1
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He A, Wan L, Zhang Y, Yan Z, Guo P, Han D, Tan W. Structure-based investigation of a DNA aptamer targeting PTK7 reveals an intricate 3D fold guiding functional optimization. Proc Natl Acad Sci U S A 2024; 121:e2404060121. [PMID: 38985770 PMCID: PMC11260122 DOI: 10.1073/pnas.2404060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
DNA aptamers have emerged as novel molecular tools in disease theranostics owing to their high binding affinity and specificity for protein targets, which rely on their ability to fold into distinctive three-dimensional (3D) structures. However, delicate atomic interactions that shape the 3D structures are often ignored when designing and modeling aptamers, leading to inefficient functional optimization. Challenges persist in determining high-resolution aptamer-protein complex structures. Moreover, the experimentally determined 3D structures of DNA molecules with exquisite functions remain scarce. These factors impede our comprehension and optimization of some important DNA aptamers. Here, we performed a streamlined solution NMR-based structural investigation on the 41-nt sgc8c, a prominent DNA aptamer used to target membrane protein tyrosine kinase 7, for cancer theranostics. We show that sgc8c prefolds into an intricate three-way junction (3WJ) structure stabilized by long-range tertiary interactions and extensive base-base stackings. Delineated by NMR chemical shift perturbations, site-directed mutagenesis, and 3D structural information, we identified essential nucleotides constituting the key functional elements of sgc8c that are centralized at the core of 3WJ. Leveraging the well-established structure-function relationship, we efficiently engineered two sgc8c variants by modifying the apical loop and introducing L-DNA base pairs to simultaneously enhance thermostability, biostability, and binding affinity for both protein and cell targets, a feat not previously attained despite extensive efforts. This work showcases a simplified NMR-based approach to comprehend and optimize sgc8c without acquiring the complex structure, and offers principles for the sophisticated structure-function organization of DNA molecules.
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Affiliation(s)
- Axin He
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Liqi Wan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Yuchao Zhang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Zhenzhen Yan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Pei Guo
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Da Han
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai200127, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang310022, China
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2
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Perdomo VA, Kim T. Molecular Dynamics Simulations of RNA Motifs to Guide the Architectural Parameters and Design Principles of RNA Nanostructures. Methods Mol Biol 2023; 2709:3-29. [PMID: 37572270 DOI: 10.1007/978-1-0716-3417-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/14/2023]
Abstract
Molecular dynamics (MD) simulations can be used to investigate the stability and conformational characteristics of RNA nanostructures. However, MD simulations of an RNA nanostructure is computationally expensive due to the size of nanostructure and the number of atoms. Alternatively, MD simulations of RNA motifs can be used to estimate the conformational stability of constructed RNA nanostructure due to their small sizes. In this chapter, we introduce the preparation and MD simulations of two RNA kissing loop (KL) motifs, a linear KL complex and a bent KL complex, and an RNA nanoring. The initial solvated system and topology files of each system will be prepared by two major force fields, AMBER and CHARMM force fields. MD simulations will be performed by NAMD simulation package, which can accept both force fields. In addition, we will introduce the use of the AMBER cpptraj program and visual molecular dynamics (VMD) for data analysis. We will also discuss how MD simulations of two KL motifs can be used to estimate the conformation and stability of RNA nanoring as well as to explain the vibrational characteristics of RNA nanoring.
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Affiliation(s)
| | - Taejin Kim
- Physical Sciences Department, West Virginia University Institute of Technology, Beckley, WV, USA.
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3
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Chauhan N, Karanastasis A, Ullal CK, Wang X. Homologous pairing in short double-stranded DNA-grafted colloidal microspheres. Biophys J 2022; 121:4819-4829. [PMID: 36196058 PMCID: PMC9811663 DOI: 10.1016/j.bpj.2022.09.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 01/07/2023] Open
Abstract
Homologous pairing (HP), i.e., the pairing of similar or identical double-stranded DNA, is an insufficiently understood fundamental biological process. HP is now understood to also occur without protein mediation, but crucial mechanistic details remain poorly established. Unfortunately, systematic studies of sequence dependence are not practical due to the enormous number of nucleotide permutations and multiple possible conformations involved in existing biophysical strategies even when using as few as 150 basepairs. Here, we show that HP can occur in DNA as short as 18 basepairs in a colloidal microparticle-based system. Exemplary systematic studies include resolving opposing reports of the impact of % AT composition, validating the impact of nucleotide order and triplet framework and revealing isotropic bendability to be crucial for HP. These studies are enabled by statistical analysis of crystal size and fraction within coexisting fluid-crystal phases of double-stranded DNA-grafted colloidal microspheres, where crystallization is predicated by HP.
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Affiliation(s)
- Neha Chauhan
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Apostolos Karanastasis
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Chaitanya K Ullal
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Xing Wang
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois; Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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4
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Mak CH. Nucleic acid folding simulations using a physics-based atomistic free energy model. J Chem Phys 2022; 156:174114. [PMID: 35525642 DOI: 10.1063/5.0086304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Performing full-resolution atomistic simulations of nucleic acid folding has remained a challenge for biomolecular modeling. Understanding how nucleic acids fold and how they transition between different folded structures as they unfold and refold has important implications for biology. This paper reports a theoretical model and computer simulation of the ab initio folding of DNA inverted repeat sequences. The formulation is based on an all-atom conformational model of the sugar-phosphate backbone via chain closure, and it incorporates three major molecular-level driving forces-base stacking, counterion-induced backbone self-interactions, and base pairing-via separate analytical theories designed to capture and reproduce the effects of the solvent without requiring explicit water and ions in the simulation. To accelerate computational throughput, a mixed numerical/analytical algorithm for the calculation of the backbone conformational volume is incorporated into the Monte Carlo simulation, and special stochastic sampling techniques were employed to achieve the computational efficiency needed to fold nucleic acids from scratch. This paper describes implementation details, benchmark results, and the advantages and technical challenges with this approach.
