadenosine (c3A) are crucial for atomic mutagenesis studies of functional RNAs. They were the key for our current mechanistic understanding of ribosomal peptide bond formation and of phosphodiester cleavage in recently discovered small ribozymes, such as twister and pistol RNAs. Here, we present a comprehensive study on the impact of c3A and the thus far underinvestigated 3-deazaguanosine (c3G) on RNA properties. We found that these nucleosides can decrease thermodynamic stability of base pairing to a significant extent. The effects are much more pronounced for 3-deazapurine nucleosides compared to their constitutional isomers of 7-deazapurine nucleosides (c7G, c7A). We furthermore investigated base pair opening dynamics by solution NMR spectroscopy and revealed significantly enhanced imino proton exchange rates. Additionally, we solved the X-ray structure of a c3A-modified RNA and visualized the hydration pattern of the minor groove. Importantly, the characteristic water molecule that is hydrogen-bonded to the purine N3 atom and always observed in a natural double helix is lacking in the 3-deazapurine-modified counterpart. Both, the findings by NMR and X-ray crystallographic methods hence provide a rationale for the reduced pairing strength. Taken together, our comparative study is a first major step towards a comprehensive understanding of this important class of nucleoside modifications.
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Affiliation(s)
- Raphael Bereiter
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Maximilian Himmelstoß
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eva Renard
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Elisabeth Mairhofer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Michaela Egger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
| | - Eric Ennifar
- Architecture et Réactivité de l'ARN - CNRS UPR 9002, Université de Strasbourg, Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innsbruck, Austria
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32
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Santermans S, Schanovsky F, Gupta M, Hellings G, Heyns M, Van Roy W, Martens K. The Significance of Nonlinear Screening and the pH Interference Mechanism in Field-Effect Transistor Molecular Sensors. ACS Sens 2021; 6:1049-1056. [PMID: 33496586 DOI: 10.1021/acssensors.0c02285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electrolyte screening is well known for its detrimental impact on the sensitivity of liquid-gated field-effect transistor (FET) molecular sensors and is mostly described by the linearized Debye-Hückel model. However, charged and pH-sensitive FET sensing surfaces can limit the FET molecular sensitivity beyond the Debye-Hückel screening formalism. Pre-existing surface charges can lead to the breakdown of Debye-Hückel screening and induce enhanced nonlinear Poisson-Boltzmann screening. Moreover, the charging of the pH-sensitive surface groups interferes with biomolecule sensing resulting in a pH interference mechanism. With analytical equations and TCAD simulations, we highlight that the Debye-Hückel approximation can underestimate screening and overestimate FET molecular sensitivity by more than an order of magnitude. Screening strengthens significantly beyond Debye-Hückel in the proximity of even moderately charged surfaces and biomolecule charge densities (≥1 × 1012 q/cm2). We experimentally show the strong impact of both nonlinear screening and the pH interference effect on charge-based biomolecular sensing using a model system based on the covalent binding of single-stranded DNA on silicon FET sensors. The DNA signal increases from 24 mV at pH 7 to 96 mV at pH 3 in 1.5 mM PBS for a DNA density of 7 × 1012 DNA/cm2. Our model quantitatively explains the signal's pH dependence with roughly equal nonlinear screening and pH interference contributions. This work shows the importance of reducing the net charge and the pH sensitivity of the sensing surface to improve molecular sensing. Therefore, tailoring the gate dielectric and functional layer of FET sensors is a promising route to strong silicon FET molecular sensitivity boosts.
