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Sojitra D, Biswas Hathiwala M, Hathiwala G, Bishoyi AK. Significance of genetic code module structure in gene expression and GC content enhancement in RNA sequences. Biosystems 2024; 237:105135. [PMID: 38320621 DOI: 10.1016/j.biosystems.2024.105135] [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: 10/16/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/08/2024]
Abstract
The existent algebraic models of the genetic code contribute to the understanding of the physio-chemical characteristics of the amino acids. However, the process of translating a gene into a phenotype is highly complex. Moreover, the intricacy of gene expression gets further multiplied due to the biases in the codon usage. This paper explores an algebraic structure called module on the set of codons as well as on that of RNA sequences. We study the potential implications of these structures on gene expression and the GC content of an RNA sequence. The base order {C,U,G,A} appears to possess greater biological significance than many of the orders previously studied. We have developed a novel algorithm to generate RNA sequences with high GC content, aiming to enhance the thermostability of biomolecules. The insights gained from this investigation may have applications in biomolecular modeling and docking, protein engineering, drug development, and related fields.
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Affiliation(s)
- Devangi Sojitra
- Department of Mathematics, Marwadi University, Rajkot, 360003, Gujarat, India.
| | | | - Gautam Hathiwala
- Department of Mathematics, Marwadi University, Rajkot, 360003, Gujarat, India.
| | - Ashok Kumar Bishoyi
- Department of Microbiology, Marwadi University, Rajkot, 360003, Gujarat, India.
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2
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Banerjee D, Tateishi-Karimata H, Toplishek M, Ohyama T, Ghosh S, Takahashi S, Trajkovski M, Plavec J, Sugimoto N. In-Cell Stability Prediction of RNA/DNA Hybrid Duplexes for Designing Oligonucleotides Aimed at Therapeutics. J Am Chem Soc 2023; 145:23503-23518. [PMID: 37873979 DOI: 10.1021/jacs.3c06706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In cells, the formation of RNA/DNA hybrid duplexes regulates gene expression and modification. The environment inside cellular organelles is heterogeneously crowded with high concentrations of biomolecules that affect the structure and stability of RNA/DNA hybrid duplexes. However, the detailed environmental effects remain unclear. Therefore, the mechanistic details of the effect of such molecular crowding were investigated at the molecular level by using thermodynamic and nuclear magnetic resonance analyses, revealing structure-dependent destabilization of the duplexes under crowded conditions. The transition from B- to A-like hybrid duplexes due to a change in conformation of the DNA strand guided by purine-pyrimidine asymmetry significantly increased the hydration number, which resulted in greater destabilization by the addition of cosolutes. By quantifying the individual contributions of environmental factors and the bulk structure of the duplex, we developed a set of parameters that predict the stability of hybrid duplexes with conformational dissimilarities under diverse crowding conditions. A comparison of the effects of environmental conditions in living cells and in vitro crowded solutions on hybrid duplex formation using the Förster resonance energy transfer technique established the applicability of our parameters to living cells. Moreover, our derived parameters can be used to estimate the efficiency of transcriptional inhibition, genome editing, and silencing techniques in cells. This supports the usefulness of our parameters for the visualization of cellular mechanisms of gene expression and the development of nucleic acid-based therapeutics targeting different cells.
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Affiliation(s)
- Dipanwita Banerjee
- 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
| | - Maria Toplishek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - 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
| | - Marko Trajkovski
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN → FIST Centre of Excellence, Trg Osvobodilne fronte 13, SI-1001 Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia
| | - 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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3
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Singh A, Yadav RK, Shati A, Kamboj NK, Hasssan H, Bharadwaj S, Rana R, Yadava U. Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations. PLoS One 2023; 18:e0278755. [PMID: 36753480 PMCID: PMC9907842 DOI: 10.1371/journal.pone.0278755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 02/09/2023] Open
Abstract
Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.
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Affiliation(s)
- Akanksha Singh
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | | | - Ali Shati
- Department of Biology, Faculty of Science, King Khaild University, Abha, Saudi Arabia
| | - Nitin Kumar Kamboj
- School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India
| | - Hesham Hasssan
- Department of Pathology, College of Medicine, King Khaild University, Abha, Saudi Arabia
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (SB); (RR); (UY)
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
- * E-mail: (SB); (RR); (UY)
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
- * E-mail: (SB); (RR); (UY)
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Aspas-Caceres J, Rico-Pasto M, Pastor I, Ritort F. Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems. ENTROPY 2022; 24:e24070895. [PMID: 35885118 PMCID: PMC9320289 DOI: 10.3390/e24070895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022]
Abstract
Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.