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Affiliation(s)
- Chi H Mak
- Departments of Chemistry and Quantitative and Computational Biology, and Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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5
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Stachowski K, Norris A, Potter D, Wysocki V, Foster M. Mechanisms of Cre recombinase synaptic complex assembly and activation illuminated by Cryo-EM. Nucleic Acids Res 2022; 50:1753-1769. [PMID: 35104890 PMCID: PMC8860596 DOI: 10.1093/nar/gkac032] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 12/15/2022] Open
Abstract
Cre recombinase selectively recognizes DNA and prevents non-specific DNA cleavage through an orchestrated series of assembly intermediates. Cre recombines two loxP DNA sequences featuring a pair of palindromic recombinase binding elements and an asymmetric spacer region, by assembly of a tetrameric synaptic complex, cleavage of an opposing pair of strands, and formation of a Holliday junction intermediate. We used Cre and loxP variants to isolate the monomeric Cre-loxP (54 kDa), dimeric Cre2-loxP (110 kDa), and tetrameric Cre4-loxP2 assembly intermediates, and determined their structures using cryo-EM to resolutions of 3.9, 4.5 and 3.2 Å, respectively. Progressive and asymmetric bending of the spacer region along the assembly pathway enables formation of increasingly intimate interfaces between Cre protomers and illuminates the structural bases of biased loxP strand cleavage order and half-the-sites activity. Application of 3D variability analysis to the tetramer data reveals constrained conformational sampling along the pathway between protomer activation and Holliday junction isomerization. These findings underscore the importance of protein and DNA flexibility in Cre-mediated site selection, controlled activation of alternating protomers, the basis for biased strand cleavage order, and recombination efficiency. Such considerations may advance development of site-specific recombinases for use in gene editing applications.
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Affiliation(s)
- Kye Stachowski
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew S Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Devante Potter
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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6
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Glazier R, Shinde P, Ogasawara H, Salaita K. Spectroscopic Analysis of a Library of DNA Tension Probes for Mapping Cellular Forces at Fluid Interfaces. ACS APPLIED MATERIALS & INTERFACES 2021; 13:2145-2164. [PMID: 33417432 DOI: 10.1021/acsami.0c09774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Oligonucleotide-based probes offer the highest spatial resolution, force sensitivity, and molecular specificity for cellular tension sensing and have been developed to measure a variety of molecular forces mediated by individual receptors in T cells, platelets, fibroblasts, B-cells, and immortalized cancer cell lines. These fluorophore-oligonucleotide conjugate probes are designed with a stem-loop structure that engages cell receptors and reversibly unfolds due to mechanical strain. With the growth of recent work bridging molecular mechanobiology and biomaterials, there is a need for a detailed spectroscopic analysis of DNA tension probes that are used for cellular imaging. In this manuscript, we conducted an analysis of 19 DNA hairpin-based tension probe variants using molecular dynamics simulations, absorption spectroscopy, and fluorescence imaging (epifluorescence and fluorescence lifetime imaging microscopy). We find that tension probes are highly sensitive to their molecular design, including donor and acceptor proximity and pairing, DNA stem-loop structure, and conjugation chemistry. We demonstrate the impact of these design features using a supported lipid bilayer model of podosome-like adhesions. Finally, we discuss the requirements for tension imaging in various biophysical contexts and offer a series of experimental recommendations, thus providing a guide for the design and application of DNA hairpin-based molecular tension probes.
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Affiliation(s)
- Roxanne Glazier
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Pushkar Shinde
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hiroaki Ogasawara
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Khalid Salaita
- Wallace H. Coulter Department of Biomedical Engineering at Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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7
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Xu N, You Y, Liu C, Balasov M, Lun LT, Geng Y, Fung CP, Miao H, Tian H, Choy TT, Shi X, Fan Z, Zhou B, Akhmetova K, Din RU, Yang H, Hao Q, Qian P, Chesnokov I, Zhu G. Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA. Nucleic Acids Res 2020; 48:11146-11161. [PMID: 32986843 PMCID: PMC7641730 DOI: 10.1093/nar/gkaa751] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 08/18/2020] [Accepted: 09/19/2020] [Indexed: 01/08/2023] Open
Abstract
The six-subunit origin recognition complex (ORC), a DNA replication initiator, defines the localization of the origins of replication in eukaryotes. The Orc6 subunit is the smallest and the least conserved among ORC subunits. It is required for DNA replication and essential for viability in all species. Orc6 in metazoans carries a structural homology with transcription factor TFIIB and can bind DNA on its own. Here, we report a solution structure of the full-length human Orc6 (HsOrc6) alone and in a complex with DNA. We further showed that human Orc6 is composed of three independent domains: N-terminal, middle and C-terminal (HsOrc6-N, HsOrc6-M and HsOrc6-C). We also identified a distinct DNA-binding domain of human Orc6, named as HsOrc6-DBD. The detailed analysis of the structure revealed novel amino acid clusters important for the interaction with DNA. Alterations of these amino acids abolish DNA-binding ability of Orc6 and result in reduced levels of DNA replication. We propose that Orc6 is a DNA-binding subunit of human/metazoan ORC and may play roles in targeting, positioning and assembling the functional ORC at the origins.
