1
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Shi J, Xu W, Yu H, Wang X, Jin F, Zhang Q, Zhang H, Peng Q, Abdurahman A, Wang M. A Highly Luminescent Metallo-Supramolecular Radical Cage. J Am Chem Soc 2023; 145:24081-24088. [PMID: 37796113 DOI: 10.1021/jacs.3c07477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
Luminescent metal-radicals have recently received increasing attention due to their unique properties and promising applications in materials science. However, the luminescence of metal-radicals tends to be quenched after formation of metallo-complexes. It is challenging to construct metal-radicals with highly luminescent properties. Herein, we report a highly luminescent metallo-supramolecular radical cage (LMRC) constructed by the assembly of a tritopic terpyridinyl ligand RL with tris(2,4,6-trichlorophenyl)methyl (TTM) radical and Zn2+. Electrospray ionization-mass spectrometry (ESI-MS), traveling-wave ion mobility-mass spectrometry (TWIM-MS), X-ray crystallography, electron paramagnetic resonance (EPR) spectroscopy, and superconducting quantum interference device (SQUID) confirm the formation of a prism-like supramolecular radical cage. LMRC exhibits a remarkable photoluminescence quantum yield (PLQY) of 65%, which is 5 times that of RL; meanwhile, LMRC also shows high photostability. Notably, significant magnetoluminescence can be observed for the high-concentration LMRC (15 wt % doped in PMMA film); however, the magnetoluminescence of 0.1 wt % doped LMRC film vanishes, revealing negligible spin-spin interactions between two radical centers in LMRC.
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Affiliation(s)
- Junjuan Shi
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Wei Xu
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Hao Yu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Xing Wang
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM) & School of Flexible Electronics (Future Technologies), Nanjing Tech University (Nanjing Tech), Nanjing, Jiangsu 211816, China
| | - Feng Jin
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Qingming Zhang
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Houyu Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
| | - Qiming Peng
- Key Laboratory of Flexible Electronics (KLOFE), Institute of Advanced Materials (IAM) & School of Flexible Electronics (Future Technologies), Nanjing Tech University (Nanjing Tech), Nanjing, Jiangsu 211816, China
| | - Alim Abdurahman
- State Key Laboratory of Integrated Optoelectronics, College of Electronic Science and Engineering, Changchun, Jilin 130012, China
| | - Ming Wang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, Jilin 130012, China
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2
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Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
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3
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Hu Y, Wang Y, Singh J, Sun R, Xu L, Niu X, Huang K, Bai G, Liu G, Zuo X, Chen C, Qin PZ, Fang X. Phosphorothioate-Based Site-Specific Labeling of Large RNAs for Structural and Dynamic Studies. ACS Chem Biol 2022; 17:2448-2460. [PMID: 36069699 PMCID: PMC10186269 DOI: 10.1021/acschembio.2c00199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Pulsed electron-electron double resonance (PELDOR) spectroscopy, X-ray scattering interferometry (XSI), and single-molecule Förster resonance energy transfer (smFRET) are molecular rulers that provide inter- or intramolecular pair-wise distance distributions in the nanometer range, thus being ideally suitable for structural and dynamic studies of biomolecules including RNAs. The prerequisite for such applications requires site-specific labeling of biomolecules with spin labels, gold nanoparticles, and fluorescent tags, respectively. Recently, site-specific labeling of large RNAs has been achieved by a combination of transcription of an expanded genetic alphabet containing A-T/G-C base pairs and NaM-TPT3 unnatural base pair (UBP) with post-transcriptional modifications at UBP bases by click chemistry or amine-NHS ester reactions. However, due to the bulky sizes of functional groups or labeling probes used, such strategies might cause structural perturbation and decrease the accuracy of distance measurements. Here, we synthesize an α-thiophosphorylated variant of rTPT3TP (rTPT3αS), which allows for post-transcriptional site-specific labeling of large RNAs at the internal α-phosphate backbone via maleimide-modified probes. Subsequent PELDOR, XSI, and smFRET measurements result in narrower distance distributions than labeling at the TPT3 base. The presented strategy provides a new route to empower the molecular rulers for structural and dynamic studies of large RNA and its complex.
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Affiliation(s)
- Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yan Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jaideep Singh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Ruirui Sun
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lilei Xu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaolin Niu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keyun Huang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Xiaobing Zuo
- X-ray Science Division, Argonne National Laboratory, Lemont Illinois 60439, United States
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter Z Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing 100084, China
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4
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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5
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Cui X, Zhang Z, Yang Y, Li S, Lee C. Organic radical materials in biomedical applications: State of the art and perspectives. EXPLORATION (BEIJING, CHINA) 2022; 2:20210264. [PMID: 37323877 PMCID: PMC10190988 DOI: 10.1002/exp.20210264] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/24/2022] [Indexed: 06/17/2023]
Abstract
Owing to their unique chemical reactivities and paramagnetism, organic radicals with unpaired electrons have found widespread exploration in physical, chemical, and biological fields. However, most radicals are too short-lived to be separated and only a few of them can maintain stable radical forms via stereochemical strategies. How to utilize these raw radicals for developing stable radical-containing materials have long been a research hotspot for many years. This perspective introduces fundamental characteristics of organic radical materials and highlights their applications in biomedical fields, particularly for bioimaging, biosensing, and photo-triggered therapies. Molecular design of these radical materials is considered with reference to their outstanding imaging and therapeutic performances. Various challenges currently limiting the wide applications of these organic radical materials and their future development are also discussed.
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Affiliation(s)
- Xiao Cui
- Department of ChemistryInstitution Center of Super‐Diamond and Advanced Films (COSDAF)City University of Hong KongKowloonHong Kong SARChina
| | - Zhen Zhang
- Department of ChemistryInstitution Center of Super‐Diamond and Advanced Films (COSDAF)City University of Hong KongKowloonHong Kong SARChina
| | - Yuliang Yang
- College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Shengliang Li
- College of Pharmaceutical SciencesSoochow UniversitySuzhouChina
| | - Chun‐Sing Lee
- Department of ChemistryInstitution Center of Super‐Diamond and Advanced Films (COSDAF)City University of Hong KongKowloonHong Kong SARChina
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6
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Zhuo B, Ou X, Li J. Structure and Mechanical Stabilities of the Three-Way Junction Motifs in Prohead RNA. J Phys Chem B 2021; 125:12125-12134. [PMID: 34719230 DOI: 10.1021/acs.jpcb.1c04681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The core structure of phi29 prohead RNA (pRNA) is composed of three major helices organized into three-way junction pRNA (3WJ-pRNA) and has stout structural rigidity along the coaxial helices. Prohead RNAs of the other Bacillus subtilis bacteriophages such as GA1 and SF5 share similar secondary structure and function with phi29; whether these pRNAs have similar mechanical rigidity remains to be elucidated. In this study, we constructed the tertiary structures of GA1 and SF5 3WJ-pRNAs by comparative modeling. Both GA1 and SF5 3WJ-pRNAs adopt a similar structure, in which three helices are organized as the three-way junction and two of the three helices are stacked coaxially. Moreover, detailed structural features of GA1 and SF5 3WJ-pRNAs are also similar to those of phi29 3WJ-pRNA: all of the bases of the coaxial helices are paired, and all of the adenines in the junction region are paired, which eliminates the interference of A-minor tertiary interactions. Hence, the coaxial helices tightly join to each other, and the major groove between them is very narrow. Two Mg2+ ions can thus fit into this major groove and form double Mg clamps. A steered molecular dynamics simulation was used to study the mechanical properties of these 3WJ-pRNAs. Both GA1 and SF5 3WJ-pRNAs show strong resistance to applied force in the direction of their coaxial helices. Such mechanical stability can be attributed to the Mg clamps.