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Affiliation(s)
- Sybren Santermans
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
| | - Franz Schanovsky
- Global TCAD Solutions GmbH, Bösendorferstraße 1/12, 1010 Wien, Austria
| | - Mihir Gupta
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Physics and Astronomy, University of Leuven, Celestijnenlaan 200d, 3001 Leuven, Belgium
| | | | - Marc Heyns
- IMEC, Kapeldreef 75, 3001 Leuven, Belgium
- Department of Materials Engineering, University of Leuven, Kasteelpark Arenberg 44, 3001 Leuven, Belgium
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33
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Nakatsuka N, Faillétaz A, Eggemann D, Forró C, Vörös J, Momotenko D. Aptamer Conformational Change Enables Serotonin Biosensing with Nanopipettes. Anal Chem 2021; 93:4033-4041. [PMID: 33596063 DOI: 10.1021/acs.analchem.0c05038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report artificial nanopores in the form of quartz nanopipettes with ca. 10 nm orifices functionalized with molecular recognition elements termed aptamers that reversibly recognize serotonin with high specificity and selectivity. Nanoscale confinement of ion fluxes, analyte-specific aptamer conformational changes, and related surface charge variations enable serotonin sensing. We demonstrate detection of physiologically relevant serotonin amounts in complex environments such as neurobasal media, in which neurons are cultured in vitro. In addition to sensing in physiologically relevant matrices with high sensitivity (picomolar detection limits), we interrogate the detection mechanism via complementary techniques such as quartz crystal microbalance with dissipation monitoring and electrochemical impedance spectroscopy. Moreover, we provide a novel theoretical model for structure-switching aptamer-modified nanopipette systems that supports experimental findings. Validation of specific and selective small-molecule detection, in parallel with mechanistic investigations, demonstrates the potential of conformationally changing aptamer-modified nanopipettes as rapid, label-free, and translatable nanotools for diverse biological systems.
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Affiliation(s)
- Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Alix Faillétaz
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Dominic Eggemann
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Csaba Forró
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
| | - Dmitry Momotenko
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich CH-8092, Switzerland
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34
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Gheorghiu A, Coveney PV, Arabi AA. The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface Focus 2020; 10:20190120. [PMID: 33178413 PMCID: PMC7653342 DOI: 10.1098/rsfs.2019.0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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35
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Casalino L, Nierzwicki Ł, Jinek M, Palermo G. Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics. ACS Catal 2020; 10:13596-13605. [PMID: 33520346 PMCID: PMC7842700 DOI: 10.1021/acscatal.0c03566] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
CRISPR-Cas9 is a cutting-edge genome editing technology, which uses the endonuclease Cas9 to introduce mutations at desired sites of the genome. This revolutionary tool is promising to treat a myriad of human genetic diseases. Nevertheless, the molecular basis of DNA cleavage, which is a fundamental step for genome editing, has not been established. Here, quantum-classical molecular dynamics (MD) and free energy methods are used to disclose the two-metal-dependent mechanism of phosphodiester bond cleavage in CRISPR-Cas9. Ab initio MD reveals a conformational rearrangement of the Mg2+-bound RuvC active site, which entails the relocation of H983 to act as a general base. Then, the DNA cleavage proceeds through a concerted associative pathway fundamentally assisted by the joint dynamics of the two Mg2+ ions. This clarifies previous controversial experimental evidence, which could not fully establish the catalytic role of the conserved H983 and the metal cluster conformation. The comparison with other two-metal-dependent enzymes supports the identified mechanism and suggests a common catalytic strategy for genome editing and recombination. Overall, the non-target DNA cleavage catalysis described here resolves a fundamental open question in the CRISPR-Cas9 biology and provides valuable insights for improving the catalytic efficiency and the metal-dependent function of the Cas9 enzyme, which are at the basis of the development of genome editing tools.