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Affiliation(s)
- Naining Xu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oral and Maxillofacial Surgery, Peking University ShenzhenHospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518036, China
| | - Yingying You
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- Department of Oncology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Changdong Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Maxim Balasov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Lee Tung Lun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Yanyan Geng
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Chun Po Fung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Haitao Miao
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Honglei Tian
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - To To Choy
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Xiao Shi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Zhuming Fan
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Bo Zhou
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Katarina Akhmetova
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Rahman Ud Din
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Hongyu Yang
- Department of Oral and Maxillofacial Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University, Shenzhen, 518036, China
| | - Quan Hao
- School of Biomedical Sciences, University of Hong Kong, 21 Sassoon Road, Hong Kong SAR, 00000, China
| | - Peiyuan Qian
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
| | - Igor Chesnokov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Guang Zhu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, 00000, China
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8
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Serobian A, Pracey CP, Thomas DS, Denny WA, Ball GE, Wakelin LPG. Structures and dynamics of DNA complexes of the desmethyl analog of the cytotoxin MLN944: Insights into activity when a methyl isn't futile. J Mol Recognit 2020; 33:e2843. [PMID: 32253794 DOI: 10.1002/jmr.2843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/11/2020] [Indexed: 01/04/2023]
Abstract
Structure activity relationships for tricyclic-carboxamide topoisomerase II poisons indicate that cytotoxicity is enhanced by the presence of methyl, and other, groups in the position peri to the carboxamide. Linked dimers of phenazine-1-carboxamides are potent cytotoxins and one phenazine dimer, MLN944 (alternatively XR5944), has been in clinical trial. MLN944 is a template inhibitor of transcription, whereas corresponding monomers are not. Nevertheless, its cytotoxic potency is also diminished by removal of its peri methyl groups. Here, we describe NMR and molecular dynamic studies of the interaction of desmethyl MLN944 with d(ATGCAT)2 , d(TATGCATA)2 , and d(TACGCGTA)2 to investigate the influence of the nine-methyl group on the structure of MLN944 complexes. As with MLN944, the carboxamide group hydrogen bonds to the phenazine ring nitrogen, the ligand sandwiches the central GC base pairs in the major groove, and the protonated linker amines hydrogen bond primarily to the O6 atom of the guanines. Molecular dynamics studies reveal that the linker exists in multiple conformations, none of which produce an ideal set of hydrogen bonds. In distinction, however, the carboxamide-to-phenazine ring nitrogen hydrogen bond is weaker, the overall helix winding is less and the NMR resonances are broader in the desmethyl complexes. Exchange between free and complexed DNA, quantified using two-dimensional NOESY spectra, is faster for the desmethyl MLN944 complexes than for MLN944 complexes. Overall, the data suggest that desmethyl MLN944 DNA complexes are "looser" and more unwound at the binding site, leading to faster dissociation rates, which could account for the diminished efficacy of the desmethyl analog.
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Affiliation(s)
- Andre Serobian
- Department of Pharmacology, School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
| | - Christopher P Pracey
- School of Chemistry, Faculty of Science, UNSW Sydney, Sydney, New South Wales, Australia
| | - Donald S Thomas
- NMR Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, New South Wales, Australia
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, Faculty of Health and Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Graham E Ball
- School of Chemistry, Faculty of Science, UNSW Sydney, Sydney, New South Wales, Australia
| | - Laurence P G Wakelin
- Department of Pharmacology, School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, New South Wales, Australia
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9
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Xu G, Zhao J, Liu N, Yang M, Zhao Q, Li C, Liu M. Structure-guided post-SELEX optimization of an ochratoxin A aptamer. Nucleic Acids Res 2019; 47:5963-5972. [PMID: 31062016 PMCID: PMC6582339 DOI: 10.1093/nar/gkz336] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/30/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
SELEX is the cornerstone for aptamer research with broad applications in biosensors and medicine. To improve the affinity of selected aptamers, we propose a structure-guided post-SELEX approach, an optimization method based on the precise secondary structure of the aptamer–ligand complex. We demonstrate this approach using the Ochratoxin A (OTA) aptamer. Guided by the structure, we designed a new aptamer whose affinity is improved by more than 50-fold. We also determined the high-resolution NMR structure of the new aptamer-OTA complex and elucidated the discriminatory recognition mechanism of one atomic difference between two analogs, OTA and OTB. The aptamer forms an unusual hairpin structure containing an intramolecular triple helix, which is not seen in the previously determined aptamer complex. The π–π stacking, the hydrophobic interaction, hydrogen bonds and halogen bonds between OTA and the aptamer contribute to the recognition of OTA, and the halogen bonds play an important role in discriminating between OTA and OTB. Our results demonstrate that the structure-guided post-SELEX approach improves aptamers affinity. An improved OTA biosensor system might be developed using this new strategy.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Qiang Zhao
- University of Chinese Academy of Sciences, Beijing 100029, P.R. China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
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10
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Shen BW, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target. Nucleic Acids Res 2017; 45:1516-1528. [PMID: 28180307 PMCID: PMC5415892 DOI: 10.1093/nar/gkw1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/15/2016] [Accepted: 11/17/2016] [Indexed: 01/06/2023] Open
Abstract
R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar ‘PD-D/ExK’ restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage.
