1
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Nakata M, Kosaka N, Kawauchi K, Miyoshi D. Quantitative Effects of the Loop Region on Topology, Thermodynamics, and Cation Binding of DNA G-quadruplexes. ACS OMEGA 2024; 9:35028-35036. [PMID: 39157113 PMCID: PMC11325513 DOI: 10.1021/acsomega.4c05008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 08/20/2024]
Abstract
The thermal stability of G-quadruplexes is important for their biological roles. G-quadruplexes are stable in the presence of cations such as K+ and Na+ because these cations coordinate in the G-quartet of four guanine bases. It is well known that the number of G-quartets and the configuration of the guanine bases affect the binding affinity of the cation. Recently, structures formed in the loop regions connecting the guanine stretches have attracted significant attention, because the loop region affects G-quadruplex properties, such as topology, thermal stability, and interactions with proteins and small molecules. Considering these effects, the loop region can also affect the binding affinity of the cations. Here, we designed a series of G-quadruplex-forming DNA sequences that contain a hairpin in a loop region and investigated the effects of the sequence and structure of the loop region on the cation binding affinity as well as the thermal stability of the G-quadruplex as a whole. First, structural analysis of the DNA sequences showed that the hairpin at the loop plays a key role in determining G4 topology (strand orientation). Second, in the case of the G-quadruplexes with the hairpin-forming loop region, it was found that a longer loop length led to a higher thermodynamic stability of the G-quadruplex as well as higher cation binding affinity. In contrast, an unstructured loop region did not lead to such effects. Interestingly, the cation binding affinity was correlated to the thermodynamic stability of the hairpin structure at the loop region. It was quantitatively demonstrated that the stable loop region stabilized the whole G-quadruplex structure, which induced higher cation binding affinity. These systematic and quantitative results showed that the loop region is one of the determinants of cation binding and expanded the possibilities of drug development targeting G4s by stabilizing the loop region.
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Affiliation(s)
- Minori Nakata
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Kosaka
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Keiko Kawauchi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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2
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. Sci Rep 2024; 14:4132. [PMID: 38374280 PMCID: PMC10876929 DOI: 10.1038/s41598-024-53841-3] [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: 06/26/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces, but they are not optimized for studies in constrained environments as they require attachment to micron-scale probes such as beads or cantilevers. Nanomechanical devices are a promising alternative, but this requires versatile designs that can be tuned to respond to a wide range of forces. We investigate the properties of a nanoscale force sensitive DNA origami device which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, has a binary (open or closed) response to an applied force by undergoing a reversible structural transition. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). The DNA oligonucleotide design parameters also strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show the opening force is tunable in real time by adding a single DNA oligonucleotide. These results establish the potential of the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Jessica O Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Carlos E Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Michael G Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA.
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3
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Arteaga S, Dolenz BJ, Znosko BM. Competitive Influence of Alkali Metals in the Ion Atmosphere on Nucleic Acid Duplex Stability. ACS OMEGA 2024; 9:1287-1297. [PMID: 38222622 PMCID: PMC10785066 DOI: 10.1021/acsomega.3c07563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
The nonspecific atmosphere around nucleic acids, often termed the ion atmosphere, encompasses a collection of weak ion-nucleic acid interactions. Although nonspecific, the ion atmosphere has been shown to influence nucleic acid folding and structural stability. Studies investigating the composition of the ion atmosphere have shown competitive occupancy of the atmosphere between metal ions in the same solution. Many studies have investigated single ion effects on nucleic acid secondary structure stability; however, no comprehensive studies have investigated how the competitive occupancy of mixed ions in the ion atmosphere influences nucleic acid secondary structure stability. Here, six oligonucleotides were optically melted in buffers containing molar quantities, or mixtures, of either XCl (X = Li, K, Rb, or Cs) or NaCl. A correction factor was developed to better predict RNA duplex stability in solutions containing mixed XCl/NaCl. For solutions containing a 1:1 mixture of XCl/NaCl, one alkali metal chloride contributed more to duplex stability than the other. Overall, there was a 54% improvement in predictive capabilities with the correction factor compared with the standard 1.0 M NaCl nearest-neighbor models. This correction factor can be used in models to better predict RNA secondary structure in solutions containing mixed XCl/NaCl.
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Affiliation(s)
- Sebastian
J. Arteaga
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Bruce J. Dolenz
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
| | - Brent M. Znosko
- Department of Chemistry, Saint Louis University, Saint
Louis, Missouri 63103, United States
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4
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Weigert N, Schweiger AL, Gross J, Matthes M, Corbacioglu S, Sommer G, Heise T. Detection of a 7SL RNA-derived small non-coding RNA using Molecular Beacons in vitro and in cells. Biol Chem 2023; 404:1123-1136. [PMID: 37632732 DOI: 10.1515/hsz-2023-0185] [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: 04/14/2023] [Accepted: 08/11/2023] [Indexed: 08/28/2023]
Abstract
Small non-coding RNAs (sncRNA) are involved in many steps of the gene expression cascade and regulate processing and expression of mRNAs by the formation of ribonucleoprotein complexes (RNP) such as the RNA-induced silencing complex (RISC). By analyzing small RNA Seq data sets, we identified a sncRNA annotated as piR-hsa-1254, which is likely derived from the 3'-end of 7SL RNA2 (RN7SL2), herein referred to as snc7SL RNA. The 7SL RNA is an abundant long non-coding RNA polymerase III transcript and serves as structural component of the cytoplasmic signal recognition particle (SRP). To evaluate a potential functional role of snc7SL RNA, we aimed to define its cellular localization by live cell imaging. Therefore, a Molecular Beacon (MB)-based method was established to compare the subcellular localization of snc7SL RNA with its precursor 7SL RNA. We designed and characterized several MBs in vitro and tested those by live cell fluorescence microscopy. Using a multiplex approach, we show that 7SL RNA localizes mainly to the endoplasmic reticulum (ER), as expected for the SRP, whereas snc7SL RNA predominately localizes to the nucleus. This finding suggests a fundamentally different function of 7SL RNA and its derivate snc7SL RNA.
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Affiliation(s)
- Nina Weigert
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Anna-Lena Schweiger
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Jonas Gross
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Marie Matthes
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Selim Corbacioglu
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Gunhild Sommer
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
| | - Tilman Heise
- Department for Pediatric Hematology, Oncology and Stem Cell Transplantation, University Hospital Regensburg, Franz-Josef-Strauß Allee 11, D-93053 Regensburg, Germany
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5
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Linko V, Keller A. Stability of DNA Origami Nanostructures in Physiological Media: The Role of Molecular Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301935. [PMID: 37093216 DOI: 10.1002/smll.202301935] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Programmable, custom-shaped, and nanometer-precise DNA origami nanostructures have rapidly emerged as prospective and versatile tools in bionanotechnology and biomedicine. Despite tremendous progress in their utilization in these fields, essential questions related to their structural stability under physiological conditions remain unanswered. Here, DNA origami stability is explored by strictly focusing on distinct molecular-level interactions. In this regard, the fundamental stabilizing and destabilizing ionic interactions as well as interactions involving various enzymes and other proteins are discussed, and their role in maintaining, modulating, or decreasing the structural integrity and colloidal stability of DNA origami nanostructures is summarized. Additionally, specific issues demanding further investigation are identified. This review - through its specific viewpoint - may serve as a primer for designing new, stable DNA objects and for adapting their use in applications dealing with physiological media.