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Affiliation(s)
- Lorenzo Casalino
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, Riverside, California 92521, United States
| | - Martin Jinek
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
| | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California Riverside, Riverside, California 92521, United States
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36
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Zhang J, Fakharzadeh A, Pan F, Roland C, Sagui C. Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids. Nucleic Acids Res 2020; 48:9899-9917. [PMID: 32821947 PMCID: PMC7515735 DOI: 10.1093/nar/gkaa665] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/27/2020] [Accepted: 08/04/2020] [Indexed: 11/13/2022] Open
Abstract
Expansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich's ataxia. Non-canonical structures are linked to this expansion. DNA triplexes and R-loops are believed to arrest transcription, which results in frataxin deficiency and eventual neurodegeneration. We present a systematic in silico characterization of the possible DNA triplexes that could be assembled with GAA and TTC strands; the two hybrid duplexes [r(GAA):d(TTC) and d(GAA):r(UUC)] in an R-loop; and three hybrid triplexes that could form during bidirectional transcription when the non-template DNA strand bonds with the hybrid duplex (collapsed R-loops, where the two DNA strands remain antiparallel). For both Y·R:Y and R·R:Y DNA triplexes, the parallel third strand orientation is more stable; both parallel and antiparallel protonated d(GA+A)·d(GAA):d(TTC) triplexes are stable. Apparent contradictions in the literature about the R·R:Y triplex stability is probably due to lack of molecular resolution, since shifting the third strand by a single nucleotide alters the stability ranking. In the collapsed R-loops, antiparallel d(TTC+)·d(GAA):r(UUC) is unstable, while parallel d(GAA)·r(GAA):d(TTC) and d(GA+A)·r(GAA):d(TTC) are stable. In addition to providing new structural perspectives for specific therapeutic aims, our results contribute to a systematic structural basis for the emerging field of quantitative R-loop biology.
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Affiliation(s)
- Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Feng Pan
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA.,Department of Statistics, Florida State University, Tallahassee, FL 32306, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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37
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Delivery of ionizable hydrophilic drugs based on pharmaceutical formulation of ion pairs and ionic liquids. Eur J Pharm Biopharm 2020; 156:203-218. [DOI: 10.1016/j.ejpb.2020.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022]
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38
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Baisden JT, Boyer JA, Zhao B, Hammond SM, Zhang Q. Visualizing a protonated RNA state that modulates microRNA-21 maturation. Nat Chem Biol 2020; 17:80-88. [PMID: 33106660 DOI: 10.1038/s41589-020-00667-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 08/02/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
MicroRNAs are evolutionarily conserved small, noncoding RNAs that regulate diverse biological processes. Due to their essential regulatory roles, microRNA biogenesis is tightly regulated, where protein factors are often found to interact with specific primary and precursor microRNAs for regulation. Here, using NMR relaxation dispersion spectroscopy and mutagenesis, we reveal that the precursor of oncogenic microRNA-21 exists as a pH-dependent ensemble that spontaneously reshuffles the secondary structure of the entire apical stem-loop region, including the Dicer cleavage site. We show that the alternative excited conformation transiently sequesters the bulged adenine into a noncanonical protonated A+-G mismatch, conferring a substantial enhancement in Dicer processing over its ground conformational state. These results indicate that microRNA maturation efficiency may be encoded in the intrinsic dynamic ensemble of primary and precursor microRNAs, providing a potential means of regulating microRNA biogenesis in response to environmental and cellular stimuli.
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Affiliation(s)
- Jared T Baisden
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua A Boyer
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bo Zhao
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott M Hammond
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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39
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Hybrid Biopolymer and Lipid Nanoparticles with Improved Transfection Efficacy for mRNA. Cells 2020; 9:cells9092034. [PMID: 32899484 PMCID: PMC7563888 DOI: 10.3390/cells9092034] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Hybrid nanoparticles from lipidic and polymeric components were assembled to serve as vehicles for the transfection of messenger RNA (mRNA) using different portions of the cationic lipid DOTAP (1,2-Dioleoyl-3-trimethylammonium-propane) and the cationic biopolymer protamine as model systems. Two different sequential assembly approaches in comparison with a direct single-step protocol were applied, and molecular organization in correlation with biological activity of the resulting nanoparticle systems was investigated. Differences in the structure of the nanoparticles were revealed by thorough physicochemical characterization including small angle neutron scattering (SANS), small angle X-ray scattering (SAXS), and cryogenic transmission electron microscopy (cryo-TEM). All hybrid systems, combining lipid and polymer, displayed significantly increased transfection in comparison to lipid/mRNA and polymer/mRNA particles alone. For the hybrid nanoparticles, characteristic differences regarding the internal organization, release characteristics, and activity were determined depending on the assembly route. The systems with the highest transfection efficacy were characterized by a heterogenous internal organization, accompanied by facilitated release. Such a system could be best obtained by the single step protocol, starting with a lipid and polymer mixture for nanoparticle formation.