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, USA
| | - Daniel F Heiter
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, USA
| | - Keith D Lunnen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA, USA
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11
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Ghosh S, Mallick S, Das U, Verma A, Pal U, Chatterjee S, Nandy A, Saha KD, Maiti NC, Baishya B, Suresh Kumar G, Gmeiner WH. Curcumin stably interacts with DNA hairpin through minor groove binding and demonstrates enhanced cytotoxicity in combination with FdU nucleotides. Biochim Biophys Acta Gen Subj 2017; 1862:485-494. [PMID: 29107813 DOI: 10.1016/j.bbagen.2017.10.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 10/11/2017] [Accepted: 10/26/2017] [Indexed: 12/12/2022]
Abstract
We report, based on biophysical studies and molecular mechanical calculations that curcumin binds DNA hairpin in the minor groove adjacent to the loop region forming a stable complex. UV-Vis and fluorescence spectroscopy indicated interaction of curcumin with DNA hairpin. In this novel binding motif, two ɣ H of curcumin heptadiene chain are closely positioned to the A16-H8 and A17-H8, while G12-H8 is located in the close proximity of curcumin α H. Molecular dynamics (MD) simulations suggest, the complex is stabilized by noncovalent forces including; π-π stacking, H-bonding and hydrophobic interactions. Nuclear magnetic resonance (NMR) spectroscopy in combination with molecular dynamics simulations indicated curcumin is bound in the minor groove, while circular dichroism (CD) spectra suggested minute enhancement in base stacking and a little change in DNA helicity, without significant conformational change of DNA hairpin structure. The DNA:curcumin complex formed with FdU nucleotides rather than Thymidine, demonstrated enhanced cytotoxicity towards oral cancer cells relative to the only FdU substituted hairpin. Fluorescence co-localization demonstrated stability of the complex in biologically relevant conditions, including its cellular uptake. Acridine orange/EtBr staining further confirmed the enhanced cytotoxic effects of the complex, suggesting apoptosis as mode of cell death. Thus, curcumin can be noncovalently complexed to small DNA hairpin for cellular delivery and the complex showed increased cytotoxicity in combination with FdU nucleotides, demonstrating its potential for advanced cancer therapy.
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Affiliation(s)
- Supratim Ghosh
- Chittaranjan National Cancer Institute, Kolkata, WB 700026, India.
| | - Sumana Mallick
- CSIR-Indian Institute of Chemical Biology, Kolkata, WB 700032, India
| | - Upasana Das
- Chittaranjan National Cancer Institute, Kolkata, WB 700026, India
| | - Ajay Verma
- Centre of BioMedical Research, Lucknow, UP 226014, India
| | - Uttam Pal
- CSIR-Indian Institute of Chemical Biology, Kolkata, WB 700032, India
| | | | - Abhishek Nandy
- CSIR-Indian Institute of Chemical Biology, Kolkata, WB 700032, India
| | - Krishna D Saha
- CSIR-Indian Institute of Chemical Biology, Kolkata, WB 700032, India
| | | | - Bikash Baishya
- Centre of BioMedical Research, Lucknow, UP 226014, India
| | - G Suresh Kumar
- CSIR-Indian Institute of Chemical Biology, Kolkata, WB 700032, India
| | - William H Gmeiner
- Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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12
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Zhang Q, Lv H, Wang L, Chen M, Li F, Liang C, Yu Y, Jiang F, Lu A, Zhang G. Recent Methods for Purification and Structure Determination of Oligonucleotides. Int J Mol Sci 2016; 17:E2134. [PMID: 27999357 PMCID: PMC5187934 DOI: 10.3390/ijms17122134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides that can interact with target molecules through specific three-dimensional structures. The excellent features, such as high specificity and affinity for target proteins, small size, chemical stability, low immunogenicity, facile chemical synthesis, versatility in structural design and engineering, and accessible for site-specific modifications with functional moieties, make aptamers attractive molecules in the fields of clinical diagnostics and biopharmaceutical therapeutics. However, difficulties in purification and structural identification of aptamers remain a major impediment to their broad clinical application. In this mini-review, we present the recently attractive developments regarding the purification and identification of aptamers. We also discuss the advantages, limitations, and prospects for the major methods applied in purifying and identifying aptamers, which could facilitate the application of aptamers.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Chromatography, High Pressure Liquid/methods
- Chromatography, Ion Exchange/methods
- Chromatography, Reverse-Phase/methods
- Crystallography, X-Ray/methods
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/ultrastructure
- Electrophoresis, Gel, Two-Dimensional/methods
- Nuclear Magnetic Resonance, Biomolecular/methods
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Affiliation(s)
- Qiulong Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Huanhuan Lv
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Lili Wang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Man Chen
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Fangfei Li
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Chao Liang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Yuanyuan Yu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Feng Jiang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- The State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
| | - Ge Zhang
- Institute of Integrated Bioinformedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University (HKBU), Hong Kong, China.
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU (Haimen) Institute of Science and Technology, Haimen 226100, China.
- Shenzhen Lab of Combinatorial Compounds and Targeted Drug Delivery, HKBU Institute of Research and Continuing Education, Shenzhen 518000, China.
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13
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Serobian A, Thomas DS, Ball GE, Denny WA, Wakelin LPG. The solution structure of bis(phenazine-1-carboxamide)-DNA complexes: MLN 944 binding corrected and extended. Biopolymers 2016; 101:1099-113. [PMID: 24898663 DOI: 10.1002/bip.22513] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 05/29/2014] [Accepted: 05/29/2014] [Indexed: 01/09/2023]
Abstract
MLN 944 is a bisintercalating DNA-binding antitumor agent known to be a template inhibitor of transcription. Previous (1) H NMR studies of its d(ATGCAT)2 complex concluded that its phenazine chromophores are protonated. However, we find that this is not so, which has important consequences for the charged state of the ligand, for the orientation of its 1-carboxamide group in the complex, and for the details of the interaction of its protonated interchromophore linker with the DNA base pairs. Here, we report a corrected solution structure of the MLN 944-d(ATGCAT)2 complex, and extend the study to complexes with d(TATGCATA)2 , and d(TACGCGTA)2 , using a variety of (1) H and (31) P NMR methods and molecular dynamics simulations employing the AMBER 12 force field. We find that for all three complexes MLN 944 binds as a dication, in which the chromophores are uncharged, in the DNA major groove spanning the central 2 GC base pairs in a manner that maintains the dyad symmetry of the DNA. The carboxamide group lies in the plane of the chromophore, its NH making hydrogen bonding interactions with the phenazine N10 nitrogen, and the protonated linkers form hydrogen bonds with the O6 atom of guanine. The dynamics simulations reveal extensive solvent interactions involving the linker amines, the carboxamide group, and the DNA bases.