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Affiliation(s)
- Boyang Zhuo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Xinwen Ou
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Jingyuan Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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7
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Wang Y, Kathiresan V, Chen Y, Hu Y, Jiang W, Bai G, Liu G, Qin PZ, Fang X. Posttranscriptional site-directed spin labeling of large RNAs with an unnatural base pair system under non-denaturing conditions. Chem Sci 2020; 11:9655-9664. [PMID: 33224460 PMCID: PMC7667596 DOI: 10.1039/d0sc01717e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/19/2020] [Indexed: 12/25/2022] Open
Abstract
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date.
Site-directed spin labeling (SDSL) of large RNAs for electron paramagnetic resonance (EPR) spectroscopy has remained challenging to date. We here demonstrate an efficient and generally applicable posttranscriptional SDSL method for large RNAs using an expanded genetic alphabet containing the NaM-TPT3 unnatural base pair (UBP). An alkyne-modified TPT3 ribonucleotide triphosphate (rTPT3COTP) is synthesized and site-specifically incorporated into large RNAs by in vitro transcription, which allows attachment of the azide-containing nitroxide through click chemistry. We validate this strategy by SDSL of a 419-nucleotide ribonuclease P (RNase P) RNA from Bacillus stearothermophilus under non-denaturing conditions. The effects of site-directed UBP incorporation and subsequent spin labeling on the global structure and function of RNase P are marginal as evaluated by Circular Dichroism spectroscopy, Small Angle X-ray Scattering, Sedimentation Velocity Analytical Ultracentrifugation and enzymatic assay. Continuous-Wave EPR analyses reveal that the labeling reaction is efficient and specific, and Pulsed Electron–Electron Double Resonance measurements yield an inter-spin distance distribution that agrees with the crystal structure. The labeling strategy as presented overcomes the size constraint of RNA labeling, opening new avenues of spin labeling and EPR spectroscopy for investigating the structure and dynamics of large RNAs.
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Affiliation(s)
- Yan Wang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Yaoyi Chen
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Yanping Hu
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
| | - Wei Jiang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Guangcan Bai
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Guoquan Liu
- State Key Laboratory of Natural and Biomimetic Drugs , School of Pharmaceutical Sciences , Peking University , Beijing 100191 , China
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , USA .
| | - Xianyang Fang
- Beijing Advanced Innovation Center for Structural Biology , School of Life Sciences , Tsinghua University , Beijing 100084 , China .
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8
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Zou A, Lee S, Li J, Zhou R. Retained Stability of the RNA Structure in DNA Packaging Motor with a Single Mg2+ Ion Bound at the Double Mg-Clamp Structure. J Phys Chem B 2020; 124:701-707. [DOI: 10.1021/acs.jpcb.9b06428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Aodong Zou
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, China
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Sangyun Lee
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
- Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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9
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Malygin AA, Graifer DM, Meschaninova MI, Venyaminova AG, Timofeev IO, Kuzhelev AA, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Structural rearrangements in mRNA upon its binding to human 80S ribosomes revealed by EPR spectroscopy. Nucleic Acids Res 2019; 46:897-904. [PMID: 29156000 PMCID: PMC5778603 DOI: 10.1093/nar/gkx1136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/30/2017] [Indexed: 12/21/2022] Open
Abstract
The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5′- and 3′-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two different types of ribosomal complexes with MR was observed. First, there were stable complexes where MR was fixed in the ribosomal mRNA-binding channel by the codon-anticodon interaction(s) with cognate tRNA(s). Second, we for the first time detected complexes assembled without tRNA due to the binding of MR most likely to an exposed peptide of ribosomal protein uS3 away from the mRNA channel. The analysis of interspin distances allowed the conclusion that 80S ribosomes facilitate dissociation of the duplex (MR)2: the equilibrium between the duplex and the single-stranded MR shifts to MR due to its efficient binding with ribosomes. Furthermore, we observed a significant influence of tRNA bound at the ribosomal exit (E) and/or aminoacyl (A) sites on the stability of ribosomal complexes. Our findings showed that a part of mRNA bound in the ribosome channel, which is not involved in codon-anticodon interactions, has more degrees of freedom than that interacting with tRNAs.
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Affiliation(s)
- Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia
| | - Ivan O Timofeev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Andrey A Kuzhelev
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Olesya A Krumkacheva
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,International Tomography Center SB RAS, Institutskaya str. 3a, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, pr. Lavrentjeva 8, Novosibirsk 630090, Russia.,Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russia.,N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, pr. Lavrentjeva 9, Novosibirsk 630090, Russia
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10
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Ding Y, Kathiresan V, Zhang X, Haworth IS, Qin PZ. Experimental Validation of the ALLNOX Program for Studying Protein-Nucleic Acid Complexes. J Phys Chem A 2019; 123:3592-3598. [PMID: 30978022 DOI: 10.1021/acs.jpca.9b01027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Measurement of distances between spectroscopic labels (e.g., spin labels, fluorophores) attached to specific sites of biomolecules is an important method for studying biomolecular complexes. ALLNOX (Addition of Labels and Linkers) has been developed as a program to model interlabel distances based on an input macromolecule structure. Here, we report validation of ALLNOX using measured distances between nitroxide spin labels attached to specific sites of a protein-DNA complex. The results demonstrate that ALLNOX predicts average interspin distances that matched with values measured with pairs of labels attached at the protein and/or DNA. This establishes a solid foundation for using spin labeling in conjunction with ALLNOX to investigate complexes without high-resolution structures. With its high degree of flexibility for the label or the target biomolecule, ALLNOX provides a useful tool for investigating the structure-function relationship in a large variety of biological molecules.
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Affiliation(s)
- Yuan Ding
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Venkatesan Kathiresan
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Xiaojun Zhang
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences , University of Southern California , Los Angeles , California 90089 , United States
| | - Peter Z Qin
- Department of Chemistry , University of Southern California , Los Angeles , California 90089 , United States.,Department of Biological Sciences , University of Southern California , Los Angeles , California 90089 , United States
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11
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Weinrich T, Jaumann EA, Scheffer UM, Prisner TF, Göbel MW. Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA. Beilstein J Org Chem 2018; 14:1563-1569. [PMID: 30013683 PMCID: PMC6036967 DOI: 10.3762/bjoc.14.133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/14/2018] [Indexed: 12/23/2022] Open
Abstract
TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The resulting spin-labeled palindromic duplexes could be directly investigated by PELDOR spectroscopy without further purification steps. Spin–spin distances measured by PELDOR correspond well to the values obtained from molecular models.