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40
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Belloň T, Slouka Z. Overlimiting behavior of surface-modified heterogeneous anion-exchange membranes. J Memb Sci 2020. [DOI: 10.1016/j.memsci.2020.118291] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Bastin G, Loison P, Vernex-Loset L, Dupire F, Challant J, Majou D, Boudaud N, Krier G, Gantzer C. Structural Organizations of Qβ and MS2 Phages Affect Capsid Protein Modifications by Oxidants Hypochlorous Acid and Peroxynitrite. Front Microbiol 2020; 11:1157. [PMID: 32582098 PMCID: PMC7283501 DOI: 10.3389/fmicb.2020.01157] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022] Open
Abstract
Pathogenic enteric viruses and bacteriophages such as Qβ and MS2 are transmitted through the fecal-oral route. However, oxidants such as peroxynitrite (ONOOH) and hypochlorous acid (HClO) can prevent new infection by inactivating infectious viruses. Their virucidal effect is well recognized, and yet predicting the effects of oxidants on viruses is currently impossible because the detailed mechanisms of viral inactivation remain unclear. Our data show that ONOOH and HClO cross-linked the capsid proteins and RNA genomes of Qβ and MS2 phages. Consistently, the capsids appeared intact by transmission electron microscopy (TEM) even when 99% of the phages were inactivated by oxidation. Moreover, a precise molecular study of the capsid proteins shows that ONOOH and HClO preferentially targeted capsid protein regions containing the oxidant-sensitive amino acid C, Y, or W. Interestingly, the interaction of these amino acids was a crucial parameter defining whether they would be modified by the addition of O, Cl, or NO2 or whether it induced the loss of the protein region detected by mass spectrometry, together suggesting potential sites for cross-link formation. Together, these data show that HClO and ONOOH consistently target oxidant-sensitive amino acids regardless of the structural organization of Qβ and MS2, even though the phenotypes change as a function of the interaction with adjacent proteins/RNA. These data also indicate a potential novel mechanism of viral inactivation in which cross-linking may impair infectivity.
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Affiliation(s)
- Guillaume Bastin
- Université de Lorraine, CNRS, LCPME, Nancy, France.,ACTALIA, Food Safety Department, Saint-Lô, France
| | | | | | | | | | | | | | - Gabriel Krier
- Université de Lorraine, LCP-A2MC, EA 4632, Metz, France
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42
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Uchiyama M, Momotake A, Kobayashi N, Yamamoto Y. Specific Binding of an Anionic Phthalocyanine Derivative to G-Quadruplex DNAs. CHEM LETT 2020. [DOI: 10.1246/cl.200110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Mami Uchiyama
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Atsuya Momotake
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
| | - Nagao Kobayashi
- Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan
| | - Yasuhiko Yamamoto
- Department of Chemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
- Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Ibaraki 305-8571, Japan
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43
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Langeberg CJ, Welch WRW, McGuire JV, Ashby A, Jackson AD, Chapman EG. Biochemical Characterization of Yeast Xrn1. Biochemistry 2020; 59:1493-1507. [PMID: 32251580 DOI: 10.1021/acs.biochem.9b01035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Messenger RNA degradation is an important component of overall gene expression. During the final step of eukaryotic mRNA degradation, exoribonuclease 1 (Xrn1) carries out 5' → 3' processive, hydrolytic degradation of RNA molecules using divalent metal ion catalysis. To initiate studies of the 5' → 3' RNA decay machinery in our lab, we expressed a C-terminally truncated version of Saccharomyces cerevisiae Xrn1 and explored its enzymology using a second-generation, time-resolved fluorescence RNA degradation assay. Using this system, we quantitatively explored Xrn1's preference for 5'-monophosphorylated RNA substrates, its pH dependence, and the importance of active site mutations in the molecule's conserved catalytic core. Furthermore, we explore Xrn1's preference for RNAs containing a 5' single-stranded region both in an intermolecular hairpin structure and in an RNA-DNA hybrid duplex system. These results both expand and solidify our understanding of Xrn1, a centrally important enzyme whose biochemical properties have implications in numerous RNA degradation and processing pathways.
