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Soni H, Lako I, Placidi M, Cramer SM. Implications of AAV affinity column reuse and vector stability on product quality attributes. Biotechnol Bioeng 2024; 121:2449-2465. [PMID: 37485847 DOI: 10.1002/bit.28500] [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: 02/08/2023] [Revised: 06/21/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
In this work, the implications of AAV9 capsid design and column reuse on AAV9 vector product quality were assessed with POROS CaptureSelect (PCS) AAVX and AAV9 resins using sf9 insect cell-derived model AAV9 vectors with varying viral protein (VP) ratios. Chromatographic experiments with purified drug substance AAV9 model feeds indicated consistent vector elution profiles, independent of adeno-associated virus (AAV) VP ratio, or cycle number. In contrast, the presence of process impurities in the clarified lysate feeds resulted in clear changes in the elution patterns. This included increased aggregate content in the vector eluates over multiple cycles as well as clear differences in the performance of these affinity resin systems. The AAV9-serotype specific PCS AAV9 column, with lower vector elution pH, resulted in higher aggregate content over multiple cycles as compared to the serotype-independent PCS AAVX column. Further, the results with vectors of varying VP ratio indicated that while one vector type eluate displayed higher aggregation in both affinity columns over column reuse, the eluate with the other vector type did not exhibit changes in the aggregation profile. Interestingly, vector aggregates in the affinity eluates also contained double-stranded DNA impurities and histone proteins, with similar trends to the aggregate levels. This behavior upon column reuse indicates that these host cell impurities are likely carried over to subsequent runs due to incomplete clean-in-place (CIP). These results indicate that feed impurities, affinity resin characteristics, elution pH, column CIP, and vector stability can impact the reusability of AAV affinity columns and product quality.
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Affiliation(s)
- Harshal Soni
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Ira Lako
- Voyager Therapeutics, Cambridge, Massachusetts, USA
| | | | - Steven M Cramer
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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2
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Morrison G, Thirumalai D. Scaling regimes for wormlike chains confined to cylindrical surfaces under tension. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:6. [PMID: 38252375 DOI: 10.1140/epje/s10189-023-00384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/20/2023] [Indexed: 01/23/2024]
Abstract
We compute the free energy of confinement [Formula: see text] for a wormlike chain (WLC), with persistence length [Formula: see text], that is confined to the surface of a cylinder of radius R under an external tension f using a mean field variational approach. For long chains, we analytically determine the behavior of the chain in a variety of regimes, which are demarcated by the interplay of [Formula: see text], the Odijk deflection length ([Formula: see text]), and the Pincus length ([Formula: see text], with [Formula: see text] being the thermal energy). The theory accurately reproduces the Odijk scaling for strongly confined chains at [Formula: see text], with [Formula: see text]. For moderate values of f, the Odijk scaling is discernible only when [Formula: see text] for strongly confined chains. Confinement does not significantly alter the scaling of the mean extension for sufficiently high tension. The theory is used to estimate unwrapping forces for DNA from nucleosomes.
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Affiliation(s)
- Greg Morrison
- Department of Physics, University of Houston, Houston, TX, 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, 77005, USA
| | - D Thirumalai
- Departments of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Physics, The University of Texas at Austin, Austin, TX, 78712, USA.
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3
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Shew CY, Yoshikawa K. Crowding effect on the alignment of rod molecules confined in a spherical cavity. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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4
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Maheshwaram SK, Shet D, David SR, Lakshminarayana MB, Soni GV. Nanopore Sensing of DNA-Histone Complexes on Nucleosome Arrays. ACS Sens 2022; 7:3876-3884. [PMID: 36441954 DOI: 10.1021/acssensors.2c01865] [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
The location of nucleosomes in DNA and their structural stability are critical in regulating DNA compaction, site accessibility, and epigenetic gene regulation. Here, we combine the nanopore platform-based fast and label-free single-molecule detection technique with a voltage-dependent force rupture assay to detect distinct structures on nucleosomal arrays and then to induce breakdown of individual nucleosome complexes. Specifically, we demonstrate direct measurement of distinct nucleosome structures present on individual 12-mer arrays. A detailed event analysis showed that nucleosomes are present as a combination of complete and partial structures, during translocation through the pore. By comparing with the voltage-dependent translocation of the mononucleosomes, we find that the partial nucleosomes result from voltage-dependent structural disintegration of nucleosomes. High signal-to-noise detection of heterogeneous levels in translocation of 12-mer array molecules quantifies the heterogeneity and nucleosomal substructure sizes on the arrays. These results facilitate the understanding of electrostatic interactions responsible for the integrity of the nucleosome structure and possible mechanisms of its unraveling by chromatin remodeling enzymes. This study also has potential applications in chromatin profiling.