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Affiliation(s)
- Timo Weinrich
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Ute M Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
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12
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Weinrich T, Jaumann EA, Scheffer U, Prisner TF, Göbel MW. A Cytidine Phosphoramidite with Protected Nitroxide Spin Label: Synthesis of a Full-Length TAR RNA and Investigation by In-Line Probing and EPR Spectroscopy. Chemistry 2018; 24:6202-6207. [PMID: 29485736 DOI: 10.1002/chem.201800167] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/23/2018] [Indexed: 01/20/2023]
Abstract
EPR studies on RNA are complicated by three major obstacles related to the chemical nature of nitroxide spin labels: Decomposition while oligonucleotides are chemically synthesized, further decay during enzymatic strand ligation, and undetected changes in conformational equilibria due to the steric demand of the label. Herein possible solutions for all three problems are presented: A 2-nitrobenzyloxymethyl protective group for nitroxides that is stable under all conditions of chemical RNA synthesis and can be removed photochemically. By careful selection of ligation sites and splint oligonucleotides, high yields were achieved in the assembly of a full-length HIV-1 TAR RNA labeled with two protected nitroxide groups. PELDOR measurements on spin-labeled TAR in the absence and presence of arginine amide indicated arrest of interhelical motions on ligand binding. Finally, even minor changes in conformation due to the presence of spin labels are detected with high sensitivity by in-line probing.
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Affiliation(s)
- Timo Weinrich
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Eva A Jaumann
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany
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13
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Lawless MJ, Shimshi A, Cunningham TF, Kinde MN, Tang P, Saxena S. Analysis of Nitroxide-Based Distance Measurements in Cell Extracts and in Cells by Pulsed ESR Spectroscopy. Chemphyschem 2017; 18:1653-1660. [PMID: 28295910 DOI: 10.1002/cphc.201700115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Indexed: 11/10/2022]
Abstract
Measurements of distances in cells by pulsed ESR spectroscopy afford tremendous opportunities to study proteins in native environments that are irreproducible in vitro. However, the in-cell environment is harsh towards the typical nitroxide radicals used in double electron-electron resonance (DEER) experiments. A systematic examination is performed on the loss of the DEER signal, including contributions from nitroxide decay and nitroxide side-chain cleavage. In addition, the possibility of extending the lifetime of the nitroxide radical by use of an oxidizing agent is investigated. Using this oxidizing agent, DEER distance measurements are performed on doubly nitroxide-labeled GB1, the immunoglobulin-binding domain of protein G, at varying incubation times in the cellular environment. It is found that, by comparison of the loss of DEER signal to the loss of the CW spectrum, cleavage of the nitroxide side chain contributes to the loss of DEER signal, which is significantly greater in cells than in cell extracts. Finally, local spin concentrations are monitored at varying incubation times to show the time required for molecular diffusion of a small globular protein within the cellular milieu.
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Affiliation(s)
- Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Amit Shimshi
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
| | - Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA.,Current address: Department of Chemistry, Hanover College, 484 Ball Dr, Hanover, IN, 47243, USA
| | - Monica N Kinde
- Department of Anesthesiology, University of Pittsburgh School of Medicine, 3501 5th Avenue, Pittsburgh, PA, 15213, USA.,Current address: Division of Basic Sciences, Kansas City University of Medicine and Biosciences, 2901 St. John's Blvd., Joplin, MO, 64804, USA
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, 3501 5th Avenue, Pittsburgh, PA, 15213, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA, 15260, USA
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14
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Xu Z, Sun Y, Weber JK, Cao Y, Wang W, Jasinski D, Guo P, Zhou R, Li J. Directional mechanical stability of Bacteriophage φ29 motor's 3WJ-pRNA: Extraordinary robustness along portal axis. SCIENCE ADVANCES 2017; 3:e1601684. [PMID: 28560321 PMCID: PMC5446216 DOI: 10.1126/sciadv.1601684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 04/07/2017] [Indexed: 06/01/2023]
Abstract
The molecular motor exploited by bacteriophage φ29 to pack DNA into its capsid is regarded as one of the most powerful mechanical devices present in viral, bacterial, and eukaryotic systems alike. Acting as a linker element, a prohead RNA (pRNA) effectively joins the connector and ATPase (adenosine triphosphatase) components of the φ29 motor. During DNA packing, this pRNA needs to withstand enormous strain along the capsid's portal axis-how this remarkable stability is achieved remains to be elucidated. We investigate the mechanical properties of the φ29 motor's three-way junction (3WJ)-pRNA using a combined steered molecular dynamics and atomic force spectroscopy approach. The 3WJ exhibits strong resistance to stretching along its coaxial helices, demonstrating its super structural robustness. This resistance disappears, however, when external forces are applied to the transverse directions. From a molecular standpoint, we demonstrate that this direction-dependent stability can be attributed to two Mg clamps that cooperate and generate mechanical resistance in the pRNA's coaxial direction. Our results suggest that the asymmetric nature of the 3WJ's mechanical stability is entwined with its biological function: Enhanced rigidity along the portal axis is likely essential to withstand the strain caused by DNA condensation, and flexibility in other directions should aid in the assembly of the pRNA and its association with other motor components.
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Affiliation(s)
- Zhonghe Xu
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Sun
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Jeffrey K. Weber
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
| | - Yi Cao
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing, Jiangsu 210093, China
| | - Daniel Jasinski
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine/Department of Physiology & Cell Biology; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy, Division of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine/Department of Physiology & Cell Biology; Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Ruhong Zhou
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou, Zhejiang 310027, China
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598, USA
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Jingyuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou, Zhejiang 310027, China
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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15
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Hill AC, Schroeder SJ. Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA. RNA (NEW YORK, N.Y.) 2017; 23:521-529. [PMID: 28069889 PMCID: PMC5340915 DOI: 10.1261/rna.059220.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/24/2016] [Indexed: 06/06/2023]
Abstract
The thermodynamic stabilities of four natural prohead or packaging RNA (pRNA) three-way junction (3WJ) nanomotifs and seven phi29 pRNA 3WJ deletion mutant nanomotifs were investigated using UV optical melting on a three-component RNA system. Our data reveal that some pRNA 3WJs are more stable than the phi29 pRNA 3WJ. The stability of the 3WJ contributes to the unique self-assembly properties of pRNA. Thus, ultrastable pRNA 3WJ motifs suggest new scaffolds for pRNA-based nanotechnology. We present data demonstrating that pRNA 3WJs differentially respond to the presence of metal ions. A comparison of our data with free energies predicted by currently available RNA secondary structure prediction programs shows that these programs do not accurately predict multibranch loop stabilities. These results will expand the existing parameters used for RNA secondary structure prediction from sequence in order to better inform RNA structure-function hypotheses and guide the rational design of functional RNA supramolecular assemblies.