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Affiliation(s)
- Veikko Linko
- Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P. O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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6
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Robbins A, Hildebolt H, Neuhoff M, Beshay P, Winter JO, Castro CE, Bundschuh R, Poirier MG. Cooperative control of a DNA origami force sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546608. [PMID: 37425797 PMCID: PMC10327127 DOI: 10.1101/2023.06.26.546608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Most biomolecular systems are dependent on a complex interplay of forces. Modern force spectroscopy techniques provide means of interrogating these forces. These techniques, however, are not optimized for studies in constrained or crowded environments as they typically require micron-scale beads in the case of magnetic or optical tweezers, or direct attachment to a cantilever in the case of atomic force microscopy. We implement a nanoscale force-sensing device using a DNA origami which is highly customizable in geometry, functionalization, and mechanical properties. The device, referred to as the NanoDyn, functions as a binary (open or closed) force sensor that undergoes a structural transition under an external force. The transition force is tuned with minor alterations of 1 to 3 DNA oligonucleotides and spans tens of picoNewtons (pN). This actuation of the NanoDyn is reversible and the design parameters strongly influence the efficiency of resetting the initial state, with higher stability devices (≳10 pN) resetting more reliably during repeated force-loading cycles. Finally, we show that the opening force can be adjusted in real time by the addition of a single DNA oligonucleotide. These results establish the NanoDyn as a versatile force sensor and provide fundamental insights into how design parameters modulate mechanical and dynamic properties.
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Affiliation(s)
- Ariel Robbins
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Hazen Hildebolt
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Michael Neuhoff
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Peter Beshay
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Jessica O. Winter
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
- Department of Biomedical Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Carlos E. Castro
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Ralf Bundschuh
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Michael G. Poirier
- Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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7
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Suh S, Xing Y, Rottensteiner A, Zhu R, Oh YJ, Howorka S, Hinterdorfer P. Molecular Recognition in Confined Space Elucidated with DNA Nanopores and Single-Molecule Force Microscopy. NANO LETTERS 2023; 23:4439-4447. [PMID: 37166380 PMCID: PMC10214486 DOI: 10.1021/acs.nanolett.3c00743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/24/2023] [Indexed: 05/12/2023]
Abstract
The binding of ligands to receptors within a nanoscale small space is relevant in biology, biosensing, and affinity filtration. Binding in confinement can be studied with biological systems but under the limitation that essential parameters cannot be easily controlled including receptor type and position within the confinement and its dimensions. Here we study molecular recognition with a synthetic confined nanopore with controllable pore dimension and molecular DNA receptors at different depth positions within the channel. Binding of a complementary DNA strand is studied at the single-molecule level with atomic force microscopy. Following the analysis, kinetic association rates are lower for receptors positioned deeper inside the pore lumen while dissociation is faster and requires less force. The phenomena are explained by the steric constraints on molecular interactions in confinement. Our study is the first to explore recognition in DNA nanostructures with atomic force microscopy and lays out new tools to further quantify the effect of nanoconfinement on molecular interactions.
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Affiliation(s)
- Saanfor
Hubert Suh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yongzheng Xing
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Alexia Rottensteiner
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Rong Zhu
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Yoo Jin Oh
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
| | - Stefan Howorka
- Department
of Chemistry, University College London,
Institute of Structural and Molecular Biology, 20 Gordon Street, London WC1H OAJ, United Kingdom
| | - Peter Hinterdorfer
- Department
of Applied Experimental Biophysics, Johannes
Kepler University Linz, Institute of Biophysics, Gruberstr. 40, 4020 Linz, Austria
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8
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Kuciński M, Jakubowska-Lehrmann M, Góra A, Mirny Z, Nadolna-Ałtyn K, Szlinder-Richert J, Ocalewicz K. Population Genetic Study on the European Flounder ( Platichthys flesus) from the Southern Baltic Sea Using SNPs and Microsatellite Markers. Animals (Basel) 2023; 13:ani13091448. [PMID: 37174485 PMCID: PMC10177365 DOI: 10.3390/ani13091448] [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: 02/28/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
The European flounder (Platichthys flesus), which is closely related to the recently discovered Baltic flounder (Platichthys solemdali), is currently the third most commercially fished species in the Baltic Sea. According to the available data from the Polish Fisheries Monitoring Center and fishermen's observations, the body condition indices of the species in the Baltic Sea have declined in recent years. The aim of the present study was to obtain information on the current patterns of genetic variability and the population structure of the European flounder and to verify whether the Baltic flounder is present in the southern Baltic Sea. Moreover, we aimed to verify whether the observed decline in the body condition indices of the species in the Baltic Sea might be associated with adaptive alterations in its gene pool due to increased fishing pressure. For this purpose, 190 fish were collected from four locations along the central coastline of Poland, i.e., Mechelinki, Władysławowo, the Vistula Lagoon in 2018, and the Słupsk Bank in 2020. The fish were morphologically analyzed and then genetically screened by the application of nineteen microsatellite DNA and two diagnostic SNP markers. The examined European flounder specimens displayed a high level of genetic diversity (PIC = 0.832-0.903, I = 2.579-2.768). A lack of significant genetic differentiation (Fst = 0.004, p > 0.05) was observed in all the examined fish, indicating that the European flounder in the sampled area constitutes a single genetic cluster. A significant deficiency in heterozygotes (Fis = 0.093, p < 0.05) and overall deviations from Hardy-Weinberg expectations (H-WE) were only detected in fish sampled from the Słupsk Bank. The estimated effective population size (Ne) among the sampled fish groups varied from 712 (Słupsk Bank) to 10,115 (Władysławowo and Mechelinki). However, the recorded values of the Garza-Williamson indicator (M = 0.574-0.600) and the lack of significant (p > 0.05) differences in Heq > He under the SMM model did not support the species' population size changes in the past. The applied SNP markers did not detect the presence of the Baltic flounder among the fish sampled from the studied area. The analysis of an association between biological traits and patterns of genetic diversity did not detect any signs of directional selection or density-dependent adaptive changes in the gene pool of the examined fish that might be caused by increased fishing pressure.
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Affiliation(s)
- Marcin Kuciński
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Piłsudskiego Ave. 46, 81-378 Gdynia, Poland
| | - Magdalena Jakubowska-Lehrmann
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Agnieszka Góra
- Department of Food and Environmental Chemistry, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Zuzanna Mirny
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Katarzyna Nadolna-Ałtyn
- Department of Fisheries Resources, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Joanna Szlinder-Richert
- Department of Food and Environmental Chemistry, National Marine Fisheries Research Institute, Kołłątaja 1 Street, 81-332 Gdynia, Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Piłsudskiego Ave. 46, 81-378 Gdynia, Poland
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9
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Pundir M, De Rosa MC, Lobanova L, Abdulmawjood S, Chen X, Papagerakis S, Papagerakis P. Structural properties and binding mechanism of DNA aptamers sensing saliva melatonin for diagnosis and monitoring of circadian clock and sleep disorders. Anal Chim Acta 2023; 1251:340971. [PMID: 36925277 DOI: 10.1016/j.aca.2023.340971] [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: 11/14/2022] [Revised: 01/25/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023]
Abstract
Circadian desynchrony with the external light-dark cycle influences the rhythmic secretion of melatonin which is among the first signs of circadian rhythm sleep disorders. An accurate dim light melatonin onset (established indicator of circadian rhythm sleep disorders) measurement requires lengthy assays, and antibody affinities alterations, especially in patients with circadian rhythm disorders whose melatonin salivary levels vary significantly, making antibodies detection mostly inadequate. In contrast, aptamers with their numerous advantages (e.g., target selectivity, structural flexibility in tuning binding affinities, small size, etc.) can become preferable biorecognition molecules for salivary melatonin detection with high sensitivity and specificity. This study thoroughly characterizes the structural property and binding mechanism of a single-stranded DNA aptamer full sequence (MLT-C-1) and its truncated versions (MLT-A-2, MLT-A-4) to decipher its optimal characteristics for saliva melatonin detection. We use circular dichroism spectroscopy to determine aptamers' conformational changes under different ionic strengths and showed that aptamers display a hairpin loop structure where few base pairs in the stem play a significant role in melatonin binding and formation of aptamer stabilized structure. Through microscale thermophoresis, aptamers demonstrated a high binding affinity in saliva samples (MLT-C-1F Kd = 12.5 ± 1.7 nM; MLT-A-4F Kd = 11.2 ± 1.6 nM; MLT-A-2F Kd = 2.4 ± 2.8 nM; limit-of-detection achieved in pM, highest sensitivity attained for MLT-A-2F aptamer with the lowest detection limit of 1.35 pM). Our data suggest that aptamers are promising as biorecognition molecules and provide the baseline parameters for the development of an aptamer-based point-of-care diagnostic system for melatonin detection and accurate profiling of its fluctuations in saliva.