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Affiliation(s)
| | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | - Serene R David
- Raman Research Institute, Bangalore, Karnataka 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka 560080, India
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Garcia DA, Johnson TA, Presman DM, Fettweis G, Wagh K, Rinaldi L, Stavreva DA, Paakinaho V, Jensen RAM, Mandrup S, Upadhyaya A, Hager GL. An intrinsically disordered region-mediated confinement state contributes to the dynamics and function of transcription factors. Mol Cell 2021; 81:1484-1498.e6. [PMID: 33561389 DOI: 10.1016/j.molcel.2021.01.013] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 01/08/2021] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to specific consensus motifs within the local chromatin context. The mechanisms by which TFs navigate the nuclear environment as they search for binding sites remain unclear. Here, we used single-molecule tracking and machine-learning-based classification to directly measure the nuclear mobility of the glucocorticoid receptor (GR) in live cells. We revealed two distinct and dynamic low-mobility populations. One accounts for specific binding to chromatin, while the other represents a confinement state that requires an intrinsically disordered region (IDR), implicated in liquid-liquid condensate subdomains. Further analysis showed that the dwell times of both subpopulations follow a power-law distribution, consistent with a broad distribution of affinities on the GR cistrome and interactome. Together, our data link IDRs with a confinement state that is functionally distinct from specific chromatin binding and modulates the transcriptional output by increasing the local concentration of TFs at specific sites.
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Affiliation(s)
- David A Garcia
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Thomas A Johnson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diego M Presman
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, C1428EGA Buenos Aires, Argentina
| | - Gregory Fettweis
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Kaustubh Wagh
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Physics, University of Maryland, College Park, MD 20742, USA
| | - Lorenzo Rinaldi
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Diana A Stavreva
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, P.O. Box 1627, 70211 Kuopio, Finland
| | - Rikke A M Jensen
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - Arpita Upadhyaya
- Department of Physics, University of Maryland, College Park, MD 20742, USA; Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Gordon L Hager
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, MD 20893, USA.
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Ma Y, Yoshikawa Y, Oana H, Yoshikawa K. Marked Difference in the Conformational Transition of DNA Caused by Propanol Isomer. Polymers (Basel) 2020; 12:polym12071607. [PMID: 32707704 PMCID: PMC7407297 DOI: 10.3390/polym12071607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022] Open
Abstract
We measured the changes in the higher-order structure of DNA molecules (λ phage DNA, 48 kbp) at different concentrations of 1- and 2-propanol through single-molecular observation. It is known that 2-propanol is usually adapted for the procedure to isolate genomic DNA from living cells/organs in contrast to 1-propanol. In the present study, it was found that with an increasing concentration of 1-propanol, DNA exhibits reentrant conformational transitions from an elongated coil to a folded globule, and then to an unfolded state. On the other hand, with 2-propanol, DNA exhibits monotonous shrinkage into a compact state. Stretching experiments under direct current (DC) electrical potential revealed that single DNA molecules intermediately shrunk by 1- and 2-propanol exhibit intrachain phase segregation, i.e., coexistence of elongated and compact parts. The characteristic effect of 1-propanol causing the reentrant transition is argued in terms of the generation of water-rich nanoclusters.
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Affiliation(s)
- Yue Ma
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan; (Y.M.); (Y.Y.)
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan; (Y.M.); (Y.Y.)
| | - Hidehiro Oana
- Department of Mechanical Engineering, The University of Tokyo, Tokyo 113-8656, Japan;
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe 610-0394, Japan; (Y.M.); (Y.Y.)