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Affiliation(s)
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
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16
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Conformational Flexibility and Dynamics of the Internal Loop and Helical Regions of the Kink–Turn Motif in the Glycine Riboswitch by Site-Directed Spin-Labeling. Biochemistry 2016; 55:4295-305. [DOI: 10.1021/acs.biochem.6b00287] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jackie M. Esquiaqui
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
| | - Eileen M. Sherman
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Jing-Dong Ye
- Department
of Chemistry, University of Central Florida, 4000 Central Florida Boulevard, Orlando, Florida 32816, United States
| | - Gail E. Fanucci
- Department
of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611, United States
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17
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Hill AC, Bartley LE, Schroeder SJ. Prohead RNA: a noncoding viral RNA of novel structure and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2016; 7:428-37. [PMID: 26810250 PMCID: PMC5066667 DOI: 10.1002/wrna.1330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 11/23/2015] [Accepted: 12/02/2015] [Indexed: 12/12/2022]
Abstract
Prohead RNA (pRNA) is an essential component of the powerful Φ29-like bacteriophage DNA packaging motor. However, the specific role of this unique RNA in the Φ29 packaging motor remains unknown. This review examines pRNA as a noncoding RNA of novel structure and function. In order to highlight the reasons for exploring the structure and function of pRNA, we (1) provide an overview of Φ29-like bacteriophage and the Φ29 DNA packaging motor, including putative motor mechanisms and structures of its component parts; (2) discuss pRNA structure and possible roles for pRNA in the Φ29 packaging motor; (3) summarize pRNA self-assembly; and (4) describe the prospective therapeutic applications of pRNA. Many questions remain to be answered in order to connect what is currently known about pRNA structure to its novel function in the Φ29 packaging motor. The knowledge gained from studying the structure, function, and sequence variation in pRNA will help develop tools to better navigate the conformational landscapes of RNA. WIREs RNA 2016, 7:428-437. doi: 10.1002/wrna.1330 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Alyssa C Hill
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Susan J Schroeder
- Department of Microbiology and Plant Biology, Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
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18
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Babaylova ES, Malygin AA, Lomzov AA, Pyshnyi DV, Yulikov M, Jeschke G, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Complementary-addressed site-directed spin labeling of long natural RNAs. Nucleic Acids Res 2016; 44:7935-43. [PMID: 27269581 PMCID: PMC5027493 DOI: 10.1093/nar/gkw516] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022] Open
Abstract
Nanoscale distance measurements by pulse dipolar Electron paramagnetic resonance (EPR) spectroscopy allow new insights into the structure and dynamics of complex biopolymers. EPR detection requires site directed spin labeling (SDSL) of biomolecule(s), which remained challenging for long RNAs up-to-date. Here, we demonstrate that novel complementary-addressed SDSL approach allows efficient spin labeling and following structural EPR studies of long RNAs. We succeeded to spin-label Hepatitis C Virus RNA internal ribosome entry site consisting of ≈330 nucleotides and having a complicated spatial structure. Application of pulsed double electron–electron resonance provided spin–spin distance distribution, which agrees well with the results of molecular dynamics (MD) calculations. Thus, novel SDSL approach in conjunction with EPR and MD allows structural studies of long natural RNAs with nanometer resolution and can be applied to systems of biological and biomedical significance.
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Affiliation(s)
- Elena S Babaylova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Maxim Yulikov
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Gunnar Jeschke
- Laboratory of Physical Chemistry, ETH Zurich, Zurich 8093, Switzerland
| | - Olesya A Krumkacheva
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Matvey V Fedin
- Novosibirsk State University, Novosibirsk 630090, Russia International Tomography Center SB RAS, Novosibirsk 630090, Russia
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University, Novosibirsk 630090, Russia N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk 630090, Russia
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19
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Lomzov AA, Sviridov EA, Shernuykov AV, Shevelev GY, Pyshnyi DV, Bagryanskaya EG. Study of a DNA Duplex by Nuclear Magnetic Resonance and Molecular Dynamics Simulations. Validation of Pulsed Dipolar Electron Paramagnetic Resonance Distance Measurements Using Triarylmethyl-Based Spin Labels. J Phys Chem B 2016; 120:5125-33. [PMID: 27195671 DOI: 10.1021/acs.jpcb.6b03193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pulse dipole-dipole electron paramagnetic resonance (EPR) spectroscopy (double electron-electron resonance [DEER] or pulse electron-electron double resonance [PELDOR] and double quantum coherence [DQC]) allows for measurement of distances in biomolecules and can be used at low temperatures in a frozen solution. Recently, the possibility of distance measurement in a nucleic acid at a physiological temperature using pulse EPR was demonstrated. In these experiments, triarylmethyl (TAM) radicals with long memory time of the electron spin served as a spin label. In addition, the duplex was immobilized on modified silica gel particles (Nucleosil DMA); this approach enables measurement of interspin distances close to 4.5 nm. Nevertheless, the possible influence of TAM on the structure of a biopolymer under study and validity of the data obtained by DQC are debated. In this paper, a combination of molecular dynamics (MD) and nuclear magnetic resonance (NMR) methods was used for verification of interspin distances measured by the X-band DQC method. NMR is widely used for structural analysis of biomolecules under natural conditions (room temperature and an aqueous solution). The ultraviolet (UV) melting method and thermal series (1)H NMR in the range 5-95 °C revealed the presence of only the DNA duplex in solution at oligonucleotide concentrations 1 μM to 1.1 mM at temperatures below 40 °C. The duplex structures and conformation flexibility of native and TAM-labeled DNA complexes obtained by MD simulation were the same as the structure obtained by NMR refinement. Thus, we showed that distance measurements at physiological temperatures by the X-band DQC method allow researchers to obtain valid structural information on an unperturbed DNA duplex using terminal TAM spin labels.
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Affiliation(s)
- Alexander A Lomzov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Eugeniy A Sviridov
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Andrey V Shernuykov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Georgiy Yu Shevelev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, SB RAS , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Novosibirsk State University , Novosibirsk 630090, Russia
| | - Elena G Bagryanskaya
- Novosibirsk State University , Novosibirsk 630090, Russia.,N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS , 9 Lavrentiev Avenue, Novosibirsk 630090, Russia
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20
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Hao Y, Kieft JS. Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol 2016; 13:635-45. [PMID: 27217219 DOI: 10.1080/15476286.2016.1190075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The packaging RNA (pRNA) found in the phi29 family of bacteriophage is an essential component of a powerful molecular motor used to package the phage's DNA genome into the capsid. The pRNA forms homomultimers mediated by intermolecular "kissing-loop" interactions, thus it is an example of the unusual phenomenon of a self-associating RNA that can form symmetric higher-order multimers. Previous research showed the pRNAs from phi29 family phages have diverse self-association properties and the kissing-loop interaction is not the sole structural element dictating multimerization. We found that a 3-way junction (3wj) within each pRNA, despite not making direct intermolecular contacts, plays important roles in stabilizing the intermolecular interactions and dictating the size of the multimer formed (dimer, trimer, etc.). Specifically, the 3wj in the pRNA from phage M2 appears to favor a different conformation compared to the 3wj in the phi29 pRNA, and the M2 junction facilitates formation of a higher-order multimer that is more thermostable. This behavior provides insights into the fundamental principles of RNA self-association, and additionally may be useful to engineer fine-tuned properties into pRNAs for nanotechnology.