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Affiliation(s)
- Andre Serobian
- Department of Pharmacology, School of Medical Sciences, Faculty of Medicine, UNSW Australia, Sydney, 2052, NSW, Australia
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14
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Ding Y, Fleming AM, White HS, Burrows CJ. Differentiation of G:C vs A:T and G:C vs G:mC Base Pairs in the Latch Zone of α-Hemolysin. ACS NANO 2015; 9:11325-32. [PMID: 26506108 PMCID: PMC4876701 DOI: 10.1021/acsnano.5b05055] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The α-hemolysin (α-HL) nanopore can detect DNA strands under an electrophoretic force via many regions of the channel. Our laboratories previously demonstrated that trapping duplex DNA in the vestibule of wild-type α-HL under force could distinguish the presence of an abasic site compared to a G:C base pair positioned in the latch zone at the top of the vestibule. Herein, a series of duplexes were probed in the latch zone to establish if this region can detect more subtle features of base pairs beyond the complete absence of a base. The results of these studies demonstrate that the most sensitive region of the latch can readily discriminate duplexes in which one G:C base pair is replaced by an A:T. Additional experiments determined that while neither 8-oxo-7,8-dihydroguanine nor 7-deazaguanine opposite C could be differentiated from a G:C base pair, in contrast, the epigenetic marker 5-methylcytosine, when present in both strands of the duplex, yielded new blocking currents when compared to strands with unmodified cytosine. The results are discussed with respect to experimental design for utilization of the latch zone of α-HL to probe specific regions of genomic samples.
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Affiliation(s)
| | | | - Henry S. White
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
| | - Cynthia J. Burrows
- To whom correspondence should be addressed: Telephone: (801) 585-7290 or (801) 585-6256, or
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15
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Wunnicke D, Ding P, Yang H, Seela F, Steinhoff HJ. DNA with Parallel Strand Orientation: A Nanometer Distance Study with Spin Labels in the Watson-Crick and the Reverse Watson-Crick Double Helix. J Phys Chem B 2015; 119:13593-9. [PMID: 26121221 DOI: 10.1021/acs.jpcb.5b02935] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Parallel-stranded (ps) DNA characterized by its sugar-phosphate backbones pointing in the same direction represents an alternative pairing system to antiparallel-stranded (aps) DNA with the potential to inhibit transcription and translation. 25-mer oligonucleotides were selected containing only dA·dT base pairs to compare spin-labeled nucleobase distances over a range of 10 or 15 base pairs in ps DNA with those in aps DNA. By means of the copper(I)-catalyzed Huisgen-Meldal-Sharpless alkyne-azide cycloaddition, the spin label 4-azido-2,2,6,6-tetramethylpiperidine-1-oxyl was clicked to 7-ethynyl-7-deaza-2'-deoxyadenosine or 5-ethynyl-2'-deoxyuridine to yield 25-mer oligonucleotides incorporating two spin labels. The interspin distances between spin labeled residues were determined by pulse EPR spectroscopy. The results reveal that in ps DNA these distances are between 5 and 10% longer than in aps DNA when the labeled DNA segment is located near the center of the double helix. The interspin distance in ps DNA becomes shorter compared with aps DNA when one of the spin labels occupies a position near the end of the double helix.
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Affiliation(s)
| | - Ping Ding
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Haozhe Yang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology , Heisenbergstrasse 11, 48149 Münster, Germany
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16
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McKenna JM, Parkinson JA. HOBS methods for enhancing resolution and sensitivity in small DNA oligonucleotide NMR studies. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2015; 53:249-255. [PMID: 25353689 DOI: 10.1002/mrc.4182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/30/2014] [Accepted: 10/13/2014] [Indexed: 06/04/2023]
Abstract
(1) H NMR spectra from biopolymers give chemical shifts classified according to proton type and often suffer from signal degeneracy. Data from nucleic acids are particularly prone to this failing. Recent developments in proton broadband decoupling techniques with the promise of enhanced resolution at full sensitivity have allowed us to investigate the application of homonuclear band-selective (HOBS) decoupling to the study of small synthetic DNA molecules and to compare these with results from classical and pure shift techniques. Improved signal resolution at full sensitivity in both HOBS-1D (1) H and HOBS-2D [(1) H, (1) H] NOESY NMR data is reported for three example small DNA molecules. Comparisons of (1) H T1 and integrals of signals from HOBS-1D (1) H and HOBS-2D [(1) H, (1) H] NOESY NMR data with those of standard data collection methods are also reported. The results show that homonuclear HOBS-NOESY data are useful for data assignment purposes and have some merit for quantification purposes. In general, we show that resolution and sensitivity enhancement of (1) H NMR data for small DNA samples may be achieved without recourse to higher magnetic field strength at full sensitivity in a band-selected manner.
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Affiliation(s)
- Josiah M McKenna
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
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17
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Stuart CH, Horita DA, Thomas MJ, Salsbury FR, Lively MO, Gmeiner WH. Site-specific DNA-doxorubicin conjugates display enhanced cytotoxicity to breast cancer cells. Bioconjug Chem 2014; 25:406-13. [PMID: 24450459 PMCID: PMC3983131 DOI: 10.1021/bc4005427] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
Doxorubicin (Dox) is widely used
for breast cancer treatment but
causes serious side effects including cardiotoxicity that may adversely
impact patient lifespan even if treatment is successful. Herein, we
describe selective conjugation of Dox to a single site in a DNA hairpin
resulting in a highly stable complex that enables Dox to be used more
effectively. Selective conjugation of Dox to G15 in the hairpin loop
was verified using site-specific labeling with [2-15N]-2′-deoxyguanosine
in conjunction with [1H–15N] 2D NMR,
while 1:1 stoichiometry for the conjugate was validated by ESI-QTOF
mass spectrometry and UV spectroscopy. Molecular modeling indicated
covalently bound Dox also intercalated into the stem of the hairpin
and stability studies demonstrated the resulting Dox-conjugated hairpin
(DCH) complex had a half-life >30 h, considerably longer than alternative
covalent and noncovalent complexes. Secondary conjugation of DCH with
folic acid (FA) resulted in increased internalization into breast
cancer cells. The dual conjugate, DCH-FA, can be used for safer and
more effective chemotherapy with Dox and this conjugation strategy
can be expanded to include additional anticancer drugs.
