Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA
Abstract A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various tri...
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| Format: | Article |
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Nature Portfolio
2023-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-46572-4 |
| _version_ | 1797630214417678336 |
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| author | N. R. Jena P. K. Shukla |
| author_facet | N. R. Jena P. K. Shukla |
| author_sort | N. R. Jena |
| collection | DOAJ |
| description | Abstract A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about − 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about − 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12–14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16–21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells. |
| first_indexed | 2024-03-11T11:05:01Z |
| format | Article |
| id | doaj.art-13a302ad2bd34529b0d28f7dab93e9ee |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-11T11:05:01Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-13a302ad2bd34529b0d28f7dab93e9ee2023-11-12T12:15:36ZengNature PortfolioScientific Reports2045-23222023-11-0113111410.1038/s41598-023-46572-4Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNAN. R. Jena0P. K. Shukla1Discipline of Natural Sciences, Indian Institute of Information Technology, Design, and ManufacturingDepartment of Physics, Assam UniversityAbstract A triple helical DNA can control gene expression, help in homologous recombination, induce mutations to facilitate DNA repair mechanisms, suppress oncogene formations, etc. However, the structure and function of semisynthetic triple helical DNA are not known. To understand this, various triplets formed between eight artificial nucleobases (P, Z, J, V, B, S, X, and K) and four natural DNA bases (G, C, A, and T) are studied herein by employing a reliable density functional theoretic (DFT) method. Initially, the triple helix-forming artificial nucleobases interacted with the duplex DNA containing GC and AT base pairs, and subsequently, triple helix-forming natural bases (G and C) interacted with artificial duplex DNA containing PZ, JV, BS, and XK base pairs. Among the different triplets formed in the first category, the C-JV triplet is found to be the most stable with a binding energy of about − 31 kcal/mol. Similarly, among the second category of triplets, the Z-GC and V-GC triplets are the most stable. Interestingly, Z-GC and V-GC are found to be isoenergetic with a binding energy of about − 30 kcal/mol. The C-JV, and Z-GC or V-GC triplets are about 12–14 kcal/mol more stable than the JV and GC base pairs respectively. Microsolvation of these triplets in 5 explicit water molecules further enhanced their stability by 16–21 kcal/mol. These results along with the consecutive stacking of the C-JV triplet (C-JV/C-JV) data indicate that the synthetic nucleobases can form stable semisynthetic triple helical DNA. However, consideration of a full-length DNA containing one or more semisynthetic bases or base pairs is necessary to understand the formation of semisynthetic DNA in living cells.https://doi.org/10.1038/s41598-023-46572-4 |
| spellingShingle | N. R. Jena P. K. Shukla Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA Scientific Reports |
| title | Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA |
| title_full | Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA |
| title_fullStr | Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA |
| title_full_unstemmed | Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA |
| title_short | Structure and stability of different triplets involving artificial nucleobases: clues for the formation of semisynthetic triple helical DNA |
| title_sort | structure and stability of different triplets involving artificial nucleobases clues for the formation of semisynthetic triple helical dna |
| url | https://doi.org/10.1038/s41598-023-46572-4 |
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