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Affiliation(s)
- Jaime Aspas-Caceres
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain; (J.A.-C.); (M.R.-P.); (I.P.)
| | - Marc Rico-Pasto
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain; (J.A.-C.); (M.R.-P.); (I.P.)
| | - Isabel Pastor
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain; (J.A.-C.); (M.R.-P.); (I.P.)
| | - Felix Ritort
- Small Biosystems Lab, Condensed Matter Physics Department, Universitat de Barcelona, Carrer de Martí i Franquès 1, 08028 Barcelona, Spain; (J.A.-C.); (M.R.-P.); (I.P.)
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
- Correspondence:
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5
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Afanasyev AY, Onufriev AV. Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach. J Chem Theory Comput 2022; 18:3911-3920. [PMID: 35544776 DOI: 10.1021/acs.jctc.1c01221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.
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Affiliation(s)
- Alexander Y Afanasyev
- Department of Biomedical Engineering and Mechanics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Alexey V Onufriev
- Departments of Computer Science and Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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Liang J, Li J, Zhong Z, Rujiralai T, Ma J. Quantifying the force in flow-cell based single-molecule stretching experiments. NANOSCALE 2021; 13:15916-15927. [PMID: 34522927 DOI: 10.1039/d1nr04748e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The flow-cell based single-molecule manipulation technique has found many applications in the study of DNA mechanics and protein-DNA interactions. However, the force in these experiments has not been fully characterized and is usually limited to a moderate force regime (<25 pN). In this work, using the "tethered-bead" assay, the hydrodynamic drag of DNA has been quantitatively evaluated based on a "bead-spring chain" model. The force derived from the Brownian motion of the bead thus contains both contributions from this equivalent hydrodynamic drag of DNA and the pulling force from the tethered bead. Next, using flow-cell based DNA pulling experiments, the linear relationship between the flow rate and total hydrodynamic force on the bead-DNA system has been demonstrated to be valid over a wide force range (0-110 pN). Consequently, the force can be directly converted from the flow rate by a linear factor that can be calibrated either by the bead's Brownian motion at low flow rates or using DNA overstretching transition. Furthermore, the hydrodynamic force and torque due to the shear flow on the bead as well as the equivalent stretching force on DNA are calculated based on theoretical models with the hydrodynamic drag on DNA also considered. The calculated force-extension curves show a good agreement with the measured ones. These results offer important insights into the force in flow-cell based single-molecule stretching experiments and provide a foundation for establishing flow-cells as a simple, low-cost, yet flexible and precise tool for single-molecule force measurements over a wide force range.
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Affiliation(s)
- Jialun Liang
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Jiaxi Li
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Zhensheng Zhong
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Thitima Rujiralai
- Division of Physical Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla, 90112, Thailand
| | - Jie Ma
- School of Physics, Sun Yat-sen University, Guangzhou 510275, Guangdong, China.
- State Key Laboratory of Optoelectronic Materials and Technologies, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
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Liu W, Zhong Z, Ma J. Simple way to correct the drift in surface-coupled optical tweezers using the laser reflection pattern. OPTICS EXPRESS 2021; 29:18769-18780. [PMID: 34154126 DOI: 10.1364/oe.423759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
The surface-coupled optical tweezers are widely used to resolve small units of motion in biology. However, such motions could readily be interfered by the drift between the trap and surface. We present a simple and low-cost method to correct the drift both actively and passively based on video tracking the distance between the laser reflection pattern and the reference bead. As a result, we achieved sub-nanometer resolution and stability for the stuck bead over a broad range of averaging time (0.002-100 s) as demonstrated by the Allan deviation analysis. The sub-nanometer resolution was further manifested with step measurement. Finally, in double-stranded DNA and DNA hairpin stretching experiments, an extension resolution of 1-2 nm with the stability over 120 s has been demonstrated under a constant force. This work thus provides an easy way to bring the benefit of nanometer resolution and long-term stability to the surface-coupled optical tweezers.
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