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Affiliation(s)
- Yumeng Hao
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver School of Medicine , Aurora , CO , USA
| | - Jeffrey S Kieft
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver School of Medicine , Aurora , CO , USA
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21
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Xu CX, Zhang X, Zhou YW, Wang H, Cao Q, Shen Y, Ji LN, Mao ZW, Qin PZ. A Nitroxide-Tagged Platinum(II) Complex Enables the Identification of DNA G-Quadruplex Binding Mode. Chemistry 2016; 22:3405-3413. [PMID: 26845489 DOI: 10.1002/chem.201504960] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We reported a novel strategy for investigating small molecule binding to G-quadruplexes (GQs). A newly synthesized dinuclear platinum(II) complex (Pt2L) containing a nitroxide radical was shown to selectively bind a GQ-forming sequence derived from human telomere (hTel). Using the nitroxide moiety as a spin label, electron paramagnetic resonance (EPR) spectroscopy was carried out to investigate binding between Pt2L and hTel GQ. Measurements indicated that two molecules of Pt2L bind with one molecule of hTel GQ. The inter-spin distance measured between the two bound Pt2L, together with molecular docking analyses, revealed that Pt2L predominately binds to the neighboring narrow and wide grooves of the G-tetrads as hTel adopts the antiparallel conformation. The design and synthesis of nitroxide tagged GQ binders, and the use of spin-labeling/EPR to investigate their interactions with GQs, will aid the development of small molecules for manipulating GQs involved in crucial biological processes.
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Affiliation(s)
- Cui-Xia Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California Los Angeles, California, 90089 (USA)
| | - Yi-Wei Zhou
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Hanqiang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Yong Shen
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Liang-Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry and Chemical Engineering, Sun Yat-Sen University Guangzhou, Guangdong, 510275 (P.R. China)
| | - Peter Z Qin
- Department of Chemistry, University of Southern California Los Angeles, California, 90089 (USA)
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22
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23
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Zhang X, Xu CX, Di Felice R, Sponer J, Islam B, Stadlbauer P, Ding Y, Mao L, Mao ZW, Qin PZ. Conformations of Human Telomeric G-Quadruplex Studied Using a Nucleotide-Independent Nitroxide Label. Biochemistry 2015; 55:360-72. [PMID: 26678746 DOI: 10.1021/acs.biochem.5b01189] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Guanine-rich oligonucleotides can form a unique G-quadruplex (GQ) structure with stacking units of four guanine bases organized in a plane through Hoogsteen bonding. GQ structures have been detected in vivo and shown to exert their roles in maintaining genome integrity and regulating gene expression. Understanding GQ conformation is important for understanding its inherent biological role and for devising strategies to control and manipulate functions based on targeting GQ. Although a number of biophysical methods have been used to investigate structure and dynamics of GQs, our understanding is far from complete. As such, this work explores the use of the site-directed spin labeling technique, complemented by molecular dynamics simulations, for investigating GQ conformations. A nucleotide-independent nitroxide label (R5), which has been previously applied for probing conformations of noncoding RNA and DNA duplexes, is attached to multiple sites in a 22-nucleotide DNA strand derived from the human telomeric sequence (hTel-22) that is known to form GQ. The R5 labels are shown to minimally impact GQ folding, and inter-R5 distances measured using double electron-electron resonance spectroscopy are shown to adequately distinguish the different topological conformations of hTel-22 and report variations in their occupancies in response to changes of the environment variables such as salt, crowding agent, and small molecule ligand. The work demonstrates that the R5 label is able to probe GQ conformation and establishes the base for using R5 to study more complex sequences, such as those that may potentially form multimeric GQs in long telomeric repeats.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Cui-Xia Xu
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Rosa Di Felice
- Department of Physics and Astronomy, University of Southern California , Los Angeles, California 90089, United States.,Center S3, CNR institute of Nanoscience , Modena, Italy
| | - Jiri Sponer
- Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic.,Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Barira Islam
- Central European Institute of Technology (CEITEC), Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Yuan Ding
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Lingling Mao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Zong-Wan Mao
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University , Guangzhou 510275, China
| | - Peter Z Qin
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
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24
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Malygin AA, Graifer DM, Meschaninova MI, Venyaminova AG, Krumkacheva OA, Fedin MV, Karpova GG, Bagryanskaya EG. Doubly Spin-Labeled RNA as an EPR Reporter for Studying Multicomponent Supramolecular Assemblies. Biophys J 2015; 109:2637-2643. [PMID: 26682820 PMCID: PMC4699879 DOI: 10.1016/j.bpj.2015.10.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/21/2015] [Accepted: 10/30/2015] [Indexed: 02/06/2023] Open
Abstract
mRNAs are involved in complicated supramolecular complexes with human 40S and 80S ribosomes responsible for the protein synthesis. In this work, a derivative of nonaribonucleotide pUUCGUAAAA with nitroxide spin labels attached to the 5'-phosphate and to the C8 atom of the adenosine in sixth position (mRNA analog) was used for studying such complexes using double electron-electron resonance/pulsed electron-electron double resonance spectroscopy. The complexes were assembled with participation of tRNA(Phe), which targeted triplet UUC of the derivative to the ribosomal peptidyl site and predetermined location of the adjacent GUA triplet coding for Val at the aminoacyl (A) site. The interspin distances were measured between the two labels of mRNA analog attached to the first nucleotide of the peptidyl site bound codon and to the third nucleotide of the A site bound codon, in the absence/presence of second tRNA bound at the A site. The values of the obtained interspin distances agree with those calculated for available near-atomic structures of similar complexes of 40S and 80S ribosomes, showing that neither 60S subunit nor tRNA at the A site have a noticeable effect on arrangement of mRNA at the codon-anticodon interaction area. In addition, the shapes of distance distributions in four studied ribosomal complexes allowed conclusions on conformational flexibility of mRNA in these complexes. Overall, the results of this study are the first, to our knowledge, demonstration of double electron-electron resonance/pulsed electron-electron double resonance application for measurements of intramolecular distances in multicomponent supramolecular complexes involving intricate cellular machineries and for evaluating dynamic properties of ligands bound to these machineries.
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Affiliation(s)
- Alexey A Malygin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Dmitri M Graifer
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Maria I Meschaninova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Aliya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Olesya A Krumkacheva
- International Tomography Center SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia
| | - Matvey V Fedin
- International Tomography Center SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Galina G Karpova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
| | - Elena G Bagryanskaya
- N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry SB RAS, Novosibirsk, Russia; Novosibirsk State University, Novosibirsk, Russia.
