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Szatylowicz H, Marek PH, Stasyuk OA, Krygowski TM, Solà M. Substituted adenine quartets: interplay between substituent effect, hydrogen bonding, and aromaticity. RSC Adv 2020; 10:23350-23358. [PMID: 35520336 PMCID: PMC9054646 DOI: 10.1039/d0ra04585c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 06/03/2020] [Indexed: 11/22/2022] Open
Abstract
Adenine, one of the components of DNA/RNA helices, has the ability to form self-organizing structures with cyclic hydrogen bonds (A4), similar to guanine quartets. Here, we report a computational investigation of the effect of substituents (X = NO2, Cl, F, H, Me, and NH2) on the electronic structure of 9H-adenine and its quartets (A4-N1, A4-N3, and A4-N7). DFT calculations were used to show the relationships between the electronic nature of the substituents, strength of H-bonds in the quartets, and aromaticity of five- and six-membered rings of adenine. We demonstrated how the remote substituent X modifies the proton-donating properties of the NH2 group involved in the H-bonds within quartets and how the position of the substituent and its electronic nature affect the stability of the quartets. We also showed the possible changes in electronic properties of the substituent and aromaticity of adenine rings caused by tetramer formation. The results indicate that the observed relationships depend on the A4 type. Moreover, the same substituent can both strengthen and weaken intermolecular interactions, depending on the substitution position. Substituent effects on hydrogen bonds in adenine quartets and aromaticity of adenine rings depend on the quartet type. A4-N3 and A4-N7 quartets are more responsive to the electronic nature of substituents than A4-N1.![]()
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Affiliation(s)
- Halina Szatylowicz
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland
| | - Paulina H Marek
- Warsaw University of Technology, Faculty of Chemistry Noakowskiego 3 00-664 Warsaw Poland .,University of Warsaw, Faculty of Chemistry Pasteura 1 02-093 Warsaw Poland
| | - Olga A Stasyuk
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
| | | | - Miquel Solà
- Department of Chemistry, Institute of Computational Chemistry and Catalysis, University of Girona C/ M. Aurèlia Capmany, 69 17003 Girona Spain
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Liu H, Wang R, Yu X, Shen F, Lan W, Haruehanroengra P, Yao Q, Zhang J, Chen Y, Li S, Wu B, Zheng L, Ma J, Lin J, Cao C, Li J, Sheng J, Gan J. High-resolution DNA quadruplex structure containing all the A-, G-, C-, T-tetrads. Nucleic Acids Res 2019; 46:11627-11638. [PMID: 30285239 PMCID: PMC6265469 DOI: 10.1093/nar/gky902] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
DNA can form diverse structures, which predefine their physiological functions. Besides duplexes that carry the genetic information, quadruplexes are the most well-studied DNA structures. In addition to their important roles in recombination, replication, transcription and translation, DNA quadruplexes have also been applied as diagnostic aptamers and antidisease therapeutics. Herein we further expand the sequence and structure complexity of DNA quadruplex by presenting a high-resolution crystal structure of DNA1 (5′-AGAGAGATGGGTGCGTT-3′). This is the first quadruplex structure that contains all the internal A-, G-, C-, T-tetrads, A:T:A:T tetrads and bulged nucleotides in one single structure; as revealed by site-specific mutagenesis and biophysical studies, the central ATGGG motif plays important role in the quadruplex formation. Interestingly, our structure also provides great new insights into cation recognition, including the first-time reported Pb2+, by tetrad structures.
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Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Xiang Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Shanghai 200032, China
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Suhua Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinzhong Lin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Shanghai 200032, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,Department of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J Chem Theory Comput 2009; 5:2514-30. [DOI: 10.1021/ct900200k] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Eva Fadrná
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Nad’a Špačková
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Joanna Sarzyñska
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jaroslav Koča
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Modesto Orozco
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Thomas E. Cheatham
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Tadeusz Kulinski
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
| | - Jiří Šponer
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic, Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61 704 Poznań, Poland, Joint IRB-BSC program on Computational Biology, Institute for Research in Biomedicine, Baldiri Reixac 10-12, 08028 Barcelona, Spain, Barcelona Supercomputing
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