Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration
DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and...
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| Format: | Article |
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MDPI AG
2022-05-01
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| Series: | Life |
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| Online Access: | https://www.mdpi.com/2075-1729/12/5/759 |
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| author | Robert T. Young Luke Czapla Zoe O. Wefers Benjamin M. Cohen Wilma K. Olson |
| author_facet | Robert T. Young Luke Czapla Zoe O. Wefers Benjamin M. Cohen Wilma K. Olson |
| author_sort | Robert T. Young |
| collection | DOAJ |
| description | DNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules that control its processing and govern its packaging. The chemical composition of base pairs directs the spatial disposition and fluctuations of successive residues. The observed arrangements of these moieties in high-resolution protein–DNA crystal structures provide one of the best available estimates of the natural, sequence-dependent structure and deformability of the double-helical molecule. Here, we update the set of knowledge-based elastic potentials designed to describe the observed equilibrium structures and configurational fluctuations of the ten unique base-pair steps. The large number of currently available structures makes it possible to characterize the configurational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., tetrameric context. Use of these knowledge-based potentials shows promise in accounting for known effects of sequence in long chain molecules, e.g., the degree of curvature reported in classic gel mobility studies and the recently reported sequence-dependent responses of supercoiled minicircles to nuclease cleavage. |
| first_indexed | 2024-03-10T03:33:48Z |
| format | Article |
| id | doaj.art-6a86a8b72db2478e928483e7d71c3558 |
| institution | Directory Open Access Journal |
| issn | 2075-1729 |
| language | English |
| last_indexed | 2024-03-10T03:33:48Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Life |
| spelling | doaj.art-6a86a8b72db2478e928483e7d71c35582023-11-23T11:51:03ZengMDPI AGLife2075-17292022-05-0112575910.3390/life12050759Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain ConfigurationRobert T. Young0Luke Czapla1Zoe O. Wefers2Benjamin M. Cohen3Wilma K. Olson4Department of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USADepartment of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USADepartment of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USADepartment of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USADepartment of Chemistry & Chemical Biology, Center for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USADNA carries more than the list of biochemical ingredients that drive the basic functions of living systems. The sequence of base pairs includes a multitude of structural and energetic signals, which determine the degree to which the long, threadlike molecule moves and how it responds to proteins and other molecules that control its processing and govern its packaging. The chemical composition of base pairs directs the spatial disposition and fluctuations of successive residues. The observed arrangements of these moieties in high-resolution protein–DNA crystal structures provide one of the best available estimates of the natural, sequence-dependent structure and deformability of the double-helical molecule. Here, we update the set of knowledge-based elastic potentials designed to describe the observed equilibrium structures and configurational fluctuations of the ten unique base-pair steps. The large number of currently available structures makes it possible to characterize the configurational preferences of the DNA base-pair steps within the context of their immediate neighbors, i.e., tetrameric context. Use of these knowledge-based potentials shows promise in accounting for known effects of sequence in long chain molecules, e.g., the degree of curvature reported in classic gel mobility studies and the recently reported sequence-dependent responses of supercoiled minicircles to nuclease cleavage.https://www.mdpi.com/2075-1729/12/5/759DNA sequence-dependent structureDNA deformabilityDNA sequence contextDNA curvatureDNA minicircles |
| spellingShingle | Robert T. Young Luke Czapla Zoe O. Wefers Benjamin M. Cohen Wilma K. Olson Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration Life DNA sequence-dependent structure DNA deformability DNA sequence context DNA curvature DNA minicircles |
| title | Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration |
| title_full | Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration |
| title_fullStr | Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration |
| title_full_unstemmed | Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration |
| title_short | Revisiting DNA Sequence-Dependent Deformability in High-Resolution Structures: Effects of Flanking Base Pairs on Dinucleotide Morphology and Global Chain Configuration |
| title_sort | revisiting dna sequence dependent deformability in high resolution structures effects of flanking base pairs on dinucleotide morphology and global chain configuration |
| topic | DNA sequence-dependent structure DNA deformability DNA sequence context DNA curvature DNA minicircles |
| url | https://www.mdpi.com/2075-1729/12/5/759 |
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