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25
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Sun Y, Borbat PP, Grigoryants VM, Myers WK, Freed JH, Scholes CP. Pulse dipolar ESR of doubly labeled mini TAR DNA and its annealing to mini TAR RNA. Biophys J 2015; 108:893-902. [PMID: 25692594 DOI: 10.1016/j.bpj.2014.12.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/07/2014] [Accepted: 12/03/2014] [Indexed: 12/27/2022] Open
Abstract
Pulse dipolar electron-spin resonance in the form of double electron electron resonance was applied to strategically placed, site-specifically attached pairs of nitroxide spin labels to monitor changes in the mini TAR DNA stem-loop structure brought on by the HIV-1 nucleocapsid protein NCp7. The biophysical structural evidence was at Ångstrom-level resolution under solution conditions not amenable to crystallography or NMR. In the absence of complementary TAR RNA, double labels located in both the upper and the lower stem of mini TAR DNA showed in the presence of NCp7 a broadened distance distribution between the points of attachment, and there was evidence for several conformers. Next, when equimolar amounts of mini TAR DNA and complementary mini TAR RNA were present, NCp7 enhanced the annealing of their stem-loop structures to form duplex DNA-RNA. When duplex TAR DNA-TAR RNA formed, double labels initially located 27.5 Å apart at the 3'- and 5'-termini of the 27-base mini TAR DNA relocated to opposite ends of a 27 bp RNA-DNA duplex with 76.5 Å between labels, a distance which was consistent with the distance between the two labels in a thermally annealed 27-bp TAR DNA-TAR RNA duplex. Different sets of double labels initially located 26-27 Å apart in the mini TAR DNA upper stem, appropriately altered their interlabel distance to ~35 Å when a 27 bp TAR DNA-TAR RNA duplex formed, where the formation was caused either through NCp7-induced annealing or by thermal annealing. In summary, clear structural evidence was obtained for the fraying and destabilization brought on by NCp7 in its biochemical function as an annealing agent and for the detailed structural change from stem-loop to duplex RNA-DNA when complementary RNA was present.
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Affiliation(s)
- Yan Sun
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, New York
| | - Vladimir M Grigoryants
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - William K Myers
- Department of Chemistry, University at Albany, State University of New York, Albany, New York
| | - Jack H Freed
- Department of Chemistry and Chemical Biology and ACERT, Cornell University, Ithaca, New York
| | - Charles P Scholes
- Department of Chemistry, University at Albany, State University of New York, Albany, New York.
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26
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Tangprasertchai NS, Zhang X, Ding Y, Tham K, Rohs R, Haworth IS, Qin PZ. An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids. Methods Enzymol 2015; 564:427-53. [PMID: 26477260 PMCID: PMC4641853 DOI: 10.1016/bs.mie.2015.07.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The technique of site-directed spin labeling (SDSL) provides unique information on biomolecules by monitoring the behavior of a stable radical tag (i.e., spin label) using electron paramagnetic resonance (EPR) spectroscopy. In this chapter, we describe an approach in which SDSL is integrated with computational modeling to map conformations of nucleic acids. This approach builds upon a SDSL tool kit previously developed and validated, which includes three components: (i) a nucleotide-independent nitroxide probe, designated as R5, which can be efficiently attached at defined sites within arbitrary nucleic acid sequences; (ii) inter-R5 distances in the nanometer range, measured via pulsed EPR; and (iii) an efficient program, called NASNOX, that computes inter-R5 distances on given nucleic acid structures. Following a general framework of data mining, our approach uses multiple sets of measured inter-R5 distances to retrieve "correct" all-atom models from a large ensemble of models. The pool of models can be generated independently without relying on the inter-R5 distances, thus allowing a large degree of flexibility in integrating the SDSL-measured distances with a modeling approach best suited for the specific system under investigation. As such, the integrative experimental/computational approach described here represents a hybrid method for determining all-atom models based on experimentally-derived distance measurements.
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Affiliation(s)
| | - Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Yuan Ding
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Kenneth Tham
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
| | - Remo Rohs
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Ian S. Haworth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California, USA,Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA,Corresponding author:
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27
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Combining NMR and EPR to Determine Structures of Large RNAs and Protein–RNA Complexes in Solution. Methods Enzymol 2015; 558:279-331. [DOI: 10.1016/bs.mie.2015.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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28
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Hao Y, Kieft JS. Diverse self-association properties within a family of phage packaging RNAs. RNA (NEW YORK, N.Y.) 2014; 20:1759-74. [PMID: 25246655 PMCID: PMC4201828 DOI: 10.1261/rna.045948.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/18/2014] [Indexed: 05/24/2023]
Abstract
The packaging RNA (pRNA) found in phi29 bacteriophage is an essential component of a molecular motor that packages the phage's DNA genome. The pRNA forms higher-order multimers by intermolecular "kissing" interactions between identical molecules. The phi29 pRNA is a proven building block for nanotechnology and a model to explore the rare phenomenon of naturally occurring RNA self-association. Although the self-association properties of the phi29 pRNA have been extensively studied and this pRNA is used in nanotechnology, the characteristics of phylogenetically related pRNAs with divergent sequences are comparatively underexplored. These diverse pRNAs may lend new insight into both the rules governing RNA self-association and for RNA engineering. Therefore, we used a combination of biochemical and biophysical methods to resolve ambiguities in the proposed secondary structures of pRNAs from M2, GA1, SF5, and B103 phage, and to discover that different naturally occurring pRNAs form multimers of different stoichiometry and thermostability. Indeed, the M2 pRNA formed multimers that were particularly thermostable and may be more useful than phi29 pRNA for many applications. To determine if diverse pRNA behaviors are conferred by different kissing loop sequences, we designed and tested chimeric RNAs based on our revised secondary structural models. We found that although the kissing loops are essential for self-association, the critical determinant of multimer stability and stoichiometry is likely the diverse three-way junctions found in these RNAs. Using known features of RNA three-way junctions and solved structures of phi29 pRNA's junction, we propose a model for how different junctions affect self-association.
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Affiliation(s)
- Yumeng Hao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, Colorado 80045, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Aurora, Colorado 80045, USA Howard Hughes Medical Institute, University of Colorado Denver, School of Medicine, Aurora, Colorado 80045, USA
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29
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Barros SA, Chenoweth DM. Recognition of nucleic acid junctions using triptycene-based molecules. Angew Chem Int Ed Engl 2014; 53:13746-50. [PMID: 25257803 DOI: 10.1002/anie.201407061] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Indexed: 12/24/2022]
Abstract
The modulation of nucleic acids by small molecules is an essential process across the kingdoms of life. Targeting nucleic acids with small molecules represents a significant challenge at the forefront of chemical biology. Nucleic acid junctions are ubiquitous structural motifs in nature and in designed materials. Herein, we describe a new class of structure-specific nucleic acid junction stabilizers based on a triptycene scaffold. Triptycenes provide significant stabilization of DNA and RNA three-way junctions, providing a new scaffold for the development of nucleic acid junction binders with enhanced recognition properties. Additionally, we report cytotoxicity and cell uptake data in two human ovarian carcinoma cell lines.