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Affiliation(s)
- Meenakshi Pundir
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Maria C De Rosa
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada.
| | - Liubov Lobanova
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada
| | - Shahad Abdulmawjood
- Department of Chemistry, Faculty of Science, Carleton University, 1125 Colonel by Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Xiongbiao Chen
- Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada; Department of Mechanical Engineering, School of Engineering, University of Saskatchewan, 57 Campus Dr, S7K 5A9, Saskatoon, Canada.
| | - Silvana Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Laboratory of Oral, Head and Neck Cancer - Personalized Diagnostics and Therapeutics, Department of Surgery, College of Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Michigan, 1500 E Medical Center Dr, Ann Arbor, MI, 48109, United States.
| | - Petros Papagerakis
- Laboratory of Precision Oral Health and Chronobiology, College of Dentistry, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, S7N 5E4, Canada; Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7K 5A9, Canada.
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10
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Arteaga SJ, Adams MS, Meyer NL, Richardson KE, Hoener S, Znosko BM. Thermodynamic determination of RNA duplex stability in magnesium solutions. Biophys J 2023; 122:565-576. [PMID: 36540026 PMCID: PMC9941723 DOI: 10.1016/j.bpj.2022.12.025] [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] [Received: 08/08/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
The prediction of RNA secondary structure and thermodynamics from sequence relies on free energy minimization and nearest neighbor parameters. Currently, algorithms used to make these predictions are based on parameters from optical melting studies performed in 1 M NaCl. However, many physiological and biochemical buffers containing RNA include much lower concentrations of monovalent cations and the presence of divalent cations. In order to improve these algorithms, thermodynamic data was previously collected for RNA duplexes in solutions containing 71, 121, 221, and 621 mM Na+. From this data, correction factors for free energy (ΔG°37) and melting temperature (Tm) were derived. Despite these newly derived correction factors for sodium, the stabilizing effects of magnesium have been ignored. Here, the same RNA duplexes were melted in solutions containing 0.5, 1.5, 3.0, and 10.0 mM Mg2+ in the absence of monovalent cations. Correction factors for Tm and ΔG°37 were derived to scale the current parameters to a range of magnesium concentrations. The Tm correction factor predicts the melting temperature within 1.2°C, and the ΔG°37 correction factor predicts the free energy within 0.30 kcalmol. These newly derived magnesium correction factors can be incorporated into algorithms that predict RNA secondary structure and stability from sequence.
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Affiliation(s)
| | - Miranda S Adams
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri
| | - Nicole L Meyer
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri
| | | | - Scott Hoener
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri
| | - Brent M Znosko
- Department of Chemistry, Saint Louis University, Saint Louis, Missouri.
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11
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Kimchi O, Brenner MP, Colwell LJ. Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the LandscapeFold Algorithm. Methods Mol Biol 2023; 2586:49-77. [PMID: 36705898 DOI: 10.1007/978-1-0716-2768-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Here we detail the LandscapeFold secondary structure prediction algorithm and how it is used. The algorithm was previously described and tested in (Kimchi O et al., Biophys J 117(3):520-532, 2019), though it was not named there. The algorithm directly enumerates all possible secondary structures into which up to two RNA or single-stranded DNA sequences can fold. It uses a polymer physics model to estimate the configurational entropy of structures including complex pseudoknots. We detail each of these steps and ways in which the user can adjust the algorithm as desired. The code is available on the GitHub repository https://github.com/ofer-kimchi/LandscapeFold .
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Affiliation(s)
- Ofer Kimchi
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA. .,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Michael P Brenner
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Lucy J Colwell
- Department of Chemistry, University of Cambridge, Cambridge, UK
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12
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Li X, Dai X, Pan Y, Sun Y, Yang B, Chen K, Wang Y, Xu JF, Dong Y, Yang YR, Yan LT, Liu D. Studies on the Synergistic Effect of Tandem Semi-Stable Complementary Domains on Sequence-Defined DNA Block Copolymers. J Am Chem Soc 2022; 144:21267-21277. [DOI: 10.1021/jacs.2c08930] [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)
- Xin Li
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaobin Dai
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yufan Pan
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yawei Sun
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (Huadong), Qingdao 258000, China
| | - Bo Yang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Kun Chen
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - You Wang
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiang-Fei Xu
- Key Lab of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid Interface and Chemical Thermodynamics, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yuhe Renee Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Li-Tang Yan
- State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Engineering Research Center of Advanced Rare Earth Materials (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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13
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Sakovina L, Vokhtantsev I, Vorobyeva M, Vorobyev P, Novopashina D. Improving Stability and Specificity of CRISPR/Cas9 System by Selective Modification of Guide RNAs with 2'-fluoro and Locked Nucleic Acid Nucleotides. Int J Mol Sci 2022; 23:13460. [PMID: 36362256 PMCID: PMC9655745 DOI: 10.3390/ijms232113460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 09/01/2023] Open
Abstract
The genome editing approach using the components of the CRISPR/Cas system has found wide application in molecular biology, fundamental medicine and genetic engineering. A promising method is to increase the efficacy and specificity of CRISPR/Cas-based genome editing systems by modifying their components. Here, we designed and chemically synthesized guide RNAs (crRNA, tracrRNA and sgRNA) containing modified nucleotides (2'-O-methyl, 2'-fluoro, LNA-locked nucleic acid) or deoxyribonucleotides in certain positions. We compared their resistance to nuclease digestion and examined the DNA cleavage efficacy of the CRISPR/Cas9 system guided by these modified guide RNAs. The replacement of ribonucleotides with 2'-fluoro modified or LNA nucleotides increased the lifetime of the crRNAs, while other types of modification did not change their nuclease resistance. Modification of crRNA or tracrRNA preserved the efficacy of the CRISPR/Cas9 system. Otherwise, the CRISPR/Cas9 systems with modified sgRNA showed a remarkable loss of DNA cleavage efficacy. The kinetic constant of DNA cleavage was higher for the system with 2'-fluoro modified crRNA. The 2'-modification of crRNA also decreased the off-target effect upon in vitro dsDNA cleavage.
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Affiliation(s)
- Lubov Sakovina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ivan Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Pavel Vorobyev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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14
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Kashima M, Kamitani M, Nomura Y, Mori-Moriyama N, Betsuyaku S, Hirata H, Nagano AJ. DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate. PLANT METHODS 2022; 18:99. [PMID: 35933383 PMCID: PMC9356424 DOI: 10.1186/s13007-022-00930-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/24/2022] [Indexed: 06/09/2023]
Abstract
BACKGROUND Quantification of gene expression such as RNA-Seq is a popular approach to study various biological phenomena. Despite the development of RNA-Seq library preparation methods and sequencing platforms in the last decade, RNA extraction remains the most laborious and costly step in RNA-Seq of tissue samples of various organisms. Thus, it is still difficult to examine gene expression in thousands of samples. RESULTS Here, we developed Direct-RT buffer in which homogenization of tissue samples and direct-lysate reverse transcription can be conducted without RNA purification. The DTT concentration in Direct-RT buffer prevented RNA degradation but not RT in the lysates of several plant tissues, yeast, and zebrafish larvae. Direct reverse transcription on these lysates in Direct-RT buffer produced comparable amounts of cDNA to those synthesized from purified RNA. To maximize the advantage of the Direct-RT buffer, we integrated Direct-RT and targeted RNA-Seq to develop a cost-effective, high-throughput quantification method for the expressions of hundreds of genes: DeLTa-Seq (Direct-Lysate reverse transcription and Targeted RNA-Seq). The DeLTa-Seq method could drastically improve the efficiency and accuracy of gene expression analysis. DeLTa-Seq analysis of 1056 samples revealed the temperature-dependent effects of jasmonic acid and salicylic acid in Arabidopsis thaliana. CONCLUSIONS The DeLTa-Seq method can realize large-scale studies using thousands of animal, plant, and microorganism samples, such as chemical screening, field experiments, and studies focusing on individual variability. In addition, Direct-RT is also beneficial for gene expression analysis in small tissues from which it is difficult to purify enough RNA for the experiments.