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Affiliation(s)
- Christopher H Stuart
- Department of Cancer Biology, ‡Department of Molecular Medicine and Translation Science, Wake Forest School of Medicine, and §Department of Biochemistry, Wake Forest School of Medicine , Winston-Salem, North Carolina 27157, United States
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18
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Gmeiner WH, Salsbury F, Olsen CM, Marky LA. The stability of a model substrate for topoisomerase 1-mediated DNA religation depends on the presence of mismatched base pairs. J Nucleic Acids 2011; 2011:631372. [PMID: 21904666 PMCID: PMC3166759 DOI: 10.4061/2011/631372] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/07/2011] [Accepted: 06/11/2011] [Indexed: 12/20/2022] Open
Abstract
Topoisomerase 1 (Top1) enzymes regulate DNA superhelicity by forming covalent cleavage complexes that undergo controlled rotation. Substitution of nucleoside analogs at the +1 position of the DNA duplex relative to the Top1 cleavage site inhibits DNA religation. The reduced efficiency for Top1-mediated religation contributes to the anticancer activity of widely used anticancer drugs including fluoropyrimidines and gemcitabine. In the present study, we report that mismatched base pairs at the +1 position destabilize the duplex DNA components for a model Top1 cleavage complex formation even though one duplex component does not directly include a mismatched base pair. Molecular dynamics simulations reveal G-dU and G-FdU mismatched base pairs, but not a G-T mismatched base pair, increase flexibility at the Top1 cleavage site, and affect coupling between the regions required for the religation reaction to occur. These results demonstrate that substitution of dT analogs into the +1 position of the non-scissile strand alters the stability and flexibility of DNA contributing to the reduced efficiency for Top1-mediated DNA religation. These effects are inherent in the DNA duplex and do not require formation of the Top1:DNA complex. These results provide a biophysical rationale for the inhibition of Top1-mediated DNA religation by nucleotide analog substitution.
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Affiliation(s)
- William H Gmeiner
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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19
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Gerlach B, Kleinschmidt JA, Böttcher B. Conformational changes in adeno-associated virus type 1 induced by genome packaging. J Mol Biol 2011; 409:427-38. [PMID: 21463638 DOI: 10.1016/j.jmb.2011.03.062] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 03/21/2011] [Accepted: 03/28/2011] [Indexed: 01/26/2023]
Abstract
Adeno-associated virus (AAV) is frequently used as a vector for gene therapy. The viral capsid consists of three structural proteins (VP1, VP2, and VP3) that have a common C-terminal core (VP3), with N-terminal extensions of increasing length in VP2 and VP1. The capsid encloses a single-stranded genome of up to 4.7 kb, which is packaged into empty capsids. The N-terminal extension of VP1 carries a phospholipase domain that becomes accessible during infection in the endosomal pathway. We have used cryo-electron microscopy and image reconstruction to determine subnanometer-resolution structures of recombinant AAV1 that has packaged different amounts of a 3.6-kb recombinant genome. The maps show that the AAV1 capsid undergoes continuous conformational changes upon packaging of the genome. The rearrangements occur at the inner capsid surface and lead to constrictions of the pores at the 5-fold symmetry axes and to subtle movements of the β-sheet regions of the capsid proteins. In fully packaged particles, the genome forms stem-like features that contact the inner capsid surface at the 3-fold symmetry axes. We think that the reorganization of the inner surface has an impact on the viral life cycle during infection, preparing the externalization of phospholipase domains through the pores at the 5-fold symmetry axes and possibly genome release.
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Affiliation(s)
- Britta Gerlach
- Division of Tumor Virology, German Cancer Research Center, Im Neuenheimerfeld, Heidelberg, Germany
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20
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Ghosh S, Salsbury FR, Horita DA, Gmeiner WH. Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif. Nucleic Acids Res 2011; 39:4490-8. [PMID: 21296761 PMCID: PMC3105383 DOI: 10.1093/nar/gkr029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We report, based on semi-empirical calculations, that Zn(2+) binds duplex DNA containing consecutive FdU-dA base pairs in the major groove with distorted trigonal bipyramidal geometry. In this previously uncharacterized binding motif, O4 and F5 on consecutive FdU are axial ligands while three water molecules complete the coordination sphere. NMR spectroscopy confirmed Zn(2+) complexation occurred with maintenance of base pairing while a slight hypsochromic shift in circular dichroism (CD) spectra indicated moderate structural distortion relative to B-form DNA. Zn(2+) complexation inhibited ethidium bromide (EtBr) intercalation and stabilized FdU-substituted duplex DNA (ΔT(m) > 15 °C). Mg(2+) neither inhibited EtBr complexation nor had as strong of a stabilizing effect. DNA sequences that did not contain consecutive FdU were not stabilized by Zn(2+). A lipofectamine preparation of the Zn(2+)-DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn(2+)-DNA complexes for cancer treatment.