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Affiliation(s)
- Stephanie A Barros
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104 (USA)
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30
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Barros SA, Chenoweth DM. Recognition of Nucleic Acid Junctions Using Triptycene-Based Molecules. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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31
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Helmling C, Bessi I, Wacker A, Schnorr KA, Jonker HRA, Richter C, Wagner D, Kreibich M, Schwalbe H. Noncovalent spin labeling of riboswitch RNAs to obtain long-range structural NMR restraints. ACS Chem Biol 2014; 9:1330-9. [PMID: 24673892 DOI: 10.1021/cb500050t] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Paramagnetic relaxation enhancement (PRE) NMR is a powerful method to study structure, dynamics and function of proteins. Up to now, the application of PRE NMR on RNAs is a significant challenge due to the limited size of chemically synthesized RNA. Here, we present a noncovalent spin labeling strategy to spin label RNAs in high yields required for NMR studies. The approach requires the presence of a helix segment composed of about 10 nucleotides (nt) but is not restricted by the size of the RNA. We show successful application of this strategy on the 2'dG sensing aptamer domain of Mesoplasma florum (78 nt). The aptamer domain was prepared in two fragments. A larger fragment was obtained by biochemical means, while a short spin labeled fragment was prepared by chemical solid-phase synthesis. The two fragments were annealed noncovalently by hybridization. We performed NMR, cw-EPR experiments and gel shift assays to investigate the stability of the two-fragment complex. NMR analysis in (15)N-TROSY and (1)H,(1)H-NOESY spectra of both unmodified and spin labeled aptamer domain show that the fragmented system forms a stable hybridization product, is in structural agreement with the full length aptamer domain and maintains its function. Together with structure modeling, experimentally determined (1)H-Γ2 rates are in agreement with reported crystal structure data and show that distance restraints up to 25 Å can be obtained from NMR PRE data of RNA.
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Affiliation(s)
- Christina Helmling
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Irene Bessi
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Anna Wacker
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Kai A. Schnorr
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Hendrik R. A. Jonker
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Christian Richter
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Dominic Wagner
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Michael Kreibich
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry
and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
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32
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Esquiaqui JM, Sherman EM, Ionescu SA, Ye JD, Fanucci GE. Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling. Biochemistry 2014; 53:3526-8. [PMID: 24849816 PMCID: PMC4059530 DOI: 10.1021/bi500404b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Site-directed
spin labeling with continuous wave electron paramagnetic
resonance (EPR) spectroscopy was utilized to characterize dynamic
features of the kink–turn motif formed through a leader–linker
interaction in the Vibrio cholerae glycine riboswitch.
Efficient incorporation of spin-labels into select sites within the
phosphate backbone of the leader–linker region proceeded via
splinted ligation of chemically synthesized spin-labeled oligonucleotides
to in vitro transcribed larger RNA fragments. The
resultant nitroxide EPR line shapes have spectral characteristics
consistent with a kink–turn motif and reveal differential backbone
dynamics that are modulated by the presence of magnesium, potassium,
and glycine.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida , P.O. Box 117200, Gainesville, Florida 32611, United States
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33
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Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat Commun 2014; 5:3890. [DOI: 10.1038/ncomms4890] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/15/2014] [Indexed: 02/08/2023] Open
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34
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Duss O, Yulikov M, Jeschke G, Allain FHT. EPR-aided approach for solution structure determination of large RNAs or protein-RNA complexes. Nat Commun 2014; 5:3669. [PMID: 24828280 DOI: 10.1038/ncomms4669] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 03/14/2014] [Indexed: 12/18/2022] Open
Abstract
High-resolution structural information on RNA and its functionally important complexes with proteins is dramatically underrepresented compared with proteins but is urgently needed for understanding cellular processes at the molecular and atomic level. Here we present an EPR-based protocol to help solving large RNA and protein-RNA complex structures in solution by providing long-range distance constraints between rigid fragments. Using enzymatic ligation of smaller RNA fragments, large doubly spin-labelled RNAs can be obtained permitting the acquisition of long distance distributions (>80 Å) within a large protein-RNA complex. Using a simple and fast calculation in torsion angle space of the spin-label distributions with the program CYANA, we can derive simple distance constraints between the spin labels and use them together with short-range distance restraints derived from NMR to determine the structure of a 70 kDa protein-RNA complex composed of three subcomplexes.
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Affiliation(s)
- Olivier Duss
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
| | - Maxim Yulikov
- Institute for Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Gunnar Jeschke
- Institute for Physical Chemistry, ETH Zürich, Zürich 8093, Switzerland
| | - Frédéric H-T Allain
- Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich 8093, Switzerland
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35
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Esquiaqui JM, Sherman EM, Ye JD, Fanucci GE. Site-directed spin-labeling strategies and electron paramagnetic resonance spectroscopy for large riboswitches. Methods Enzymol 2014; 549:287-311. [PMID: 25432754 DOI: 10.1016/b978-0-12-801122-5.00013-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genetic regulation effected by RNA riboswitches is governed by ligand-induced structural reorganization with modulation of RNA conformation and dynamics. Characterization of the conformational states of riboswitches in the presence or absence of salts and ligands is important for understanding how interconversion of riboswitch RNA folding states influences function. The methodology of site-directed spin labeling (SDSL) coupled with electron paramagnetic resonance (EPR) spectroscopy is suitable for such studies, wherein site-specific incorporation of a nitroxide radical spin probe allows for local dynamics and conformational changes to be investigated. This chapter reviews a strategy for SDSL-EPR studies of large riboswitches and uses the full length 232 nucleotide (nt) kink-turn motif-containing Vibrio cholerae (VC) glycine riboswitch as an example. Spin-labeling strategies and the challenges of incorporating spin labels into large riboswitches are reviewed and the approach to overcome these challenges is described. Results are subsequently presented illustrating changes in dynamics within the labeled region of the VC glycine riboswitch as observed using SDSL-EPR.
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Affiliation(s)
- Jackie M Esquiaqui
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Eileen M Sherman
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA
| | - Jing-Dong Ye
- Department of Chemistry, University of Central Florida, Orlando, Florida, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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36
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Zhang X, Dantas Machado AC, Ding Y, Chen Y, Lu Y, Duan Y, Tham KW, Chen L, Rohs R, Qin PZ. Conformations of p53 response elements in solution deduced using site-directed spin labeling and Monte Carlo sampling. Nucleic Acids Res 2013; 42:2789-97. [PMID: 24293651 PMCID: PMC3936745 DOI: 10.1093/nar/gkt1219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein-DNA interactions.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA and Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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37
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Chen Y, Zhang X, Dantas Machado AC, Ding Y, Chen Z, Qin PZ, Rohs R, Chen L. Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion. Nucleic Acids Res 2013; 41:8368-76. [PMID: 23836939 PMCID: PMC3783167 DOI: 10.1093/nar/gkt584] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.
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Affiliation(s)
- Yongheng Chen
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA, Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital & State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan 410008, China, Department of Chemistry, Norris Comprehensive Cancer Center, Department of Physics and Astronomy and Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
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38
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Fedorova OS, Tsvetkov YD. Pulsed electron double resonance in structural studies of spin-labeled nucleic acids. Acta Naturae 2013; 5:9-32. [PMID: 23556128 PMCID: PMC3612823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This review deals with the application of the pulsed electron double resonance (PELDOR) method to studies of spin-labeled DNA and RNA with complicated spatial structures, such as tetramers, aptamers, riboswitches, and three- and four-way junctions. The use of this method for studying DNA damage sites is also described.