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Affiliation(s)
- Makoto Kashima
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Fuchinobe 5-10-1, Chuoku, , Sagamihara 252-5258 Japan
| | - Mari Kamitani
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113 Japan
| | - Yasuyuki Nomura
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
| | - Natsumi Mori-Moriyama
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
| | - Shigeyuki Betsuyaku
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
| | - Hiromi Hirata
- Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Fuchinobe 5-10-1, Chuoku, , Sagamihara 252-5258 Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017 Japan
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15
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Wang L, Cui J, Tanner JA, Shiu SCC. Self-Assembly of DNA Tiles with G-Quadruplex DNAzyme Catalytic Activity for Sensing Applications. ACS APPLIED BIO MATERIALS 2022; 5:3788-3794. [PMID: 35916910 DOI: 10.1021/acsabm.2c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA tiles form through self-assembly of a small number of DNA strands that interact through basic repeated interactions, allowing the growth of nanoscale structures seeded by molecular inputs. If an approach for catalytic signal amplification can be integrated into the resultant nanostructure, then one can anticipate biosensing or diagnostic applications mediated by DNA tile self-assembly. Here, two-dimensional DNA tiles with split quadruplexes were designed as diagnostic tools for nucleic acid sensing without the use of protein enzymes. The presence of a target sequence leads to formation of extended microscale structures with arrayed multiple G-quadruplexes across the tile plane, with catalytic activity coupled to a colorimetric reporter. Such a mechanism has potential for low-cost signal amplification using unmodified DNA without the use of protein enzymes for biosensing.
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Affiliation(s)
- Lin Wang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Jingyu Cui
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Hong Kong, China
| | - Julian A Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Hong Kong, China.,Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam Hong Kong, China
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16
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Satpathi S, Endoh T, Sugimoto N. Applicability of the nearest-neighbour model for pseudoknot RNAs. Chem Commun (Camb) 2022; 58:5952-5955. [PMID: 35451430 DOI: 10.1039/d1cc07094k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The validity of the nearest-neighbour (NN) model was verified in an RNA pseudoknot (PK) structure. The thermodynamic parameters of the second hairpin stem (S2) region, which separates the PK from a hairpin structure, were monitored using CD and UV melting. Different PKs with identical NN base pairs in the S2 region exhibited similar thermodynamic parameters, highlighting the validity of the NN model in this RNA tertiary structure motif.
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Affiliation(s)
- Sagar Satpathi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Kobe, 650-0047, Japan.
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17
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Xin Y, Piskunen P, Suma A, Li C, Ijäs H, Ojasalo S, Seitz I, Kostiainen MA, Grundmeier G, Linko V, Keller A. Environment-Dependent Stability and Mechanical Properties of DNA Origami Six-Helix Bundles with Different Crossover Spacings. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107393. [PMID: 35363419 DOI: 10.1002/smll.202107393] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/14/2022] [Indexed: 05/25/2023]
Abstract
The internal design of DNA nanostructures defines how they behave in different environmental conditions, such as endonuclease-rich or low-Mg2+ solutions. Notably, the inter-helical crossovers that form the core of such DNA objects have a major impact on their mechanical properties and stability. Importantly, crossover design can be used to optimize DNA nanostructures for target applications, especially when developing them for biomedical environments. To elucidate this, two otherwise identical DNA origami designs are presented that have a different number of staple crossovers between neighboring helices, spaced at 42- and 21- basepair (bp) intervals, respectively. The behavior of these structures is then compared in various buffer conditions, as well as when they are exposed to enzymatic digestion by DNase I. The results show that an increased number of crossovers significantly improves the nuclease resistance of the DNA origami by making it less accessible to digestion enzymes but simultaneously lowers its stability under Mg2+ -free conditions by reducing the malleability of the structures. Therefore, these results represent an important step toward rational, application-specific DNA nanostructure design.
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Affiliation(s)
- Yang Xin
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Petteri Piskunen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Antonio Suma
- Dipartimento di Fisica, Università di Bari and Sezione INFN di Bari, Bari, 70126, Italy
| | - Changyong Li
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Heini Ijäs
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Sofia Ojasalo
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Iris Seitz
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
| | - Veikko Linko
- Biohybrid Materials, Department of Bioproducts and Biosystems, Aalto University, P.O. Box 16100, Aalto, 00076, Finland
| | - Adrian Keller
- Technical and Macromolecular Chemistry, Paderborn University, Warburger Str. 100, 33098, Paderborn, Germany
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18
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Wahl A, Huptas C, Neuhaus K. Comparison of rRNA depletion methods for efficient bacterial mRNA sequencing. Sci Rep 2022; 12:5765. [PMID: 35388078 PMCID: PMC8986838 DOI: 10.1038/s41598-022-09710-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 03/28/2022] [Indexed: 11/18/2022] Open
Abstract
Current methods of high-throughput RNA sequencing of prokaryotes, including transcriptome analysis or ribosomal profiling, need deep sequencing to achieve sufficient numbers of effective reads (e.g., mapping to mRNA) in order to also find weakly expressed genetic elements. The fraction of high-quality reads mapping to coding RNAs (i.e., mRNA) is mainly influenced by the large content of rRNA and, to a lesser extent, tRNA in total RNA. Thus, depletion of rRNA increases coverage and thus sequencing costs. RiboZero, a depletion kit based on probe hybridisation and rRNA-removal was found to be most efficient in the past, but it was discontinued in 2018. To facilitate comparability with previous experiments and to help choose adequate replacements, we compare three commercially available rRNA depletion kits also based on hybridization and magnetic beads, i.e., riboPOOLs, RiboMinus and MICROBExpress, with the former RiboZero. Additionally, we constructed biotinylated probes for magnetic bead capture and rRNA depletion in this study. Based on E. coli, we found similar efficiencies in rRNA depletion for riboPOOLs and the self-made depletion method; both comparable to the former RiboZero, followed by RiboMinus, succeeded by MICROBExpress. Further, our in-house protocol allows customized species-specific rRNA or even tRNA depletion or depletion of other RNA targets. Both, the self-made biotinylated probes and riboPOOLs, were most successful in reducing the rRNA content and thereby increasing sequencing depth concerning mRNA reads. Additionally, the number of reads matching to weakly expressed genes are increased. In conclusion, the self-made specific biotinylated probes and riboPOOLs are an adequate replacement for the former RiboZero. Both are very efficient in depleting rRNAs, increasing mRNA reads and thus sequencing efficiency.
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Affiliation(s)
- Anika Wahl
- Core Facility Microbiome, ZIEL - Institute for Food and Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Christopher Huptas
- Chair for Microbial Ecology, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food and Health, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany.
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19
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Ohira M, Katashima T, Naito M, Aoki D, Yoshikawa Y, Iwase H, Takata SI, Miyata K, Chung UI, Sakai T, Shibayama M, Li X. Star-Polymer-DNA Gels Showing Highly Predictable and Tunable Mechanical Responses. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2108818. [PMID: 35034389 DOI: 10.1002/adma.202108818] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Dynamically crosslinked gels are appealing materials for applications that require time-dependent mechanical responses. DNA duplexes are ideal crosslinkers for building such gels because of their excellent sequence addressability and flexible tunability in bond energy. However, the mechanical responses of most DNA gels are complicated and unpredictable. Here, a DNA gel with a highly homogeneous gel network and well predictable mechanical behaviors is demonstrated by using a pair of star-polymer-DNA precursors with presimulated DNA sequences showing the two-state transition. The melting curve analysis of the DNA gels reveals the good correspondence between the thermodynamic potentials of the DNA crosslinkers and the presimulated values by DNA calculators. Stress-relaxation tests and dissociation kinetics measurements show that the macroscopic relaxation time of the DNA gels is approximately equal to the lifetime of the DNA crosslinkers over 4 orders of magnitude from 0.1-2000 s. Furthermore, a series of durability tests find the DNA gels are hysteresis-less and self-healable after the applications of repeated temperature and mechanical stimuli. These results demonstrate the great potential of star-polymer-DNA precursors for building gels with predictable and tunable viscoelastic properties, suitable for applications such as stress-response extracellular matrices, injectable solids, and soft robotics.
