Molecular crowding stabilizes folded RNA structure by the excluded volume effect

Kilburn, Duncan, Roh, Joon Ho, Guo, Liang, Briber, Robert M., Woodson, Sarah A.·2010·Journal of the American Chemical Society

Cited by (211)

Items 101–200 of 211

  1. The chaperone-like activity of the hepatitis C virus IRES and CRE elements regulates genome dimerization
    Cristina Romero‐López, Alicia Barroso-del Jesus, Alfredo Berzal‐Herranz · 2017 · Scientific Reports
  2. Enzyme-Mediated Temporal Control over the Conformational Disposition of a Condensed Protein in Macromolecular Crowded Media
    Ekta Shandilya, Arshdeep Singh Bains, Subhabrata Maiti · 2023 · The Journal of Physical Chemistry B
  3. Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch
    Vinit Kumar, Tamaki Endoh, Kentaro Murakami, Naoki Sugimoto · 2012 · Chemical Communications
  4. Control of stability and structure of nucleic acids using cosolutes
    Hisae Tateishi-Karimta, Naoki Sugimoto · 2013 · Methods
  5. Epitranscriptomic technologies and analyses
    Xiaoyu Li, Liang‐Hu Qu, Jinran Lin, Jinying Peng, Jianhua Yang, Chengqi Yi, Yang Yu, Qiangfeng Cliff Zhang, Keren Zhou · 2020 · Science China Life Sciences
  6. Structural Analyses of Intrinsically Disordered Proteins by Small-Angle X-Ray Scattering
    Amin Sagar, Dmitri I. Svergun, Pau Bernadó · 2020 · Methods in molecular biology
  7. Segregation and phase inversion of strongly and weakly fluctuating Brownian particle mixtures and a chain of such particle mixtures in spherical containers
    Akinori Awazu · 2014 · Physical Review E
  8. Alternative RNA Conformations: Companion or Combatant
    Payal Gupta, Rushikesh M. Khadake, Shounok Panja, Krushna Shinde, Ambadas B. Rode · 2022 · Genes
  9. The Metabolome Weakens RNA Thermodynamic Stability and Strengthens RNA Chemical Stability
    Sieg, Jacob P., McKinley, Lauren N., Huot, Melanie J., Yennawar, Neela H., Bevilacqua, Philip C. · 2022 · Biochemistry
  10. Transcriptome-wide measurement of plant RNA secondary structure
    Shawn W. Foley, Lee E. Vandivier, Pavel P. Kuksa, Brian D. Gregory · 2015 · Current Opinion in Plant Biology
  11. Polymer additives in liquid electrolytes for advanced lithium batteries
    Kefeng Wang, Man Zhang, Jingxiao Ren, Wei Wei, Jianwei Nai · 2025 · Nanoscale
  12. The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements
    Katharina F. Hohmann, Anja Blümler, Alexander Heckel, Boris Fürtig · 2021 · Nucleic Acids Research
  13. Molecular Crowding Modulates SARS‐CoV‐2 Aptamer Affinity
    Ting Song, Miao Sun, Jialü Zhang, Yinzhu Lu, Shuang Wan, Chaoyong James Yang, Yanling Song · 2023 · Small Structures
  14. Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement
    Chenjie Feng, Ya-Lan Tan, Yu-Xuan Cheng, Ya-Zhou Shi, Zhi-Jie Tan · 2021 · Frontiers in Molecular Biosciences
  15. Divergent LIN28-mRNA associations result in translational suppression upon the initiation of differentiation
    Shen Mynn Tan, Gabriel M. Altschuler, Tian Yun Zhao, Haw Siang Ang, Henry He Yang, Bing Lim, Leah A. Vardy, Winston Hide, Andrew M. Thomson, Ricky R. Lareu · 2014 · Nucleic Acids Research
  16. Protocell Effects on RNA Folding, Function, and Evolution
    Ranajay Saha, J. Choi, Irene A. Chen · 2024 · Accounts of Chemical Research