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Affiliation(s)
- Conner J Langeberg
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - William R W Welch
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - John V McGuire
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Alison Ashby
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Alexander D Jackson
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Erich G Chapman
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
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44
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Metzger KF, Padutsch W, Pekarsky A, Kopp J, Voloshin AM, Kühnel H, Maurer M. IGF1 inclusion bodies: A QbD based process approach for efficient USP as well as early DSP unit operations. J Biotechnol 2020; 312:23-34. [DOI: 10.1016/j.jbiotec.2020.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 12/20/2022]
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45
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Lawler R, Caliendo C, Ju H, Kim JY, Lee SW, Jang SS. Effect of the Side-Chain Length in Perfluorinated Sulfonic and Phosphoric Acid-Based Membranes on Nanophase Segregation and Transport: A Molecular Dynamics Simulation Approach. J Phys Chem B 2020; 124:1571-1580. [PMID: 32026694 DOI: 10.1021/acs.jpcb.9b10408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of side-chain length on the nanophase-segregated structure and transport in perfluorinated sulfonic acid (PFSA)-based and perfluorinated phosphoric acid (PFPA)-based membranes is investigated at 20 and 5 wt % water content conditions using a molecular dynamics simulation method. It is found using the pair correlation analysis that the longer side chain leads to more developed local water structures in the water phase at 20 wt % water content, observable in both membrane chemistries albeit more distinct in PFPA-based membranes. It is also confirmed from the structure factor analysis that large-scale nanophase segregation is enhanced with increasing side-chain length for PFPA membranes, whereas no significant change is observed at these scales for PFSA membranes. Next, it is revealed that the proton transport is increased by 0.004 S/cm in PFSA-based membranes with increasing side-chain length due to the enhanced vehicular and hopping mechanisms, whereas the proton transport in PFPA-based membranes is decreased by 0.002 S/cm despite improved nanophase segregation. As confirmed by the pair correlation function analysis, the diminished proton transport in PFPA-based membranes is attributed to the molecular association of phosphate groups with hydronium ions via hydrogen bond in the longer side-chain case, which is namely a hydronium-mediated bridge configuration. Such bridge configurations and correspondingly similar trends in proton transport are also observed at 5 wt % water content condition to a lesser extent. Our simulation study demonstrates that the proton transport is affected by the hydrogen-bonding network as well as by the nanophase segregation.
