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Sengupta S, Bhattacharjee SM, Mishra G. Large bubble drives circular DNA melting. Phys Chem Chem Phys 2024. [PMID: 39027987 DOI: 10.1039/d4cp01536c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulations. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.
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Affiliation(s)
- Souradeep Sengupta
- Department of Physics, Ashoka University, Sonipat, Haryana - 131029, India.
| | | | - Garima Mishra
- Department of Physics, Ashoka University, Sonipat, Haryana - 131029, India.
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Basov A, Dorohova A, Malyshko V, Moiseev A, Svidlov A, Bezhenar M, Nechipurenko Y, Dzhimak S. Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17. Int J Mol Sci 2023; 24:12137. [PMID: 37569512 PMCID: PMC10418495 DOI: 10.3390/ijms241512137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/13/2023] Open
Abstract
The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.
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Affiliation(s)
- Alexandr Basov
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
| | - Anna Dorohova
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Vadim Malyshko
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia; (A.B.); (V.M.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Arkadii Moiseev
- Scientific Department, Kuban State Agrarian University, Krasnodar 350004, Russia;
| | - Alexandr Svidlov
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| | - Maria Bezhenar
- Department of Function Theory, Kuban State University, Krasnodar 350040, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Stepan Dzhimak
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia; (A.D.); (A.S.); (S.D.)
- Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center of the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
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Abstract
We study dsDNA (double strand DNA) melting in detail within varying strip-like confinement in a two-dimensional lattice model. The interplay between reduced configurational entropy and attractive base-pairing energy results in a non-monotonic melting profile of DNA. Structural transitions associated with confined DNA melting reveal a stretched or extended state for very strong confinement. By using the exact enumeration method, we investigate the emergence of a local denatured zone e.g. bubbles during DNA melting. The survival time of a single bubble within varying strip width is studied from the Fokker-Planck formalism by considering the bubble size as a reaction co-ordinate. We show that a simple lattice model can capture the sequence heterogeneity effect on DNA melting and bubble dynamics within the strip. Different time scales of bubble zipping for different DNA sequences are found, which may have potential applications in denaturation mapping.
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Affiliation(s)
- Dibyajyoti Mohanta
- Department of Physics, IIT (BHU), Varanasi 221005, India.
- The Institute of Mathematical Sciences, C.I.T Campus, Taramani, Chennai 600113, India
- Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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Majumdar D. Elasticity of a DNA chain dotted with bubbles under force. Phys Rev E 2021; 103:052412. [PMID: 34134228 DOI: 10.1103/physreve.103.052412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/04/2021] [Indexed: 11/07/2022]
Abstract
The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles, respectively, when the strands of the DNA are subjected to a force along the same direction, here called a stretching force. The force-temperature phase diagram shows the existence of a tricritical point, where the first-order force-induced zipping transition becomes continuous. On the other hand, when the forces are being applied in opposite directions, here called an unzipping force, the transition remains first order, with the possibility of vanishing of the low-temperature reentrant phase for a semiflexible DNA. Moreover, we found that the bulk elasticity changes only if an external force penetrates the bound phase and affects the bubble states.
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Affiliation(s)
- Debjyoti Majumdar
- Institute of Physics, Bhubaneswar, Odisha 751005, India and Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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