  17. Optimal Design of a Small-Molecule Crowding Electrolyte and Molecular Dynamics Simulation of an Electrode–Electrolyte Interface for Aqueous Supercapacitors with a Wide Operating Temperature Range
    Di Wu, Huajie Feng, Li Hua Xu, Wen Yu Zhang, Zhong Jie Zhang, Xiangying Chen, Peng Cui · 2022 · ACS Applied Energy Materials
  18. Cross-diffusion in a colloid–polymer aqueous system
    Michele S. McAfee, Onofrio Annunziata · 2013 · Fluid Phase Equilibria
  19. Proton Intercalation into an Open‐Tunnel Bronze Phase with Near‐Zero Volume Change
    Kosuke Kawai, Seong‐Hoon Jang, Yuta Igarashi, Koji Yazawa, Kazuma Gotoh B, Jun Kikkawa, Atsuo Yamada, Yoshitaka Tateyama, Masashi Okubo · 2024 · Angewandte Chemie International Edition
  20. Visualization of liquid-liquid phase transitions using a tiny G-quadruplex binding protein
    Bikash Ranjan Sahoo, Xiexiong Deng, Ee Lin Wong, Nathan Clark, Harry Yang, Alexey Kovalenko, Subramanian Vivekanandan, Bryan B. Guzmán, Sarah Elizabeth Harris, Budheswar Dehury et al. · 2025 · Nature Communications
  21. Understanding chain looping kinetics in polymer solutions: crowding effects of microviscosity and collapse
    Yukun Bian, Xiuli Cao, Peng Li, Nanrong Zhao · 2018 · Soft Matter
  22. An in Vitro Cytomimetic of In‐Cell RNA Folding
    Hyejin Yoo, Caitlin M. Davis · 2022 · ChemBioChem
  23. Comparison of Interactions of Diamine and Mg2+ with RNA Tertiary Structures: Similar versus Differential Effects on the Stabilities of Diverse RNA Folds
    Robert J. Trachman, David E. Draper · 2013 · Biochemistry
  24. Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg2+, and Trimethylamine N-Oxide
    Peter McPhie, Patrick Brown, Bin Chen, Theodore Kwaku Dayie, Allen P. Minton · 2016 · Biochemistry
  25. Polymer brush-induced depletion interactions and clustering of membrane proteins
    Anvy Moly Tom, Won Kyu Kim, Changbong Hyeon · 2021 · The Journal of Chemical Physics
  26. Effect of Molecular Crowding on Complexation of Metal Ions and 8-Quinolinol-5-Sulfonic Acid
    Akihisa Miyagawa, Hiroyuki Komatsu, Shigenori Nagatomo, Kiyoharu Nakatani · 2021 · The Journal of Physical Chemistry B
  27. RNA structure, binding, and coordination in Arabidopsis
    Shawn W. Foley, Marianne C. Kramer, Brian D. Gregory · 2017 · Wiley Interdisciplinary Reviews - RNA
  28. Molecular Crowding Inhibits U-Insertion/Deletion RNA Editing In Vitro: Consequences for the In Vivo Reaction
    Venkata Subbaraju Katari, Lea van Esdonk, H. Ulrich Göringer · 2013 · PLoS ONE
  29. Duplex Formation and the Origins of Homochirality
    David S. Ross, David W. Deamer · 2022 · Astrobiology
  30. Fitness Landscapes and Evolution of Catalytic RNA
    Ranajay Saha, Alberto Vázquez-Salazar, Aditya Nandy, Irene A. Chen · 2024 · Annual Review of Biophysics
  31. Chain-Length-Dependent Autocatalytic Hydrolysis of Fatty Acid Anhydrides in Polyethylene Glycol
    Cao Cao, Qing-Biao Wang, Linjun Tang, Bing-Qiang Ge, Zhong‐Xiu Chen, Shaoping Deng · 2014 · The Journal of Physical Chemistry B
  32. Differential Effects of Strand Asymmetry on the Energetics and Structural Flexibility of DNA Internal Loops
    T. Thao Tran, Brian L. Cannon · 2017 · Biochemistry
  33. Protein crowding impedes pressure-induced unfolding of staphylococcal nuclease
    Suntao Wang, Mark W. Täte, Sol Michael Gruner · 2012 · Biochimica et Biophysica Acta (BBA) - General Subjects