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Affiliation(s)
- Robin Lawler
- Computational NanoBio Technology Laboratory, School of Materials Science and Engineering , Georgia Institute of Technology , 771 Ferst Drive NW , Atlanta , Georgia 30332 , United States.,School of Chemical and Biomolecular Engineering , Georgia Institute of Technology , 311 Ferst Drive NW , Atlanta , Georgia 30332 , United States
| | - Charles Caliendo
- Computational NanoBio Technology Laboratory, School of Materials Science and Engineering , Georgia Institute of Technology , 771 Ferst Drive NW , Atlanta , Georgia 30332 , United States
| | - Hyunchul Ju
- Department of Mechanical Engineering , Inha University , 100 Inha-ro , Michuhol-gu, Incheon 22212 , Republic of Korea
| | - Jin Young Kim
- Center for Hydrogen Fuel Cell Research , Korea Institute of Science and Technology (KIST) , Seoul 02792 , Republic of Korea
| | - Seung Woo Lee
- G. W. Woodruff School of Mechanical Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Strategic Energy Institute , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Seung Soon Jang
- Computational NanoBio Technology Laboratory, School of Materials Science and Engineering , Georgia Institute of Technology , 771 Ferst Drive NW , Atlanta , Georgia 30332 , United States.,Strategic Energy Institute , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States.,Institute for Electronics and Nanotechnology , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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Metzger KFJ, Voloshin A, Schillinger H, Kühnel H, Maurer M. Adsorptive filtration: A case study for early impurity reduction in an Escherichia coli production process. Biotechnol Prog 2019; 36:e2948. [PMID: 31837191 DOI: 10.1002/btpr.2948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/22/2019] [Accepted: 12/08/2019] [Indexed: 11/10/2022]
Abstract
Primary recovery of intracellular products from Escherichia coli requires cell disruption which leads to a massive release of process-related impurities burdening subsequent downstream process (DSP) unit operations. Especially, DNA and endotoxins challenge purification operations due to their size and concentrations. Consequently, an early reduction in impurities will not only simplify the production process but also increase robustness while alleviating the workload afterward. In the present work, we studied the proof of concept whether a nonwoven anion exchange filter material decreases soluble impurities immediately at the clarification step of E. coli DSP. In a first attempt, endotoxin burden was reduced by 4.6-fold and the DNA concentration by 3.6-fold compared to conventional depth filtration. A design of experiment for the adsorptive filtration approach was carried out to analyze the influence of different critical process parameters (CPPs) on impurity reduction. We showed that depending on the CPPs chosen, a DNA lowering of more than 3 log values, an endotoxin decrease of approximately 7 logs, and a minor HCP clearance of at least 0.3 logs could be achieved. Thus, we further revealed a chromatography column protecting effect when using adsorptive filtration beforehand.
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Affiliation(s)
- Karl F J Metzger
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,Bioprocess Engineering, Austrian Centre of Industrial Biotechnology, Wien, AT, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Wien, AT, Austria
| | - Alexei Voloshin
- 3M Company, Separation and Purification Sciences Division, 3M Center, Saint Paul, Minnesota
| | - Harald Schillinger
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,3M Österreich, 3M Separation and Purification Sciences Division, Wien, AT, Austria
| | - Harald Kühnel
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria
| | - Michael Maurer
- Life Sciences, University of Applied Sciences Campus Vienna, Wien, AT, Austria.,Bioprocess Engineering, Austrian Centre of Industrial Biotechnology, Wien, AT, Austria
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Abstract
RNA is a versatile biomolecule with a broad range of biological functions that go far beyond its initially described role as a simple information carrier. The development of chemical methods to control, manipulate and modify RNA has the potential to yield new insights into its many functions and properties. Traditionally, most of these methods involved the chemical modification of RNA structure using solid-state synthesis or enzymatic transformations. However, over the past 15 years, the direct functionalization of RNA by selective acylation of the 2'-hydroxyl (2'-OH) group has emerged as a powerful alternative that enables the simple modification of both synthetic and transcribed RNAs. In this Review, we discuss the chemical properties and design of effective reagents for RNA 2'-OH acylation, highlighting the unique problem of 2'-OH reactivity in the presence of water. We elaborate on how RNA 2'-OH acylation is being exploited to develop selective chemical probes that enable interrogation of RNA structure and function, and describe new developments and applications in the field.
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48
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RNA base-pairing complexity in living cells visualized by correlated chemical probing. Proc Natl Acad Sci U S A 2019; 116:24574-24582. [PMID: 31744869 DOI: 10.1073/pnas.1905491116] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA structure and dynamics are critical to biological function. However, strategies for determining RNA structure in vivo are limited, with established chemical probing and newer duplex detection methods each having deficiencies. Here we convert the common reagent dimethyl sulfate into a useful probe of all 4 RNA nucleotides. Building on this advance, we introduce PAIR-MaP, which uses single-molecule correlated chemical probing to directly detect base-pairing interactions in cells. PAIR-MaP has superior resolution compared to alternative experiments, can resolve multiple sets of pairing interactions for structurally dynamic RNAs, and enables highly accurate structure modeling, including of RNAs containing multiple pseudoknots and extensively bound by proteins. Application of PAIR-MaP to human RNase MRP and 2 bacterial messenger RNA 5' untranslated regions reveals functionally important and complex structures undetected by prior analyses. PAIR-MaP is a powerful, experimentally concise, and broadly applicable strategy for directly visualizing RNA base pairs and dynamics in cells.