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Affiliation(s)
- Masashi Ohira
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8685, Japan
| | - Takuya Katashima
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8685, Japan
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Daisuke Aoki
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Yusuke Yoshikawa
- Neutron Science Laboratory, Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan
| | - Hiroki Iwase
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Naka, Ibaraki, 319-1106, Japan
| | - Shin-Ichi Takata
- Materials and Life Science Division, J-PARC Center, Japan Atomic Energy Agency (JAEA), 2-4 Shirakata, Tokai, Ibaraki, 319-1195, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ung-Il Chung
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8685, Japan
| | - Takamasa Sakai
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8685, Japan
| | - Mitsuhiro Shibayama
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Tokai, Naka, Ibaraki, 319-1106, Japan
| | - Xiang Li
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 001-0021, Japan
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20
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Bielec K, Kowalski A, Bubak G, Witkowska Nery E, Hołyst R. Ion Complexation Explains Orders of Magnitude Changes in the Equilibrium Constant of Biochemical Reactions in Buffers Crowded by Nonionic Compounds. J Phys Chem Lett 2022; 13:112-117. [PMID: 34962392 PMCID: PMC8762655 DOI: 10.1021/acs.jpclett.1c03596] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The equilibrium constant (K) of biochemical complex formation in aqueous buffers with high concentration (>20 wt %) of nonionic compounds can vary by orders of magnitude in comparison with the K in a pure buffer. The precise molecular mechanisms of these profound changes are not known. Herein, we show up to a 1000-fold decrease of the K value of DNA hybridization (at nM concentration) in standard molecular crowder systems such as PEG, dextrans, Ficoll, and glycerol. The effect responsible for the decrease of K is the complexation of positively charged ions from a buffer by nonionic polymers/small molecules. We determined the average equilibrium constant for the complexation of ions per monomer (∼0.49 M-1). We retrieve K's original value for a pure buffer if we properly increase the ionic strength of the buffer crowded by the polymers, compensating for the loss of complexed ions.
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Affiliation(s)
- Krzysztof Bielec
- Institute
of Physical Chemistry, Polish Academy of
Sciences, 01-224 Warsaw, Poland
- Institute
of Chemical Sciences and Engineering,
EPFL CH C2 425, Bâtiment CH, Station 6, Lausanne CH-1015, Switzerland
| | - Adam Kowalski
- Institute
of Physical Chemistry, Polish Academy of
Sciences, 01-224 Warsaw, Poland
| | - Grzegorz Bubak
- Institute
of Physical Chemistry, Polish Academy of
Sciences, 01-224 Warsaw, Poland
| | | | - Robert Hołyst
- Institute
of Physical Chemistry, Polish Academy of
Sciences, 01-224 Warsaw, Poland
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21
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Singh JKD, Darley E, Ridone P, Gaston JP, Abbas A, Wickham SFJ, Baker MAB. Binding of DNA origami to lipids: maximizing yield and switching via strand displacement. Nucleic Acids Res 2021; 49:10835-10850. [PMID: 34614184 PMCID: PMC8565350 DOI: 10.1093/nar/gkab888] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023] Open
Abstract
Liposomes are widely used as synthetic analogues of cell membranes and for drug delivery. Lipid-binding DNA nanostructures can modify the shape, porosity and reactivity of liposomes, mediated by cholesterol modifications. DNA nanostructures can also be designed to switch conformations by DNA strand displacement. However, the optimal conditions to facilitate stable, high-yield DNA–lipid binding while allowing controlled switching by strand displacement are not known. Here, we characterized the effect of cholesterol arrangement, DNA structure, buffer and lipid composition on DNA–lipid binding and strand displacement. We observed that binding was inhibited below pH 4, and above 200 mM NaCl or 40 mM MgCl2, was independent of lipid type, and increased with membrane cholesterol content. For simple motifs, binding yield was slightly higher for double-stranded DNA than single-stranded DNA. For larger DNA origami tiles, four to eight cholesterol modifications were optimal, while edge positions and longer spacers increased yield of lipid binding. Strand displacement achieved controlled removal of DNA tiles from membranes, but was inhibited by overhang domains, which are used to prevent cholesterol aggregation. These findings provide design guidelines for integrating strand displacement switching with lipid-binding DNA nanostructures. This paves the way for achieving dynamic control of membrane morphology, enabling broader applications in nanomedicine and biophysics.
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Affiliation(s)
- Jasleen Kaur Daljit Singh
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.,School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Esther Darley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Pietro Ridone
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - James P Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Ali Abbas
- School of Chemical and Biomolecular Engineering, The University of Sydney, Sydney, New South Wales, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Shelley F J Wickham
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.,The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales, Australia.,School of Physics, The University of Sydney, Sydney, New South Wales, Australia
| | - Matthew A B Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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22
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Akintayo CO, Creusen G, Straub P, Walther A. Tunable and Large-Scale Model Network StarPEG-DNA Hydrogels. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00600] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Cecilia Oluwadunsin Akintayo
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
| | - Guido Creusen
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
| | - Paula Straub
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
| | - Andreas Walther
- A3BMS Lab, Active, Adaptive and Autonomous Bioinspired Materials, Department of Chemistry, University of Mainz, 55128 Mainz, Germany
- DFG Cluster of Excellence @ FIT “Living, Adaptive and Energy-Autonomous Materials Systems” (livMatS), Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Georges-Koehler-Allee 105, 79110 Freiburg, Germany
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23
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Sugimoto N, Endoh T, Takahashi S, Tateishi-Karimata H. Chemical Biology of Double Helical and Non-Double Helical Nucleic Acids: “To B or Not To B, That Is the Question”. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210131] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 17-1-20 Minatojima-minamimachi, Kobe, Hyogo 650-0047, Japan
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24
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Nakano SI, Yamashita H, Sugimoto N. Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations. Chembiochem 2021; 22:2721-2728. [PMID: 34240789 DOI: 10.1002/cbic.202100280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/28/2021] [Indexed: 11/05/2022]
Abstract
Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hirofumi Yamashita
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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25
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Takahashi S, Sugimoto N. Watson-Crick versus Hoogsteen Base Pairs: Chemical Strategy to Encode and Express Genetic Information in Life. Acc Chem Res 2021; 54:2110-2120. [PMID: 33591181 DOI: 10.1021/acs.accounts.0c00734] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nucleic acids typically form a double helix structure through Watson-Crick base-pairing. In contrast, non-Watson-Crick base pairs can form other three-dimensional structures. Although it is well-known that Watson-Crick base pairs may be more unstable than non-Watson-Crick base pairs under some conditions, the importance of non-Watson-Crick base pairs has not been widely examined. Hoogsteen base pairs, the non-Watson-Crick base pairs, contain important hydrogen-bond patterns that form the helices of nucleic acids, such as in Watson-Crick base pairs, and can form non-double helix structures such as triplexes and quadruplexes. In recent years, non-double helix structures have been discovered in cells and were reported to considerably influence gene expression. The complex behavior of these nucleic acids in cells is gradually being revealed, but the underlying mechanisms remain almost unknown.Quantitatively analyzing the structural stability of nucleic acids is important for understanding their behavior. A nucleic acid is an anionic biopolymer composed of a sugar, base, and phosphoric acid. The physicochemical factors that determine the stability of nucleic acid structures include those derived from the interactions of nucleic acid structures and those derived from the environments surrounding nucleic acids. The Gibbs free energy change (ΔG) of structure formation is the most commonly used physicochemical parameter for analyzing quantitative stability. Quantitatively understanding the intracellular behavior of nucleic acids involves describing the formation of nucleic acid structures and related reactions as ΔG. Based on this concept, we quantitatively analyzed the stability of double helix and non-double helix structures and found that decreased water activity, an important factor in crowded cellular conditions, significantly destabilize the formation of Watson-Crick base pairs but stabilizes Hoogsteen base pairs.Here, we describe a physicochemical approach to understand the regulation of gene expressions based on the stability of nucleic acid structures. We developed new methods for predicting the stability of double and non-double helices in various molecular environments by mimicking intracellular environments. Furthermore, the physicochemical approach used for analyzing gene expression regulated by non-double helix structures is useful for not only determining how gene expression is controlled by cellular environments but also for developing new technologies to chemically regulate gene expression by targeting non-double helix structures. We discuss the roles of Watson-Crick and Hoogsteen base pairs in cells based on our results and why both types of base pairing are required for life. Finally, a new concept in nucleic acid science beyond that of Watson and Crick base pairing is introduced.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
- FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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26
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DNA hybridisation kinetics using single-molecule fluorescence imaging. Essays Biochem 2021; 65:27-36. [PMID: 33491734 PMCID: PMC8056036 DOI: 10.1042/ebc20200040] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 01/05/2023]
Abstract
Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.