  34. Faltung einer RNA‐Haarnadel in der dicht gedrängten Zelle
    Mimi Gao, David Gnutt, Axel M. Orban, Bettina Appel, Francesco Righetti, Roland Winter, Franz Narberhaus, Sabine Müller, Simon Ebbinghaus · 2016 · Angewandte Chemie
  35. Polyethylene glycol perturbs the unfolding of CRABP I: A correlation between experimental and theoretical approach
    Suchismita Subadini, Krishnendu Bera, Jozef Hritz, Harekrushna Sahoo · 2021 · Colloids and Surfaces B Biointerfaces
  36. Molecular Dynamics of Anthraquinone DNA Intercalators with Polyethylene Glycol Side Chains
    Shirlene Jackson Beckford, Dabney White Dixon · 2012 · Journal of Biomolecular Structure and Dynamics
  37. In situ SAXS investigation of vinyl acetate polymerization-induced self-assembly
    Fabrice Brunel, Paul Galanopoulo, Edgar Espinosa, Muriel Lansalot, Franck D’Agosto · 2024 · Polymer Chemistry
  38. Single-molecule visualization of sequence-specific RNA binding by a designer PPR protein
    Nicholas R. Marzano, Brady Johnston, Bishnu P. Paudel, Jason W. Schmidberger, Slobodan Jergic, Till Böcking, Mark Agostino, Ian Small, Antoine M. van Oijen, Charles S. Bond · 2024 · Nucleic Acids Research
  39. Imperfect G-quadruplex as an emerging candidate for transcriptional regulation
    Sunipa Sarkar, Hisae Tateishi‐Karimata, Tatsuya Ohyama, Naoki Sugimoto · 2025 · Nucleic Acids Research
  40. Crowding-induced morphological changes in synthetic lipid vesicles determined using smFRET
    Steven D. Quinn, Lara G. Dresser, Sarah P. Graham, Donato Conteduca, Jack W Shepherd, Mark C. Leake · 2022 · Frontiers in Bioengineering and Biotechnology
  41. The Key Role of Membranes in Amyloid Formation from a Biophysical Perspective
    Clarisa M. Torres-Bugeau, Claudio D. Borsarelli, Carlos Javier Minahk, Rosana Nieves Chehín · 2011 · Current Protein and Peptide Science
  42. Discrimination between Purine and Pyrimidine-Rich RNA in Liquid–Liquid Phase-Separated Condensates with Cationic Peptides and the Effect of Artificial Crowding Agents
    Anika L. Moller, Isis A. Middleton, Grace E. Maynard, L. R. Cox, Anna Wang, Hsiu L. Li, Pall Thordarson · 2024 · Biomacromolecules
  43. Acid Dissociation Behavior of 8-Hydroxyquinoline-5-Sulfonic Acid in Molecular Crowding Environment Modeled Using Polyethylene Glycol
    Akihisa Miyagawa, Hiroyuki Komatsu, Shigenori Nagatomo, Kiyoharu Nakatani · 2022 · Journal of Molecular Liquids
  44. The significant enhancement of energy density by redox and molecular crowding synergistic effects for aqueous zinc-ion hybrid capacitors
    Junqin Zeng, Juan Yang, Chaobai Yi, Jing Huang, Liping Zheng, Xianyou Wang · 2024 · Journal of Power Sources
  45. Synergism in the Molecular Crowding of Ligand-Induced Riboswitch Folding: Kinetic/Thermodynamic Insights from Single-Molecule Spectroscopy
    Hsuan-Lei Sung, David J. Nesbitt · 2022 · The Journal of Physical Chemistry B
  46. Influence of Magnesium Ions and Crowding Agents on Structure and Stability of RNA Aptamers
    Jaskirat Kaur, Rajeev Jain, Sumangal Roychowdhury, Rajanya Roy, Krishnananda Chattopadhyay, Ipsita Roy · 2025 · Biochemistry
  47. Thermodynamic complexation mechanism of zinc ion with 8-hydroxyquinoline-5-sulfonic acid in molecular crowding environment