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Affiliation(s)
- Supratim Ghosh
- Department of Cancer Biology, Program in Molecular Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
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21
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Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2010; 107:5154-9. [PMID: 20133735 DOI: 10.1073/pnas.0913551107] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial nucleoid-associated proteins play important roles in chromosome organization and global gene regulation. We find that Lsr2 of Mycobacterium tuberculosis is a unique nucleoid-associated protein that binds AT-rich regions of the genome, including genomic islands acquired by horizontal gene transfer and regions encoding major virulence factors, such as the ESX secretion systems, the lipid virulence factors PDIM and PGL, and the PE/PPE families of antigenic proteins. Comparison of genome-wide binding data with expression data indicates that Lsr2 binding results in transcriptional repression. Domain-swapping experiments demonstrate that Lsr2 has an N-terminal dimerization domain and a C-terminal DNA-binding domain. Nuclear magnetic resonance analysis of the DNA-binding domain of Lsr2 and its interaction with DNA reveals a unique structure and a unique mechanism that enables Lsr2 to discriminately target AT-rich sequences through interactions with the minor groove of DNA. Taken together, we provide evidence that mycobacteria have employed a structurally distinct molecule with an apparently different DNA recognition mechanism to achieve a function similar to the Enterobacteriaceae H-NS, likely coordinating global gene regulation and virulence in this group of medically important bacteria.
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22
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Nucleosomes represent a physical barrier for cleavage activity of DNA topoisomerase I in vivo. Biochem J 2008; 409:651-6. [PMID: 17967163 DOI: 10.1042/bj20070893] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
DNA topoisomerase I together with the other cellular DNA topoisomerases releases the torsional stress from DNA caused by processes such as replication, transcription and recombination. Despite the well-defined knowledge of its mechanism of action, DNA topoisomerase I in vivo activity has been only partially characterized. In fact the basic question concerning the capability of the enzyme to cleave and rejoin DNA wrapped around a histone octamer remains still unanswered. By studying both in vivo and in vitro the cleavage activity of DNA topoisomerase I in the presence of camptothecin on a repeated trinucleotide sequence, (TTA)(35), lying in chromosome XIII of Saccharomyces cerevisiae, we can conclude that nucleosomes represent a physical barrier for the enzyme activity.
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23
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24
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Ulyanov NB, Mujeeb A, Du Z, Tonelli M, Parslow TG, James TL. NMR structure of the full-length linear dimer of stem-loop-1 RNA in the HIV-1 dimer initiation site. J Biol Chem 2006; 281:16168-77. [PMID: 16603544 DOI: 10.1074/jbc.m601711200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The packaging signal of HIV-1 RNA contains a stem-loop structure, SL1, which serves as the dimerization initiation site for two identical copies of the genome and is important for packaging of the RNA genome into the budding virion and for overall infectivity. SL1 spontaneously dimerizes via a palindromic hexanucleotide sequence in its apical loop, forming a metastable kissing dimer form. Incubation with nucleocapsid protein causes this form to refold to a thermodynamically stable mature linear dimer. Here, we present an NMR structure of the latter form of the full-length SL1 sequence of the Lai HIV-1 isolate. The structure was refined using nuclear Overhauser effect and residual dipolar coupling data. The structure presents a symmetric homodimer of two RNA strands of 35 nucleotides each; it includes five stems separated by four internal loops. The central palindromic stem is surrounded by two symmetric adenine-rich 1-2 internal loops, A-bulges. All three adenines in each A-bulge are stacked inside the helix, consistent with the solution structures of shorter SL1 constructs determined previously. The outer 4-base pair stems and, proximal to them, purine-rich 1-3 internal loops, or G-bulges, are the least stable parts of the molecule. The G-bulges display high conformational variability in the refined ensemble of structures, despite the availability of many structural restraints for this region. Nevertheless, most conformations share a similar structural motif: a guanine and an adenine from opposite strands form a GA mismatch stacked on the top of the neighboring stem. The two remaining guanines are exposed, one in the minor groove and another in the major groove side of the helix, consistent with secondary structure probing data for SL1. These guanines may be recognized by the nucleocapsid protein, which binds tightly to the G-bulge in vitro.
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Affiliation(s)
- Nikolai B Ulyanov
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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Bharanidharan D, Gautham N. Principal component analysis of DNA oligonucleotide structural data. Biochem Biophys Res Commun 2006; 340:1229-37. [PMID: 16414352 DOI: 10.1016/j.bbrc.2005.12.127] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 12/17/2005] [Indexed: 10/25/2022]
Abstract
The microstructure of a DNA helix is characterized by several base pair and base step parameters such as twist, rise, roll, propeller twist, etc., in addition to conformational parameters such as the backbone and the glycosidic torsion angles. Among these only a few, which are independent of all others and of each other, may be used to precisely characterize the helix. The problem however is to identify these independent parameters. We have used principal component analysis to identify a relatively small set of independent parameters, with which to characterize each DNA helix. We show that these principal components clearly discriminate between A and B DNA helical types. The calculations further suggest that the microstructure of a DNA helix is better characterized using dinucleotides.
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Affiliation(s)
- D Bharanidharan
- Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India
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Ruiz-Chica A, Medina M, Sánchez-Jiménez F, Ramírez F. Study by electronic circular dichroism spectroscopy of the interaction between aminooxy analogues of biogenic polyamines and selected oligonucleotides. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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McAteer K, Aceves-Gaona A, Michalczyk R, Buchko GW, Isern NG, Silks LAP, Miller JH, Kennedy MA. Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature. Biopolymers 2005; 75:497-511. [PMID: 15526287 DOI: 10.1002/bip.20168] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In-phase ligated DNA containing T(n)A(n) segments fail to exhibit the retarded polyacrylamide gel electrophoresis (PAGE) migration observed for in-phase ligated A(n)T(n) segments, a behavior thought to be correlated with macroscopic DNA curvature. The lack of macroscopic curvature in ligated T(n)A(n) segments is thought to be due to cancellation of bending in regions flanking the TpA steps. To address this issue, solution-state NMR, including residual dipolar coupling (RDC) restraints, was used to determine a high-resolution structure of [d(CGAGGTTTAAACCTCG)2], a DNA oligomer containing a T3A3 tract. The overall magnitude and direction of bending, including the regions flanking the central TpA step, was measured using a radius of curvature, Rc, analysis. The Rc for the overall molecule indicated a small magnitude of global bending (Rc = 138 +/- 23 nm) towards the major groove, whereas the Rc for the two halves (72 +/- 33 nm and 69 +/- 14 nm) indicated greater localized bending into the minor groove. The direction of bending in the regions flanking the TpA step is in partial opposition (109 degrees), contributing to cancellation of bending. The cancellation of bending did not correlate with a pattern of roll values at the TpA step, or at the 5' and 3' junctions, of the T3A3 segment, suggesting a simple junction/roll model is insufficient to predict cancellation of DNA bending in all T(n)A(n) junction sequence contexts. Importantly, Rc analysis of structures refined without RDC restraints lacked the precision and accuracy needed to reliably measure bending.
