Thermodynamic framework for information in nanoscale systems with memory

This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Arias-Gonzalez, J. Ricardo. 2017. Thermodynamic Framework for Information in Nanoscale Systems with Memory. The Journal of Chemical Physics 147 (20). AIP Publishing: 205101. doi:10.1063/1.5004793 and may be found at https://doi.org/10.1063/1.5004793."[EN] Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes. Published by AIP Publishing.This work was supported by the Spanish Ministry of Economy and Competitiveness (Grant No. MAT2015-71806-R).Arias-Gonzalez, JR. (2017). Thermodynamic framework for information in nanoscale systems with memory. The Journal of Chemical Physics. 147(20):1-10. https://doi.org/10.1063/1.5004793S11014720Bustamante, C., Cheng, W., & Mejia, Y. X. (2011). 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A DNA-centered explanation of the DNA polymerase translocation mechanism

[EN] DNA polymerase couples chemical energy to translocation along a DNA template with a specific directionality while it replicates genetic information. According to single-molecule manipulation experiments, the polymerase-DNA complex can work against loads greater than 50 pN. It is not known, on the one hand, how chemical energy is transduced into mechanical motion, accounting for such large forces on sub-nanometer steps, and, on the other hand, how energy consumption in fidelity maintenance integrates in this non-equilibrium cycle. Here, we propose a translocation mechanism that points to the flexibility of the DNA, including its overstretching transition, as the principal responsible for the DNA polymerase ratcheting motion. By using thermodynamic analyses, we then find that an external load hardly affects the fidelity of the copying process and, consequently, that translocation and fidelity maintenance are loosely coupled processes. The proposed translocation mechanism is compatible with single-molecule experiments, structural data and stereochemical details of the DNA- protein complex that is formed during replication, and may be extended to RNA transcription.The author thanks B. Ibarra and F.J. Cao for fruitful discussion and H.Rodriguez-Rodriguez for critical reading of the manuscript. This work was supported the Spanish Ministry of Economy and Competitiveness (grant number MAT2015-71806-R).Arias-Gonzalez, JR. (2017). A DNA-centered explanation of the DNA polymerase translocation mechanism. Scientific Reports. 7:1-8. https://doi.org/10.1038/s41598-017-08038-2S187Bustamante, C., Cheng, C. & Mejia, Y. X. Revisiting the central dogma one molecule at a time. Cell 144, 480–497 (2011).van Oijen, A. M. & Loparo, J. J. Single-molecule studies of the replisome. Annu. Rev. Biophys. 39, 429–448 (2010).Wang, H.-Y., Elston, T., Mogilner, A. & Oster, G. Force generation in RNA polymerase. Biophys. 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Single-molecule portrait of DNA and RNA double helices

This is a pre-copyedited, author-produced version of an article accepted for publication in Integrative Biology following peer review. The version of record Arias-Gonzalez, J. Ricardo. 2014. Single-Molecule Portrait of DNA and RNA Double Helices. Integr. Biol. 6 (10). Oxford University Press (OUP): 904 25. doi:10.1039/c4ib00163j is available online at: https://doi.org/10.1039/c4ib00163j[EN] The composition and geometry of the genetic information carriers were described as double-stranded right helices sixty years ago. The flexibility of their sugar¿phosphate backbones and the chemistry of their nucleotide subunits, which give rise to the RNA and DNA polymers, were soon reported to generate two main structural duplex states with biological relevance: the so-called A and B forms. Double-stranded (ds) RNA adopts the former whereas dsDNA is stable in the latter. The presence of flexural and torsional stresses in combination with environmental conditions in the cell or in the event of specific sequences in the genome can, however, stabilize other conformations. Single-molecule manipulation, besides affording the investigation of the elastic response of these polymers, can test the stability of their structural states and transition models. This approach is uniquely suited to understanding the basic features of protein binding molecules, the dynamics of molecular motors and to shedding more light on the biological relevance of the information blocks of life. Here, we provide a comprehensive single-molecule analysis of DNA and RNA double helices in the context of their structural polymorphism to set a rigorous interpretation of their material response both inside and outside the cell. From early knowledge of static structures to current dynamic investigations, we review their phase transitions and mechanochemical behaviour and harness this fundamental knowledge not only through biological sciences, but also for Nanotechnology and Nanomedicine.We are sincerely indebted to S. Hormeno, F. Moreno-Herrero, B. Ibarra, J. L. Carrascosa, J. M. Valpuesta, M. Fuentes-Perez and C. Carrasco for their work throughout the years. C. Flors and A. Villasante are acknowledged for critical revision. This work was supported by Fundacion IMDEA Nanociencia.Arias-Gonzalez, JR. (2014). Single-molecule portrait of DNA and RNA double helices. Integrative Biology. 6(10):904-925. https://doi.org/10.1039/c4ib00163jS904925610Ivanov, V. I., Minchenkova, L. E., Minyat, E. E., Frank-Kamenetskii, M. D., & Schyolkina, A. K. (1974). The B̄ to Ā transition of DNA in solution. Journal of Molecular Biology, 87(4), 817-833. doi:10.1016/0022-2836(74)90086-2FRANKLIN, R. E., & GOSLING, R. G. (1953). 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Writing, Proofreading and Editing in Information Theory