    Akihisa Miyagawa, Hiroyuki Komatsu, Shigenori Nagatomo, Kiyoharu Nakatani · 2022 · Journal of Molecular Liquids
  48. Folding Stability and Self‐Association of a Triplet‐Repeat (CAG)20 RNA Hairpin in Cytomimetic Media
    Alexander Hautke, Simon Ebbinghaus · 2020 · ChemSystemsChem
  49. Macromolecular crowding in human tenocyte and skin fibroblast cultures: A comparative analysis
    Adrian Djalali-Cuevas, Mandy Rettel, Frank Stein, Mikhail M. Savitski, Stephen R. Kearns, Jack Laurence Kelly, Manus Jonathan Paul Biggs, Ioannis A. Skoufos, Athina Tzora, Nikitas N Prassinos et al. · 2024 · Materials Today Bio
  50. Factors that influence T box riboswitch efficacy and tRNA affinity
    Chunxi Zeng, S. Zhou, Stephen C. Bergmeier, Jennifer V. Hines · 2015 · Bioorganic & Medicinal Chemistry
  51. Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint
    Marta Gabryelska, Eliza Wyszko, M. Szymański, Mariusz Popenda, Jan Barciszewski · 2013 · Biochemical Journal
  52. Cpg Methylation in G-Quadruplex and IMotif DNA Structures
    Galina E. Pozmogova · 2018 · Significances of Bioengineering & Biosciences
  53. Development and Applications of Coarse‐Grained Models for RNA
    Changbong Hyeon, Natalia A. Denesyuk, Dave Thirumalai · 2014 · Israel Journal of Chemistry
  54. Force-Induced Unzipping Transitions in an Athermal Crowded Environment
    David L. Pincus, Dave Thirumalai · 2013 · The Journal of Physical Chemistry B
  55. RNA Aptamer-Based Approach to Inhibiting Split-GFP Reconstruction and the Loss of Inhibitory Activity Using Complementary RNA
    Takuto Kamura, Yousuke Katsuda, Yusuke Fuchigami, Yua Itsuki, Yusuke Kitamura, Toshihiko Sakurai, Takeaki Ozawa, Toshihiro Ihara · 2023 · Bulletin of the Chemical Society of Japan
  56. Molecular crowding effect in Hantzch pyridine synthesis in polyethylene glycol aqueous solution
    Akihisa Miyagawa, Yasuyuki Ueda, Kiyoharu Nakatani · 2024 · Physical Chemistry Chemical Physics
  57. Quest for space: Tenacity of DNA, Protein, and Lipid macromolecules in intracellular crowded environment
    Priyanka Phogat, Aparna Bansal, Nishu Nain, Shoaib Khan, Luciano Saso, Shrikant Kukreti · 2025 · BioMolecular Concepts
  58. Unusual crowding-induced chain looping kinetics in hard-sphere fluids: a contrastive study with polymer solutions
    Yukun Bian, Ran Yan, Peng Li, Nanrong Zhao · 2019 · Soft Matter
  59. Kineto-Mechanistic Investigation of Effect of Macromolecular Crowding on the Breathing of DNA Bubble
    Manali Basu, Padmaja Prasad Mishra · 2022 · The Journal of Physical Chemistry B
  60. The solution structure of apo-iron regulatory protein 1
    O'Neil Shand, Karl W. Volz · 2013 · Gene
  61. Nonmonotonic Modulation of the Protein–Ligand Recognition Event by Inert Crowders
    Bhupendra Ramesh Dandekar, Bibhab Bandhu Majumdar, Jagannath Mondal · 2023 · The Journal of Physical Chemistry B
  62. Chelate extraction of metal ions in aqueous/chloroform system based on molecular crowding environment
    Akihisa Miyagawa, Hiroyuki Komatsu, Shigenori Nagatomo, Kiyoharu Nakatani · 2024 · Bulletin of the Chemical Society of Japan
  63. Effect of PEG-Induced Liquid–Liquid Phase Separation on DNA–Topotecan Interactions
    Dineshbabu Takkella, Jyoti Vishwakarma, Krishna Gavvala · 2025 · The Journal of Physical Chemistry B