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Affiliation(s)
- Kathleen McAteer
- Department of Computer Science and Electrical Engineering, Washington State University Tri-Cities, Richland, WA 99352
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Ruiz-Chica AJ, Medina MA, Sánchez-Jiménez F, Ramírez FJ. On the interpretation of Raman spectra of 1-aminooxy-spermine/DNA complexes. Nucleic Acids Res 2004; 32:579-89. [PMID: 14752046 PMCID: PMC373354 DOI: 10.1093/nar/gkh232] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
By FT-Raman spectroscopy, we have investigated the effect of 1-aminooxy-spermine (AOSPM) on aggregation and stability of calf-thymus DNA and selected oligonucleotide chains. AOSPM is able to mimic spermine in some macromolecular interactions, but is unable to substitute polyamines to maintain cell proliferation, suggesting pharmacological applications. Raman spectra of solutions containing AOSPM and either genomic DNA or two 15mer oligodeoxyribonucleotides, with GC or AT sequences, were recorded. Precipitation was observed for calf-thymus DNA, aggregated structures and appearance of several Z marker bands were observed for the 15mer GC sequence, and no macromolecular changes were detected for the 15mer AT sequence. Specific binding sites between the aminooxy group and the base residues were also evidenced. Assignment of the AOSPM Raman bands was supported on a normal mode calculation for the molecule NH(2)-O-CH(3), as a model. The theoretical results, in combination with the analysis of the Raman bands, demonstrated that the aminooxy group played a relevant role in the AOSPM-DNA interaction. Preferential binding by the major groove was evidenced in the absence of macromolecular changes. When either precipitation or aggregation occurred, the interaction involved both the major and minor grooves. The specific interaction between AT/GC base pairs and the aminooxy group has also been theoretically investigated. The biological relevance of this work is discussed.
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Affiliation(s)
- A J Ruiz-Chica
- Departamento de Química Física, Facultad de Ciencias, Universidad de Málaga, Málaga 29071, Spain
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Aihara H, Kwon HJ, Nunes-Düby SE, Landy A, Ellenberger T. A conformational switch controls the DNA cleavage activity of lambda integrase. Mol Cell 2003; 12:187-98. [PMID: 12887904 DOI: 10.1016/s1097-2765(03)00268-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The bacteriophage lambda integrase protein (lambda Int) belongs to a family of tyrosine recombinases that catalyze DNA rearrangements. We have determined a crystal structure of lambda Int complexed with a cleaved DNA substrate through a covalent phosphotyrosine bond. In comparison to an earlier unliganded structure, we observe a drastic conformational change in DNA-bound lambda Int that brings Tyr342 into the active site for cleavage of the DNA in cis. A flexible linker connects the central and the catalytic domains, allowing the protein to encircle the DNA. Binding specificity is achieved through direct interactions with the DNA and indirect readout of the flexibility of the att site. The conformational switch that activates lambda Int for DNA cleavage exposes the C-terminal 8 residues for interactions with a neighboring Int molecule. The protein interactions mediated by lambda Int's C-terminal tail offer a mechanism for the allosteric control of cleavage activity in higher order lambda Int complexes.
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Affiliation(s)
- Hideki Aihara
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Comolli LR, Ulyanov NB, Soto AM, Marky LA, James TL, Gmeiner WH. NMR structure of the 3' stem-loop from human U4 snRNA. Nucleic Acids Res 2002; 30:4371-9. [PMID: 12384583 PMCID: PMC137124 DOI: 10.1093/nar/gkf560] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was determined to gain insight into the structural basis for conservation of this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG tetraloop. No high resolution structure has previously been reported for a UACG tetraloop. The UACG tetraloop portion of the 3'SL was especially well defined by the NMR data, with a total of 92 NOE-derived restraints (about 15 per residue), including 48 inter-residue restraints (about 8 per residue) for the tetraloop and closing C-G base pair. Distance restraints were derived from NOESY spectra using MARDIGRAS with random error analysis. Refinement of the 20mer RNA hairpin structure was carried out using the programs DYANA and miniCarlo. In the UACG tetraloop, U and G formed a base pair stabilized by two hydrogen bonds, one between the 2'-hydroxyl proton of U and carbonyl oxygen of G, another between the imino proton of G and carbonyl oxygen O2 of U. In addition, the amino group of C formed a hydrogen bond with the phosphate oxygen of A. G adopted a syn orientation about the glycosidic bond, while the sugar puckers of A and C were either C2'-endo or flexible. The conformation of the UACG tetraloop was, overall, similar to that previously reported for UUCG tetraloops, another member of the UNCG class of tetraloops. The presence of an A, rather than a U, at the variable position, however, presents a distinct surface for interaction of the 3'SL tetraloop with either RNA or protein residues that may stabilize interactions important for active spliceosome formation. Such tertiary interactions may explain the conservation of the UACG tetraloop motif in 3'SL sequences from U4 snRNA in vertebrates.
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Affiliation(s)
- Luis R Comolli
- Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143, USA
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