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27
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Ferreira I, Amarante TD, Weber G. Salt dependent mesoscopic model for RNA at multiple strand concentrations. Biophys Chem 2021; 271:106551. [PMID: 33662903 DOI: 10.1016/j.bpc.2021.106551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/19/2021] [Indexed: 12/12/2022]
Abstract
Mesoscopic models can be used for the description of the thermodynamic properties of RNA duplexes. With the use of experimental melting temperatures, its parametrization can provide important insights into its hydrogen bonds and stacking interactions as has been done for high sodium concentrations. However, the RNA parametrization for lower salt concentrations is still missing due to the limited amount of published melting temperature data. While the Peyrard-Bishop (PB) parametrization was found to be largely independent of strand concentrations, it requires that all temperatures are provided at the same strand concentrations. Here we adapted the PB model to handle multiple strand concentrations and in this way we were able to make use of an experimental set of temperatures to model the hydrogen bond and stacking interactions at low and intermediate sodium concentrations. For the parametrizations we make a distinction between terminal and internal base pairs, and the resulting potentials were qualitatively similar as we obtained previously for DNA. The main difference from DNA parameters, was the Morse potentials at low sodium concentrations for terminal r(AU) which is stronger than d(AT), suggesting higher hydrogen bond strength.
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Affiliation(s)
- Izabela Ferreira
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Tauanne D Amarante
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
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28
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29
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Tsuruta M, Sugitani Y, Sugimoto N, Miyoshi D. Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes. Int J Mol Sci 2021; 22:ijms22020947. [PMID: 33477917 PMCID: PMC7833394 DOI: 10.3390/ijms22020947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/31/2022] Open
Abstract
Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.
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Affiliation(s)
- Mitsuki Tsuruta
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Yui Sugitani
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Correspondence: ; Tel.: +81-(07)-8303-1426
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30
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Banerjee D, Tateishi-Karimata H, Ohyama T, Ghosh S, Endoh T, Takahashi S, Sugimoto N. Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. Nucleic Acids Res 2020; 48:12042-12054. [PMID: 32663294 PMCID: PMC7708073 DOI: 10.1093/nar/gkaa572] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
The stability of Watson–Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)–Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR–Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
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Affiliation(s)
- Dipanwita Banerjee
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Hisae Tateishi-Karimata
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tatsuya Ohyama
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Saptarshi Ghosh
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Tamaki Endoh
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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31
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Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments. Nat Commun 2020; 11:5949. [PMID: 33230101 PMCID: PMC7683531 DOI: 10.1038/s41467-020-19775-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/27/2020] [Indexed: 12/02/2022] Open
Abstract
Multivalent polyions can undergo complex coacervation, producing membraneless compartments that accumulate ribozymes and enhance catalysis, and offering a mechanism for functional prebiotic compartmentalization in the origins of life. Here, we evaluate the impact of lower, more prebiotically-relevant, polyion multivalency on the functional performance of coacervates as compartments. Positively and negatively charged homopeptides with 1–100 residues and adenosine mono-, di-, and triphosphate nucleotides are used as model polyions. Polycation/polyanion pairs are tested for coacervation, and resulting membraneless compartments are analyzed for salt resistance, ability to provide a distinct internal microenvironment (apparent local pH, RNA partitioning), and effect on RNA structure formation. We find that coacervates formed by phase separation of the shorter polyions more effectively generated distinct pH microenvironments, accumulated RNA, and preserved duplexes than those formed by longer polyions. Hence, coacervates formed by reduced multivalency polyions are not only viable as functional compartments for prebiotic chemistries, they can outperform higher molecular weight analogues. Short cationic peptides and nucleotides can form complex coacervates, but the influence of reduced multivalency on coacervate functionality was not investigated. Here, the authors report that coacervates formed from short polyions generate distinct pH microenvironments, accumulate RNA and preserve nucleic acid duplexes more efficiently than their longer counterparts.
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32
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Lu S, Du J, Sun Z, Jing C. Hairpin-Structured Magnetic SERS Sensor for Tetracycline Resistance Gene tetA Detection. Anal Chem 2020; 92:16229-16235. [DOI: 10.1021/acs.analchem.0c04085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shaoyu Lu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjing Du
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhenli Sun
- MOE Key Laboratory of Resources and Environmental System Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Chuanyong Jing
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
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33
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. Proc Natl Acad Sci U S A 2020; 117:14194-14201. [PMID: 32522884 DOI: 10.1073/pnas.1920886117] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (T m) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.
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34
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Kekic T, Barisic I. In silico modelling of DNA nanostructures. Comput Struct Biotechnol J 2020; 18:1191-1201. [PMID: 32528637 PMCID: PMC7276390 DOI: 10.1016/j.csbj.2020.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023] Open
Abstract
The rise of material science and nanotechnology created a demand for a next generation of materials and procedures that can transcend the shaping of simple geometrical nano-objects. As a legacy of the technological progress made in the Human Genome Project, DNA was identified as a possible candidate. The low production costs of custom-made DNA molecules and the possibilities concerning the structural manipulation triggered significant advances in the field of DNA nanotechnology in the last decade. To facilitate the development of new DNA nanostructures and provide users an insight in less intuitive complexities and physical properties of the DNA folding, several in silico modelling tools were published. Here, we summarize the main characteristics of these specialised tools, describe the most common design principles and discuss tools and strategies used to predict the properties of DNA nanostructures.
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35
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Kuo TC, Wu MW, Lin WC, Matulis D, Yang YS, Li SY, Chen WY. Reduction of interstrand charge repulsion of DNA duplexes by salts and by neutral phosphotriesters – Contrary effects for harnessing duplex formation. J Taiwan Inst Chem Eng 2020. [DOI: 10.1016/j.jtice.2020.02.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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36
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Yu X, Buck MJ. Pioneer factors and their in vitro identification methods. Mol Genet Genomics 2020; 295:825-835. [PMID: 32296927 DOI: 10.1007/s00438-020-01675-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/02/2020] [Indexed: 11/27/2022]
Abstract
Pioneer transcription factors are a special group of transcription factors that can interact with nucleosomal DNA and initiate regulatory events. Their binding to regulatory regions is the first event in gene activation and can occur in silent or heterochromatin regions. Several research groups have endeavored to define pioneer factors and study their binding characteristics using various techniques. In this review, we describe the in vitro methods used to define and characterize pioneer factors, paying particular attention to differences in methodologies and how these differences can affect results.
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Affiliation(s)
- Xinyang Yu
- Zhuhai Precision Medical Center, Zhuhai People's Hospital (Zhuhai Hospital Affiliated With Jinan University), Zhuhai, 519000, Guangdong, P.R. China.
| | - Michael J Buck
- Department of Biochemistry, New York State Center of Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
- Department of Biomedical Informatics, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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37
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Rudeejaroonrung K, Hanpanich O, Saito K, Shimada N, Maruyama A. Cationic copolymer enhances 8–17 DNAzyme and MNAzyme activities. Biomater Sci 2020; 8:3812-3818. [DOI: 10.1039/d0bm00428f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Cationic copolymer acts as a chaperone to facilitate multiple strand assembly and enhance nucleic acid enzyme activities.
