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Beššeová I, Banáš P, Kührová P, Košinová P, Otyepka M, Šponer J. Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration. J Phys Chem B 2012; 116:9899-916. [DOI: 10.1021/jp3014817] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ivana Beššeová
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavlína Košinová
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Michal Otyepka
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- Regional Centre of Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University, tr. 17
listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska
135, 612 65 Brno, Czech Republic
- CEITEC - Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
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Das J, Mukherjee S, Mitra A, Bhattacharyya D. Non-Canonical Base Pairs and Higher Order Structures in Nucleic Acids: Crystal Structure Database Analysis. J Biomol Struct Dyn 2006; 24:149-61. [PMID: 16928138 DOI: 10.1080/07391102.2006.10507108] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Non-canonical base pairs, mostly present in the RNA, often play a prominent role towards maintaining their structural diversity. Higher order structures like base triples are also important in defining and stabilizing the tertiary folded structure of RNA. We have developed a new program BPFIND to analyze different types of canonical and non-canonical base pairs and base triples involving at least two direct hydrogen bonds formed between polar atoms of the bases or sugar O2' only. We considered 104 possible types of base pairs, out of which examples of 87 base pair types are found to occur in the available RNA crystal structures. Analysis indicates that approximately 32.7% base pairs in the functional RNA structures are non-canonical, which include different types of GA and GU Wobble base pairs apart from a wide range of base pair possibilities. We further noticed that more than 10.4% of these base pairs are involved in triplet formation, most of which play important role in maintaining long-range tertiary contacts in the three-dimensional folded structure of RNA. Apart from detection, the program also gives a quantitative estimate of the conformational deformation of detected base pairs in comparison to an ideal planar base pair. This helps us to gain insight into the extent of their structural variations and thus assists in understanding their specific role towards structural and functional diversity.
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Affiliation(s)
- Jhuma Das
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
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