  64. Predicting the Limit of Intramolecular Hydrogen Bonding with Classical Molecular Dynamics
    Francesco Colizzi, Sanja Zivanovic, Modesto Orozco · 2019 · Angewandte Chemie
  65. J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran
    Akihisa Miyagawa, Kiyoharu Nakatani · 2022 · Analytical Sciences
  66. Nucleotides and nucleic acids; oligo- and polynucleotides
    David Loakes · 2012 · Royal Society of Chemistry eBooks
  67. Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assemblyin vivo
    Richard A. Lease, Véronique Arluison, Christophe Lavelle · 2012 · Frontiers in Life Science
  68. Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins
    Hakan Alıcı, Orkun Hasekioğlu, Vladimir Nikolaevich Uversky, Orkid Coskuner‐Weber · 2022 · Elsevier eBooks
  69. Crowding-induced polymer trapping in a channel
    Jialu Chen, Liang Sun, Simin Wang, Fujia Tian, Haoqi Zhu, Ruiqin Zhang, Liang Dai · 2021 · Physical review. E
  70. Synthetic Strategies to Identify and Regulate Noncoding RNAs
    Ganesh N. Pandian, Junetha Syed, Hiroshi Sugiyama · 2015 · Springer eBooks
  71. Influences of Excluded Volume of Molecules on Signaling Processes on the Biomembrane
    Masashi Fujii, Hiraku Nishimori, Akinori Awazu · 2013 · PLoS ONE
  72. Anionic Liposomes as Optimal Membrane Fusion Carriers Enabling in Situ Multiplexed Detection of Extracellular Vesicle MicroRNAs
    Jingyuan Ma, Xiao Wang, Yuhan Cai, Guancheng Wang, Mingze Lu, Kaizheng Feng, Ying Zhao, Xue Dong Wu, Xiaoping Zhang, Haoan Wu et al. · 2025 · Advanced Science
  73. Revolutionizing molecular-crowding concepts: investigation of oxine complexation in methanol solutions
    Akihisa Miyagawa · 2025 · Bulletin of the Chemical Society of Japan
  74. Ultrasensitive, Real-Time Molecular Sensing in Unprocessed Whole Blood Using Surface-Enhanced Raman Scattering Combined with Glycocalyx-Mimicking Structures
    Mingyu Han, Eugeniu Balaur, Connie Darmanin, Brian Abbey, Paul R. Stoddart, Mya Myintzu Hlaing, Regine Stockmann, Robert Barlow, Luíza A. Nascimento, Saimon Moraes Silva et al. · 2026 · ACS Sensors
  75. Effects of osmolytes and macromolecular crowders on stable GAAA tetraloops and their preference for a CG closing base pair
    Kaethe N. Leonard, Joshua M. Blose · 2018 · PeerJ
  76. Structural Studies of a Double-Stranded RNA from Trypanosome RNA Editing by Small-Angle X-Ray Scattering
    Angela R. Criswell, Blaine H. M. Mooers · 2014 · Methods in molecular biology
  77. The effect of macromolecular crowders on dielecric constant of aqueous electrolyte solutions
    Ema Slejko, Barbara Hribar-Lee · 2021 · Journal of Molecular Liquids
  78. DNA strand exchange and hydrophobic interactions between biomolecules
    Bobo Feng · 2015 · Chalmers Publication Library (Chalmers University of Technology)
  79. Theory and simulations for crowding-induced changes in stability of proteins with applications to λ repressor
    Natalia A. Denesyuk, Dave Thirumalai · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  80. A desolvation-based molecular crowding mechanism revealed through α,β,γ,δ-tetrakis(1-methylpyridinium-4-yl)porphyrin p -toluenesulfonate–Zn complexation in alcohols
    Akihisa Miyagawa, Chisa Ito, Shigenori Nagatomo, Kiyoharu Nakatani · 2026 · Physical Chemistry Chemical Physics