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Affiliation(s)
| | - Orakan Hanpanich
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Ken Saito
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Naohiko Shimada
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Atsushi Maruyama
- School of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
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38
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Takahashi S, Sugimoto N. Stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells. Chem Soc Rev 2020; 49:8439-8468. [DOI: 10.1039/d0cs00594k] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review provides the biophysicochemical background and recent advances in stability prediction of canonical and non-canonical structures of nucleic acids in various molecular environments and cells.
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Affiliation(s)
- Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Konan University
- Kobe
- Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST)
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39
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O'Connell AA, Hanson JA, McCaskill DC, Moore ET, Lewis DC, Grover N. Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop. RNA (NEW YORK, N.Y.) 2019; 25:1779-1792. [PMID: 31548339 PMCID: PMC6859860 DOI: 10.1261/rna.070466.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
U6 RNA contains a 1 × 2-nt internal loop that folds and unfold during spliceosomal assembly and activation. The 1 × 2 loop consists of a C67•A79 base pair that forms an additional hydrogen bond upon protonation, C67•A+79, and uracil (U80) that coordinates the catalytically essential magnesium ions. We designed a series of RNA and DNA constructs with a 1 × 2 loop sequence contained in the ISL, and its modifications, to measure the thermodynamic effects of protonation and magnesium binding using UV-visible thermal denaturation experiments. We show that the wild-type RNA construct gains 0.43 kcal/mol in 1 M KCl upon lowering the pH from 7.5 to 5.5; the presence of magnesium ions increases its stability by 2.17 kcal/mol at pH 7.5 over 1 M KCl. Modifications of the helix closing base pairs from C-G to U•G causes a loss in protonation-dependent stability and a decrease in stability in the presence of magnesium ions, especially in the C68U construct. A79G single-nucleotide bulge loop construct showed the largest gain in stability in the presence of magnesium ions. The DNA wild-type construct shows a smaller effect on stability upon lowering the pH and in the presence of magnesium ions, highlighting differences in RNA and DNA structures. A U6 RNA 1 × 2 loop sequence is rare in the databases examined.
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Affiliation(s)
- Allison A O'Connell
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Jared A Hanson
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Darryl C McCaskill
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Ethan T Moore
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Daniel C Lewis
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
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40
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Ghosh S, Takahashi S, Endoh T, Tateishi-Karimata H, Hazra S, Sugimoto N. Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition. Nucleic Acids Res 2019; 47:3284-3294. [PMID: 30753582 PMCID: PMC6468326 DOI: 10.1093/nar/gkz071] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/21/2019] [Accepted: 01/29/2019] [Indexed: 01/03/2023] Open
Abstract
Recent advancement in nucleic acid techniques inside cells demands the knowledge of the stability of nucleic acid structures in molecular crowding. The nearest-neighbor model has been successfully used to predict thermodynamic parameters for the formation of nucleic acid duplexes, with significant accuracy in a dilute solution. However, knowledge about the applicability of the model in molecular crowding is still limited. To determine and predict the stabilities of DNA duplexes in a cell-like crowded environment, we systematically investigated the validity of the nearest-neighbor model for Watson–Crick self-complementary DNA duplexes in molecular crowding. The thermodynamic parameters for the duplex formation were measured in the presence of 40 wt% poly(ethylene glycol)200 for different self-complementary DNA oligonucleotides consisting of identical nearest-neighbors in a physiological buffer containing 0.1 M NaCl. The thermodynamic parameters as well as the melting temperatures (Tm) obtained from the UV melting studies revealed similar values for the oligonucleotides having identical nearest-neighbors, suggesting the validity of the nearest-neighbor model in the crowding condition. Linear relationships between the measured ΔG°37 and Tm in crowding condition and those predicted in dilute solutions allowed us to predict ΔG°37, Tm and nearest-neighbor parameters in molecular crowding using existing parameters in the dilute condition, which provides useful information about the thermostability of the self-complementary DNA duplexes in molecular crowding.
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Affiliation(s)
- Saptarshi Ghosh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Shuntaro Takahashi
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Soumitra Hazra
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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41
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Nakano SI, Ayusawa T, Tanino Y, Sugimoto N. Stabilization of DNA Loop Structures by Large Cations. J Phys Chem B 2019; 123:7687-7694. [PMID: 31465227 DOI: 10.1021/acs.jpcb.9b06074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The DNA-binding properties of large cations differ from those of metal ions due to steric exclusion from base-paired regions. In this study, the thermal stability of DNA secondary structures, including duplexes, internal loops, bulge loops, hairpin loops, dangling ends, and G-quadruplexes, was investigated in the presence of cations of different sizes. Large cations, such as tetrabutylammonium and tetrapentylammonium ions, reduced the stability of fully matched duplexes but increased the stability of duplexes with a long loop. The cations also increased the stability of G-quadruplexes with a long loop, and the degree of stabilization was greater for low-stability G-quadruplexes. Analysis of the salt concentration dependence indicates that large cations bind to the loop nucleotides, leading to counteracting the destabilization effect on base pairing. It is likely that binding occurs when loop nucleotides are sufficiently flexible to allow for greater accessibility for large cations. These results provide insight into nucleic acid interactions with large cationic molecules and suggest a potential method for stabilizing noncanonical DNA structures under intracellular conditions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Toshiya Ayusawa
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Yuichi Tanino
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
| | - Naoki Sugimoto
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan.,Frontier Institute for Biomolecular Engineering Research (FIBER) , Konan University , 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe , 650-0047 , Japan
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42
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Basílio Barbosa V, de Oliveira Martins E, Weber G. Nearest-neighbour parameters optimized for melting temperature prediction of DNA/RNA hybrids at high and low salt concentrations. Biophys Chem 2019; 251:106189. [PMID: 31129553 DOI: 10.1016/j.bpc.2019.106189] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/28/2022]
Abstract
Gene editing technologies sparked a renewed interest in the hybridization of DNA/RNA duplexes, yet little improvement on nearest-neighbour parameters was made over the past two decades. For low sodium concentration no parameter set was yet calculated. Here, we revised the existing experimental datasets and used an expanded set of sequences from which we recalculated the nearest-neighbour parameters, reducing the average temperature prediction uncertainty to 1.6 °C. Two experimental sets using temperatures extracted via different methods were used with similar results, with the curve-fitting method achieving a slight advantage in prediction quality over other methods. Additionally, we obtained new parameters for low salt with an average uncertainty of 0.98 °C. We also tested several types of salt correction factors and concluded that it is advisable to use those originally developed for RNA/RNA rather than for DNA/DNA.
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Affiliation(s)
- Vivianne Basílio Barbosa
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Erik de Oliveira Martins
- Escola Politécnica, Centro Universitário do Leste de Minas Gerais, 35170-056 Coronel Fabriciano, MG, Brazil
| | - Gerald Weber
- Departamento de Fsica, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.
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43
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Bielec K, Sozanski K, Seynen M, Dziekan Z, Ten Wolde PR, Holyst R. Kinetics and equilibrium constants of oligonucleotides at low concentrations. Hybridization and melting study. Phys Chem Chem Phys 2019; 21:10798-10807. [PMID: 31086926 DOI: 10.1039/c9cp01295h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Although DNA hybridization/melting is one of the most important biochemical reactions, the non-trivial kinetics of the process is not yet fully understood. In this work, we use Förster resonance energy transfer (FRET) to investigate the influence of temperature, ionic strength, and oligonucleotide length on the kinetic and equilibrium constants of DNA oligonucleotide binding and dissociation. We show that at low reagent concentrations and ionic strength, the time needed to establish equilibrium between single and double strand forms may be of the order of days, even for simple oligonucleotides of a length of 20 base pairs or less. We also identify and discuss the possible artifacts related to fluorescence-based experiments conducted in extremely dilute solutions. The results should prove useful for the judicious design of technologies based on DNA-matching, including sensors, DNA multiplication, sequencing, and gene manipulation.