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Affiliation(s)
- O. S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk, 630090
| | - Yu. D. Tsvetkov
- Institute of Chemical Kinetics and Combustion, Siberian Branch, Russian Academy of Sciences, Institutskaya Str. 3, Novosibirsk, 630090
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39
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Zhang H, Schwartz C, De Donatis GM, Guo P. "Push through one-way valve" mechanism of viral DNA packaging. Adv Virus Res 2012; 83:415-65. [PMID: 22748815 DOI: 10.1016/b978-0-12-394438-2.00009-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Double-stranded (ds)DNA viruses package their genomic DNA into a procapsid using a force-generating nanomotor powered by ATP hydrolysis. Viral DNA packaging motors are mainly composed of the connector channel and two DNA packaging enzymes. In 1998, it was proposed that viral DNA packaging motors exercise a mechanism similar to the action of AAA+ ATPases that assemble into ring-shaped oligomers, often hexamers, with a central channel (Guo et al. Molecular Cell, 2:149). This chapter focuses on the most recent findings in the bacteriophage ϕ29 DNA packaging nanomotor to address this intriguing notion. Almost all dsDNA viruses are composed entirely of protein, but in the unique case of ϕ29, packaging RNA (pRNA) plays an intermediate role in the packaging process. Evidence revealed that DNA packaging is accomplished via a "push through one-way valve" mechanism. The ATPase gp16 pushes dsDNA through the connector channel section by section into the procapsid. The dodecameric connector channel functions as a one-way valve that only allows dsDNA to enter but not exit the procapsid during DNA packaging. Although the roles of the ATPase gp16 and the motor connector channel are separate and independent, pRNA bridges these two components to ensure the coordination of an integrated motor. ATP induces a conformational change in gp16, leading to its stronger binding to dsDNA. Furthermore, ATP hydrolysis led to the departure of dsDNA from the ATPase/dsDNA complex, an action used to push dsDNA through the connector channel. It was found unexpectedly that by mutating the basic lysine rings of the connector channel or by changing the pH did not measurably impair DNA translocation or affect the one-way traffic property of the channel, suggesting that the positive charges in the lysine ring are not essential in gearing the dsDNA. The motor channel exercises three discrete, reversible, and controllable steps of gating, with each step altering the channel size by 31% to control the direction of translocation of dsDNA. Many DNA packaging models have been contingent upon the number of base pairs packaged per ATP relative to helical turns for B-type DNA. Both 2 and 2.5 bp per ATP have been used to argue for four, five, or six discrete steps of DNA translocation. The "push through one-way valve" mechanism renews the perception of dsDNA packaging energy calculations and provides insight into the discrepancy between 2 and 2.5 bp per ATP. Application of the DNA packaging motor in nanotechnology and nanomedicine is also addressed. Comparison with nine other DNA packaging models revealed that the "push through one-way valve" is the most agreeable mechanism to interpret most of the findings that led to historical models. The application of viral DNA packaging motors is also discussed.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Department of Pharmaceutical Sciences, and Markey Cancer Center, University of Kentucky, Lexington, KY, USA
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Höbartner C, Sicoli G, Wachowius F, Gophane DB, Sigurdsson ST. Synthesis and Characterization of RNA Containing a Rigid and Nonperturbing Cytidine-Derived Spin Label. J Org Chem 2012; 77:7749-54. [DOI: 10.1021/jo301227w] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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A three-helix junction is the interface between two functional domains of prohead RNA in 29 DNA packaging. J Virol 2012; 86:11625-32. [PMID: 22896620 DOI: 10.1128/jvi.01370-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The double-stranded-DNA bacteriophages employ powerful molecular motors to translocate genomic DNA into preformed capsids during the packaging step in phage assembly. Bacillus subtilis bacteriophage 29 has an oligomeric prohead RNA (pRNA) that is an essential component of its packaging motor. The crystal structure of the pRNA-prohead binding domain suggested that a three-helix junction constitutes both a flexible region and part of a rigid RNA superhelix. Here we define the functional role of the three-helix junction in motor assembly and DNA packaging. Deletion mutagenesis showed that a U-rich region comprising two sides of the junction plays a role in the stable assembly of pRNA to the prohead. The retention of at least two bulged residues in this region was essential for pRNA binding and thereby subsequent DNA packaging. Additional deletions resulted in the loss of the ability of pRNA to multimerize in solution, consistent with the hypothesis that this region provides the flexibility required for pRNA oligomerization and prohead binding. The third side of the junction is part of a large RNA superhelix that spans the motor. The insertion of bases into this feature resulted in a loss of DNA packaging and an impairment of initiation complex assembly. Additionally, cryo-electron microscopy (cryoEM) analysis of third-side insertion mutants showed an increased flexibility of the helix that binds the ATPase, suggesting that the rigidity of the RNA superhelix is necessary for efficient motor assembly and function. These results highlight the critical role of the three-way junction in bridging the prohead binding and ATPase assembly functions of pRNA.
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Popova AM, Hatmal MM, Frushicheva M, Price EA, Qin PZ, Haworth IS. Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations. J Phys Chem B 2012; 116:6387-96. [PMID: 22574834 PMCID: PMC3382087 DOI: 10.1021/jp303303v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The behavior of the nitroxide spin labels 1-oxyl-4-bromo-2,2,5,5-tetramethylpyrroline (R5a) and 1-oxyl-2,2,5,5-tetramethylpyrroline (R5) attached at a phosphorothioate-substituted site in a DNA duplex is modulated by the DNA in a site- and stereospecific manner. A better understanding of the mechanisms of R5a/R5 sensing of the DNA microenvironment will enhance our capability to relate information from nitroxide spectra to sequence-dependent properties of DNA. Toward this goal, electron paramagnetic resonance (EPR) spectroscopy and molecular dynamics (MD) simulations were used to investigate R5 and R5a attached as R(p) and S(p) diastereomers at phosphorothioate (pS)C(7) of d(CTACTG(pS)C(7)Y(8)TTAG). d(CTAAAGCAGTAG) (Y = T or U). X-band continuous-wave EPR spectra revealed that the dT(8) to dU(8) change alters nanosecond rotational motions of R(p)-R5a but produces no detectable differences for S(p)-R5a, R(p)-R5, and S(p)-R5. MD simulations were able to qualitatively account for these spectral variations and provide a plausible physical basis for the R5/R5a behavior. The simulations also revealed a correlation between DNA backbone B(I)/B(II) conformations and R5/R5a rotational diffusion, thus suggesting a direct connection between DNA local backbone dynamics and EPR-detectable R5/R5a motion. These results advance our understanding of how a DNA microenvironment influences nitroxide motion and the observed EPR spectra. This may enable use of R5/R5a for a quantitative description of the sequence-dependent properties of large biologically relevant DNA molecules.
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Affiliation(s)
- Anna M. Popova
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ma’mon M. Hatmal
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
| | - Maria Frushicheva
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Eric A. Price
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0744
| | - Peter Z. Qin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744
| | - Ian S. Haworth
- Department of Biochemistry, University of Southern California, Los Angeles, California 90033-1039
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121
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