  81. The application of metabolic network analysis in understanding and targeting metabolism for drug discovery
    Jiangxia Liu · 2010 · D-Scholarship@Pitt (University of Pittsburgh)
  82. Effects of osmolytes on stable UUCG tetraloops and their preference for a CG closing base pair
    Michelle E. Whittum, Joshua M. Blose · 2017 · Nucleosides Nucleotides & Nucleic Acids
  83. RNA Heterogeneity Visualized Under AFM
    J. Ding, Jason R. Stagno, Ping Yu, Shun Li, K. P. Sapkota, Jinwei Zhang, Y.-X. Wang · 2023 · Royal Society of Chemistry eBooks
  84. Proton Intercalation into an Open‐Tunnel Bronze Phase with Near‐Zero Volume Change
    Kosuke Kawai, Seong‐Hoon Jang, Yuta Igarashi, Koji Yazawa, Kazuma Gotoh B, Jun Kikkawa, Atsuo Yamada, Yoshitaka Tateyama, Masashi Okubo · 2024 · Angewandte Chemie
  85. The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding
    W.‐Matthias Leeder, Stephan Voskuhl, H. Ulrich Göringer · 2017 · Journal of Nucleic Acids
  86. Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit
    Ambadas B. Rode, Tamaki Endoh, Naoki Sugimoto · 2018 · Angewandte Chemie
  87. Diffusion and Flow on Microscopic Length Scales Studied with Fluorescence Correlation Spectroscopy
    Christoph Pieper · 2012
  88. 2010 NIST Center for Neutron Research :
    R. L. Cappelletti · 2010
  89. Shape changes and cooperativity in the folding of central domain of the 16S ribosomal RNA
    Naoto Hori, Natalia A Denesyuk, Dave Thirumalai · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  90. Scattering From Polymer Systems
    Yimin Mao, Tianbo Liu, Benjamin Chu · 2022
  91. Single-Molecule Studies Of Local And Global Nucleic-Acid Dynamics
    Eric M. Patrick · 2013 · Human Biology
  92. Large‐Scale Structural Characterization of Biopolymer Systems by Small‐Angle Neutron Scattering
    Ferenc Horkay · 2013 · Wiley eBooks
  93. Rate equation model of phototransduction into the membranous disks of mouse rod cells
    Rei Takamoto, Hiraku Nishimori, Akinori Awazu · 2015 · arXiv (Cornell University)
  94. Effect of Macromolecular Crowding on the Structure and Function of a Riboswitch Aptamer in Cells and in Vitro
    Jillian Tyrrell · 2019 · Carolina Digital Repository (University of North Carolina at Chapel Hill)
  95. A macromolecular crowding study of RNA folding and activity: polymer pore size matters! (Conference Presentation)
    Richard Börner, Erica Fiorini, Bishnu P. Paudel, David Rueda, Roland K. O. Sigel · 2016
  96. Теоретические проблемы формирования антитеневой компетенции налоговых институтов
    И. С. Вазарханов · 2011 · Terra Economicus
  97. Randomness and optimality in enhanced DNA ligation with crowding effects
    Takaharu Y. Shiraki, Ken‐ichiro Kamei, Yusuke T. Maeda · 2020 · Physical Review Research
  98. Effects of chain length of polyethylene glycol molecular crowders on a mutant Tetrahymena group I ribozyme lacking large peripheral module
    Dobirul Islam, M. M. Rahman, Shigeyoshi Matsumura, Yoshiya Ikawa · 2021 · Nucleosides Nucleotides & Nucleic Acids
  99. Fast peptide bond formation and release by the ribosomal large subunit
    Letian Bao, Anthony C. Forster · 2025 · Journal of Biological Chemistry
  100. Role of Aqueous Media in Macromolecular Crowding
    Pedro P. Madeira, Vladimir Nikolaevich Uversky, Boris Y. Zaslavsky · 2025 · Sub-cellular biochemistry/Subcellular biochemistry