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Demelenne A, Gou MJ, Nys G, Parulski C, Crommen J, Servais AC, Fillet M. Evaluation of hydrophilic interaction liquid chromatography, capillary zone electrophoresis and drift tube ion-mobility quadrupole time of flight mass spectrometry for the characterization of phosphodiester and phosphorothioate oligonucleotides. J Chromatogr A 2019; 1614:460716. [PMID: 31761437 DOI: 10.1016/j.chroma.2019.460716] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/09/2019] [Accepted: 11/14/2019] [Indexed: 01/23/2023]
Abstract
Oligonucleotide-based medicines that can modulate gene expression have numerous potential applications in targeted therapies. Most of the commercialized therapeutic oligonucleotides are chemically modified to increase their in vivo lifetime. In this work, we studied poly-deoxy(thymidylic) acids (dT) and modified phosphorothioate oligonucleotides (PS). Several analytical techniques, including ion-pair reverse phase liquid chromatography, are described in the literature to assess their quality but most of them present significant drawbacks. In the present study, dT and PS mixtures were analyzed by hydrophilic interaction liquid chromatography (HILIC) and capillary zone electrophoresis (CZE) coupled to ultraviolet detection. In HILIC, the selectivities of three types of stationary phases (dihydroxypropane, phosphorylcholine and amide) were compared. Optimal conditions were determined and consisted of an amide stationary phase with a mobile phase made up of water, acetonitrile and 15 mM ammonium acetate (pH 5.5). In those conditions, high resolving power and good repeatability were achieved. In CZE, the effect of the background electrolyte (BGE), its pH and concentration were evaluated. A BGE made up of 300 mM ammonium acetate adjusted to pH 6.0 was selected. Finally, the two techniques were compared in terms of selectivity, repeatability and peak efficiency. In the second part of the study, HILIC and CZE were both coupled to a drift-tube ion-mobility quadrupole time-of-flight MS detector (DTIMS-QTOF) to assess the added value of this coupling for oligonucleotide characterization. Indeed, by using the measured collision cross section (CCS), the evaluation of the number of nucleotides was performed. Looking across the results, HILIC and CZE coupled to DTIMS-QTOF can be considered as promising tools for the quality control of oligonucleotides.
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Affiliation(s)
- Alice Demelenne
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Marie-Jia Gou
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Gwenaël Nys
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Chloé Parulski
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Jacques Crommen
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Anne-Catherine Servais
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Quartier Hospital, Avenue Hippocrate 15, Liege 4000, Belgium.
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50
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Fast and unbiased purification of RNA-protein complexes after UV cross-linking. Methods 2019; 178:72-82. [PMID: 31586594 DOI: 10.1016/j.ymeth.2019.09.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/04/2019] [Accepted: 09/16/2019] [Indexed: 12/13/2022] Open
Abstract
Post-transcriptional regulation of gene expression in cells is facilitated by formation of RNA-protein complexes (RNPs). While many methods to study eukaryotic (m)RNPs rely on purification of polyadenylated RNA, other important regulatory RNA classes or bacterial mRNA could not be investigated at the same depth. To overcome this limitation, we developed Phenol Toluol extraction (PTex), a novel and unbiased method for the purification of UV cross-linked RNPs in living cells. PTex is a fast (2-3 h) and simple protocol. The purification principle is solely based on physicochemical properties of cross-linked RNPs, enabling us to interrogate RNA-protein interactions system-wide and beyond poly(A) RNA from a variety of species and source material. Here, we are presenting an introduction of the underlying separation principles and give a detailed discussion of the individual steps as well as incorporation of PTex in high-throughput pipelines.
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