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Affiliation(s)
- Krzysztof Bielec
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Krzysztof Sozanski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Marco Seynen
- FOM Institute AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Zofia Dziekan
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | | | - Robert Holyst
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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44
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Fatin M, Rahim Ruslinda A, Gopinath SC, Arshad MM, Hashim U, Lakshmipriya T, Tang TH, Kamarulzaman A. Co-ordinated split aptamer assembly and disassembly on Gold nanoparticle for functional detection of HIV-1 tat. Process Biochem 2019. [DOI: 10.1016/j.procbio.2018.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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45
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Khorsand B, Khammari A, Shirvanizadeh N, Zahiri J, Arab SS. OligoCOOL: A mobile application for nucleotide sequence analysis. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:201-206. [PMID: 30681253 DOI: 10.1002/bmb.21213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/25/2018] [Accepted: 01/06/2019] [Indexed: 06/09/2023]
Abstract
Today smartphones are inseparable parts of modern life and are capable of performing many desktop computers' tasks such as scientific analysis with greater convenience. Here, we present OligoCOOL, which is an Android application for analyzing nucleic sequences. This application enables users to perform several common biomedical analyses for a given nucleotide sequence. OligoCOOL is a freely accessible Android app at http://bioinf.modares.ac.ir/software/OligoCOOL, which can be a suitable tool for the experimental design in the laboratories. This application also can be used to learn the basics of nucleotide sequence analysis. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 201-206, 2019.
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Affiliation(s)
- Babak Khorsand
- Computer Engineering Department, Faculty of Engineering, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Anahita Khammari
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Niloofar Shirvanizadeh
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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46
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Hadži S, Kocman V, Oblak D, Plavec J, Lah J. Energetic Basis of AGCGA-Rich DNA Folding into a Tetrahelical Structure. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201813502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Vojč Kocman
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Domen Oblak
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Janez Plavec
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
- National Institute of Chemistry; Hajdrihova 19 Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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47
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Hadži S, Kocman V, Oblak D, Plavec J, Lah J. Energetic Basis of AGCGA‐Rich DNA Folding into a Tetrahelical Structure. Angew Chem Int Ed Engl 2019; 58:2387-2391. [DOI: 10.1002/anie.201813502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 11/09/2022]
Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
| | - Vojč Kocman
- National Institute of Chemistry Hajdrihova 19 Slovenia
| | - Domen Oblak
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
| | - Janez Plavec
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
- National Institute of Chemistry Hajdrihova 19 Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical TechnologyUniversity of Ljubljana Večna pot 113 Ljubljana Slovenia
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48
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Rinaldin M, Verweij RW, Chakraborty I, Kraft DJ. Colloid supported lipid bilayers for self-assembly. SOFT MATTER 2019; 15:1345-1360. [PMID: 30565635 PMCID: PMC6371764 DOI: 10.1039/c8sm01661e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/23/2018] [Indexed: 05/10/2023]
Abstract
The use of colloid supported lipid bilayers (CSLBs) has recently been extended to create colloidal joints, that enable the assembly of structures with internal degrees of flexibility, and to study lipid membranes on curved and closed geometries. These novel applications of CSLBs rely on previously unappreciated properties: the simultaneous fluidity of the bilayer, lateral mobility of inserted (linker) molecules and colloidal stability. Here we characterize every step in the manufacturing of CSLBs in view of these requirements using confocal microscopy and fluorescence recovery after photobleaching (FRAP). Specifically, we have studied the influence of different particle properties (roughness, surface charge, chemical composition, polymer coating) on the quality and mobility of the supported bilayer. We find that the insertion of lipopolymers in the bilayer can affect its homogeneity and fluidity. We improve the colloidal stability by inserting lipopolymers or double-stranded inert DNA into the bilayer. We include surface-mobile DNA linkers and use FRAP to characterize their lateral mobility both in their freely diffusive and bonded state. Finally, we demonstrate the self-assembly of flexibly linked structures from the CSLBs modified with surface-mobile DNA linkers. Our work offers a collection of experimental tools for working with CSLBs in applications ranging from controlled bottom-up self-assembly to model membrane studies.
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Affiliation(s)
- Melissa Rinaldin
- Huygens-Kamerlingh Onnes Lab, Universiteit Leiden
,
P.O. Box 9504
, 2300 RA Leiden
, The Netherlands
.
- Instituut-Lorentz, Universiteit Leiden
,
P.O. Box 9506
, 2300 RA Leiden
, The Netherlands
| | - Ruben W. Verweij
- Huygens-Kamerlingh Onnes Lab, Universiteit Leiden
,
P.O. Box 9504
, 2300 RA Leiden
, The Netherlands
.
| | - Indrani Chakraborty
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University
,
Tel Aviv 69978
, Israel
| | - Daniela J. Kraft
- Huygens-Kamerlingh Onnes Lab, Universiteit Leiden
,
P.O. Box 9504
, 2300 RA Leiden
, The Netherlands
.
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49
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Replacing salt correction factors with optimized RNA nearest-neighbour enthalpy and entropy parameters. Chem Phys 2019; 521:69-76. [PMID: 31598030 DOI: 10.1016/j.chemphys.2019.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We calculate the nearest-neighbour enthalpies and entropies at 5 salt concentrations of 18 RNA sequences, each for at least 9 different species concentrations, totalling 757 melting temperatures, using a melting temperature optimization method. These new parameters do not need to be salt-corrected and are shown to provide overall improved melting temperature predictions. They show a marked quadratic dependence with salt concentrations which are compensated to form linear Gibbs free energies. Two different parameter schemes were tested, with fixed or variable initial parameters. We have found that using variable initial parameters provides better predictive results than using salt correction factors and that the prediction uncertainty is considerably reduced for a validation set of independent sequences. An interpolation scheme is introduced to generate model parameters for arbitrary salt concentrations which performs better against a validation set than predictions using salt corrections.
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50
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Fatin MF, Rahim Ruslinda A, Gopinath SCB, Arshad MKM. High-performance interactive analysis of split aptamer and HIV-1 Tat on multiwall carbon nanotube-modified field-effect transistor. Int J Biol Macromol 2018; 125:414-422. [PMID: 30529550 DOI: 10.1016/j.ijbiomac.2018.12.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/27/2022]
Abstract
Interaction between split RNA aptamer and the clinically important target, HIV-1 Tat was investigated on a biosensing surface transduced by functionally choreographed multiwall carbon nanotubes (MWCNTs). Acid oxidation was performed to functionalize MWCNTs with carboxyl functional groups. X-ray photoelectron spectroscopy analysis had profound ~2.91% increment in overall oxygen group and ~1% increment was noticed with a specific carboxyl content owing to CO and OCO bonding. The interaction between split RNA aptamer and HIV-1 Tat protein was quantified by electrical measurements with the current signal (Ids) over a gate voltage (Vgs). Initially, 34.4 mV gate voltage shift was observed by the immobilization of aptamer on MWCNT. With aptamer and HIV-1 Tat interaction, the current flow was decreased with the concomitant gate voltage shift of 23.5 mV. The attainment of sensitivity with split aptamer and HIV-1 Tat interaction on the fabricated device was 600 pM. To ensure the genuine interaction of aptamer with HIV-1 Tat, other HIV-1 proteins, Nef and p24 were interacted with aptamer and they displayed the negligible interferences with gate voltage shift of 3.5 mV and 5.7 mV, which shows 4 and 2.5 folds lesser than HIV-1 Tat interaction, respectively.
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Affiliation(s)
- M F Fatin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia
| | - A Rahim Ruslinda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia.
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia; School of Bioprocess Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis, Malaysia
| | - M K Md Arshad
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia; School of Microelectronic Engineering, Universiti Malaysia Perlis, 02600 Arau, Pauh putra, Perlis, Malaysia
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