[EN] Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.This work was supported by the Spanish Ministry of Economy and Competitiveness (MINECO, Grant MAT2015-71806-R). IMDEANanociencia acknowledges support from the 'Severo Ochoa' Programme for Centres of Excellence in R&D (MINECO, Grant SEV-2016-0686). These funds covered the costs to publish in open access.Arias-Gonzalez, JR. (2018). Writing, Proofreading and Editing in Information Theory. Entropy. 20(5):1-10. https://doi.org/10.3390/e20050368S11020

Microscopically Reversible Pathways with Memory

[EN] Statistical mechanics is a physics theory that deals with ensembles of microstates of a system compatible with environmental constraints and that on average define a thermodynamic state. The evolution of a small system is normally subjected to changing constraints, as set by a protocol, and involves a stochastic dependence on previous events. Here, we generalize the dynamic trajectories described by a realization of a physical system without dissipation to include those in which the history of previous events is necessary to understand its future. This framework is then used to characterize the processes experienced by the stochastic system, as derived from ensemble averages over the available pathways. We find that the pathways that the system traces in the presence of a protocol entail different statistics from those in its absence and prove that both types of pathways are equivalent in the limit of independent events. Such equivalence implies that a thermodynamic system cannot evolve away from equilibrium in the absence of memory. These results are useful to interpret single-molecule experiments in biophysics and other fields in nanoscience, as well as an adequate platform to describe non-equilibrium processes.Work supported by Ministerio de Ciencia e Innovacion, grant number PID2019-107391RB-I00.Arias-Gonzalez, JR. (2021). Microscopically Reversible Pathways with Memory. Mathematics. 9(2):1-21. https://doi.org/10.3390/math9020127S1219

Comment on "Information management in DNA replication modeled by directional, stochastic chains with memory" [J. Chem. Phys. 145, 185103 (2016)]

Arias-Gonzalez, JR.; Aleja, D. (2020). Comment on "Information management in DNA replication modeled by directional, stochastic chains with memory" [J. Chem. Phys. 145, 185103 (2016)]. The Journal of Chemical Physics. 152(4):1-2. https://doi.org/10.1063/1.5140055S121524Arias-Gonzalez, J. R. (2016). Information management in DNA replication modeled by directional, stochastic chains with memory. The Journal of Chemical Physics, 145(18), 185103. doi:10.1063/1.4967335The Journal of Chemical Physics14518185103201

Near-field distributions of resonant modes in small dielectric objects on flat surfaces

[EN] We report numerical simulations of the coupling of waves, either propagating or evanescent, with the eigenmodes of dielectric nanocylinders and nanospheres upon substrates. The multiple interaction of light between these objects and the dielectric surface at which the evanescent waves are created is taken into account. In this way, we present an accurate procedure for predicting and controlling the creation of large field enhancements concentrated both within and near the nanoparticle compared with the angle of incidence and the state of polarization.This research was supported by the Fundacion Ramon Areces and the European Union. J. R. Arias-Gonzalez acknowledges a scholarship from the Comunidad Autonoma de Madrid.Arias-Gonzalez, JR.; Nieto-Vesperinas, M. (2000). Near-field distributions of resonant modes in small dielectric objects on flat surfaces. Optics Letters. 25(11):782-784. https://doi.org/10.1364/OL.25.000782782784251

Luminescence Dynamics of Silica-Encapsulated Quantum Dots During Optical Trapping