- Correspondence: ; Tel.: +81-774-65-6131
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Nishio T, Yoshikawa Y, Shew CY, Umezawa N, Higuchi T, Yoshikawa K. Specific effects of antitumor active norspermidine on the structure and function of DNA. Sci Rep 2019; 9:14971. [PMID: 31628357 PMCID: PMC6802174 DOI: 10.1038/s41598-019-50943-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/23/2019] [Indexed: 01/11/2023] Open
Abstract
We compared the effects of trivalent polyamines, spermidine (SPD) and norspermidine (NSPD), a chemical homologue of SPD, on the structure of DNA and gene expression. The chemical structures of SPD and NSPD are different only with the number of methylene groups between amine groups, [N-3-N-4-N] and [N-3-N-3-N], respectively. SPD plays vital roles in cell function and survival, including in mammals. On the other hand, NSPD has antitumor activity and is found in some species of plants, bacteria and algae, but not in humans. We found that both polyamines exhibit biphasic effect; enhancement and inhibition on in vitro gene expression, where SPD shows definitely higher potency in enhancement but NSPD causes stronger inhibition. Based on the results of AFM (atomic force microscopy) observations together with single DNA measurements with fluorescence microscopy, it becomes clear that SPD tends to align DNA orientation, whereas NSPD induces shrinkage with a greater potency. The measurement of binding equilibrium by NMR indicates that NSPD shows 4-5 times higher affinity to DNA than SPD. Our theoretical study with Monte Carlo simulation provides the insights into the underlying mechanism of the specific effect of NSPD on DNA.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Chwen-Yang Shew
- Doctoral Program in Chemistry, The Graduate Center of the City University of New York, New York, 10016, USA.
- Department of Chemistry, College of Staten Island, Staten Island, New York, 10314, USA.
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan.
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Bolaños Quiñones VA, Zhu H, Solovev AA, Mei Y, Gracias DH. Origami Biosystems: 3D Assembly Methods for Biomedical Applications. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800230] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Vladimir A. Bolaños Quiñones
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Hong Zhu
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Alexander A. Solovev
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - Yongfeng Mei
- Department of Materials Science State Key Laboratory of ASIC and Systems Fudan University Shanghai 200433 P. R. China
| | - David H. Gracias
- Department of Chemical and Biomolecular Engineering Johns Hopkins University 3400 N Charles Street, 221 Maryland Hall Baltimore MD 21218 USA
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Nishio T, Yoshikawa Y, Fukuda W, Umezawa N, Higuchi T, Fujiwara S, Imanaka T, Yoshikawa K. Branched-Chain Polyamine Found in Hyperthermophiles Induces Unique Temperature-Dependent Structural Changes in Genome-Size DNA. Chemphyschem 2018; 19:2299-2304. [PMID: 29931720 PMCID: PMC6175440 DOI: 10.1002/cphc.201800396] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/31/2022]
Abstract
A pentavalent branched‐chain polyamine, N4‐bis(aminopropyl)spermidine 3(3)(3)4, is a unique polycation found in the hyperthermophilic archaeon Thermococcus kodakarensis, which grows at temperatures between 60 and 100 °C. We studied the effects of this branched‐chain polyamine on DNA structure at different temperatures up to 80 °C. Atomic force microscopic observation revealed that 3(3)(3)4 induces a mesh‐like structure on a large DNA (166 kbp) at 24 °C. With an increase in temperature, DNA molecules tend to unwind, and multiple nano‐loops with a diameter of 10–50 nm are generated along the DNA strand at 80 °C. These results were compared to those obtained with linear‐chain polyamines, homocaldopentamine 3334 and spermidine, the former of which is a structural isomer of 3(3)(3)4. These specific effects are expected to neatly concern with its role on high‐temperature preference in hyperthermophiles.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
| | - Wakao Fukuda
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Shinsuke Fujiwara
- School of Science and Technology, Kwansei-gakuin University, Sanda, 669-1337, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
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Abstract
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the bioinformatics, physics and biology of nucleosome positioning. The purpose of this review is to cover a practical aspect of this field, namely, to provide a guide to the multitude of nucleosome positioning resources available online. These include almost 300 experimental datasets of genome-wide nucleosome occupancy profiles determined in different cell types and more than 40 computational tools for the analysis of experimental nucleosome positioning data and prediction of intrinsic nucleosome formation probabilities from the DNA sequence. A manually curated, up to date list of these resources will be maintained at http://generegulation.info.
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Dršata T, Lankaš F. Multiscale modelling of DNA mechanics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:323102. [PMID: 26194779 DOI: 10.1088/0953-8984/27/32/323102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mechanical properties of DNA are important not only in a wide range of biological processes but also in the emerging field of DNA nanotechnology. We review some of the recent developments in modeling these properties, emphasizing the multiscale nature of the problem. Modern atomic resolution, explicit solvent molecular dynamics simulations have contributed to our understanding of DNA fine structure and conformational polymorphism. These simulations may serve as data sources to parameterize rigid base models which themselves have undergone major development. A consistent buildup of larger entities involving multiple rigid bases enables us to describe DNA at more global scales. Free energy methods to impose large strains on DNA, as well as bead models and other approaches, are also briefly discussed.
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Affiliation(s)
- Tomáš Dršata
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 166 10 Prague, Czech Republic. Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University Prague, Albertov 6, 128 43 Prague, Czech Republic
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