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry C, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://pubs.acs.org/doi/10.1021/acs.jpcc.6b11867."[EN] The trade-off between photobrightening and photobleaching controls the emission stability of colloidal quantum dots. This balance is critical in optical trapping configurations, where irradiances that confine and simultaneously excite the nanocrystals in the focal region cannot be indefinitely lowered. In this work, we studied the photobrightening and bleaching behaviors of two types of silica-encapsulated quantum dots excited upon two-photon absorption in an optical trap. The first type consists of alloyed CdSeZnS quantum dots covered with a silica shell. We found that the dynamics of these as-prepared architectures are similar to those previously reported for bare surface-deposited quantum dots, where thousands of times smaller irradiances were used. We then analyzed the same quantum dot systems treated with an extra intermediate sulfur passivating shell for the better understanding of the surface traps influence in the temporal evolution of their emission in the optical trap. We found that these latter systems exhibit better homogeneity in their photodynamic behavior compared to the untreated ones. These features strengthen the value of quantum dot preparations in optical manipulation as well as for applications where both long and maximal emission stability in physiological and other polar media are required.The authors thank A. Blanco and D. Granados for fruitful discussion and S. de Lorenzo for technical help. H.R-R. is supported by an FPI-UAM fellowship and M. A. by a contract from Fundacion IMDEA Nanociencia. The research leading to these results has received funding from the Spanish Ministry of Economy and Competitiveness (grant numbers MAT2015-71806-R and FIS2015-67367-C2-1-P), from Comunidad de Madrid (S2013/MIT-2740) and from UAM-Banco Santander (CEAL-AL/2015-15).Rodríguez-Rodríguez, H.; Acebrón, M.; Juárez, B.; Arias-Gonzalez, JR. (2017). Luminescence Dynamics of Silica-Encapsulated Quantum Dots During Optical Trapping. The Journal of Physical Chemistry C. 121(18):10124-10130. https://doi.org/10.1021/acs.jpcc.6b11867S10124101301211

Effect of modified atmosphere packaging (MAP) and UC-C irradiation on postharvest quality of red raspberries

Red raspberries (Rubus idaeus L.) are highly appreciated by consumers. However, their postharvest shelf life scarcely exceeds 5 d under the refrigeration temperatures usually applied during commercialization, due to their high susceptibility to dehydration, softening and rot incidence. Thus, the objective of this study was to investigate the ability of UV-C radiation (UV1: 2 kJ m-2 and UV2: 4 kJ m-2 ), passive modified atmosphere packaging (MAP) with transmission rates (TR) for O2 and CO2 of 1805 mL d-1 and 1570 mL d-1 (MAP1), and 902 mL d-1 and 785 mL d-1 (MAP2), respectively, and the combination of both technologies to prolong raspberries’ shelf life at 6¿ C. Their influence on respiration, physicochemical parameters, and microbiological and nutritional quality was assessed during 12 d of storage. The combination of 4 kJ m-2 UV-C radiation and a packaging film with O2 and CO2 transmission rates of 902 mL d-1 and 785 mL d-1, respectively, produced a synergistic effect against rot development, delaying senescence of the fruit. The UV2MAP2 and MAP2 samples only showed 1.66% rot incidence after 8 d of storage. The UV2MAP2 samples also had higher bioactive content (1.76 g kg-1 of gallic acid equivalents (GAE), 1.08 g kg-1 of catechin equivalents (CE) and 0.32 g kg-1 of cyanidin 3-O-glucoside equivalents (CGE)) than the control samples at the end of their shelf life. Moreover, the mass loss was minimal (0.56%), and fruit color and firmness were maintained during shelf life. However, the rest of the batches were not suitable for commercialization after 4 d due to excessive mold development. © 2021 by the authors. Licensee MDPI, Basel, Switzerland

Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA

"This document is the Accepted Manuscript version of a Published Work that appeared in final form in The Journal of Physical Chemistry Letters, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://pubs.acs.org/doi/10.1021/acs.jpclett.8b00722."[EN] TERRA is an RNA molecule transcribed from human subtelomeric regions toward chromosome ends potentially involved in regulation of heterochromatin stability, semiconservative replication, and telomerase inhibition, among others. TERRA contains tandem repeats of the sequence GGGUUA, with a strong tendency to fold into a four-stranded arrangement known as a parallel G-quadruplex. Here, we demonstrate by using single-molecule force spectroscopy that this potential is limited by the inherent capacity of RNA to self-associate randomly and further condense into entropically more favorable structures. We stretched RNA constructions with more than four and less than eight hexanucleotide repeats, thus unable to form several G-quadruplexes in tandem, flanked by non-G-rich overhangs of random sequence by optical tweezers on a one by one basis. We found that condensed RNA stochastically blocks G-quadruplex folding pathways with a near 20% probability, a behavior that is not found in DNA analogous molecules.Dedicated to the memory of Alfredo Villasante. The authors thank E. Poyatos-Racionero for auxiliary experiments. I.G. is supported by Fundacion IMDEA Nanociencia and M.G. by a Juan de la Cierva contract (FJCI-2016-28474). This research received grants from the MINECO (MAT2015-71806-R and BFU2017-89707-P). IMDEA Nanociencia acknowledges support from the "Severo Ochoa" Programme for Centres of Excellence in R&D (MINECO, Grant SEV-2016-0686).Gutiérrez, I.; Garavís, M.; De Lorenzo, S.; Villasante, A.; González, C.; Arias-Gonzalez, JR. (2018). Single-Stranded Condensation Stochastically Blocks G-Quadruplex Assembly in Human Telomeric RNA. The Journal of Physical Chemistry Letters. 9(10):2498-2503. https://doi.org/10.1021/acs.jpclett.8b00722S2498250391