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Yildirim O, Barman D, Chung M, Stone S, Geißen R, Boby ML, Sherborne BS, Tan DS. Design and synthesis of a library of C8-substituted sulfamidoadenosines to probe bacterial permeability. Bioorg Med Chem Lett 2024; 110:129844. [PMID: 38851357 PMCID: PMC11361631 DOI: 10.1016/j.bmcl.2024.129844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024]
Abstract
Gram-negative bacteria pose a major challenge in antibiotic drug discovery because their cell envelope presents a permeability barrier that affords high intrinsic resistance to small-molecule drugs. The identification of correlations between chemical structure and Gram-negative permeability would thus enable development of predictive tools to facilitate antibiotic discovery. Toward this end, have advanced a library design paradigm in which various chemical scaffolds are functionalized at different regioisomeric positions using a uniform reagent set. This design enables decoupling of scaffold, regiochemistry, and substituent effects upon Gram-negative permeability of these molecules. Building upon our recent synthesis of a library of C2-substituted sulfamidoadenosines, we have now developed an efficient synthetic route to an analogous library of regioisomeric C8-substituted congeners. The C8 library samples a region of antibiotic-relevant chemical space that is similar to that addressed by the C2 library, but distinct from that sampled by a library of analogously substituted oxazolidinones. Selected molecules were tested for accumulation in Escherichia coli in a pilot analysis, setting the stage for full comparative evaluation of these libraries in the future.
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Affiliation(s)
- Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Dipti Barman
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mia Chung
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Samantha Stone
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Raphael Geißen
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Doctoral Program, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Melissa L Boby
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | | | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Pharmacology Graduate Program, Weill Cornell Graduate School, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA; Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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2
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Stachowiak K, Zabiszak M, Grajewski J, Teubert A, Bajek A, Jastrzab R. Thermodynamic Studies of Complexes in Cu(II)/Uridine-5'-Diphosphoglucuronic Acid System. Molecules 2024; 29:3695. [PMID: 39125099 PMCID: PMC11314288 DOI: 10.3390/molecules29153695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 07/28/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024] Open
Abstract
A binary system of uridine-5'-diphosphoglucuronic acid with copper (II) ions was studied. Potentiometric studies in aqueous solutions using computer data analysis were carried out. The pH of dominance, the overall stability constants (logβ), and the equilibrium constants of the formation reaction (logKe) were determined for each complex compound formed in the studied system. Spectroscopic studies were carried out to determine the mode of coordination in the compounds studied. Cytotoxicity and metabolic activity tests of the compounds obtained showed an increase in the biological activity of the complexes tested against the free ligand. The current research may contribute to the knowledge of complex compounds of biomolecules found in the human body and may also contribute to the characterization of a group of complex compounds with potential anticancer properties.
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Affiliation(s)
- Klaudia Stachowiak
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Michal Zabiszak
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Jakub Grajewski
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
| | - Anna Teubert
- Institute of Bioorganic Chemistry, Polish Academy of Science, Zygmunta Noskowskiego 12/14, 61-704 Poznan, Poland;
| | - Anna Bajek
- Faculty of Medicine, Department of Urology and Andrology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Jagiellonska 13, 85-067 Bydgoszcz, Poland;
| | - Renata Jastrzab
- Faculty of Chemistry, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland; (K.S.); (M.Z.)
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3
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Tao YH, Schulke S, Schwaab G, Nealon GL, Pezzotti S, Hodgetts SI, Harvey AR, Havenith M, Wallace VP. Hydration water drives the self-assembly of guanosine monophosphate. Biophys J 2024; 123:931-939. [PMID: 38454599 PMCID: PMC11052693 DOI: 10.1016/j.bpj.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024] Open
Abstract
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases such as cancer. We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1) absorptivity spectra of aqueous Na2 GMP solution in comparison with the aqueous solutions of other RNA nucleotides. Distinct absorption features were observed in the spectrum of GMP, which we attribute to the intramolecular modes of the self-assemblies (i.e., G-complexes) that, at 1 M, start to form at 313 K and below. Changes in broad-band features of the terahertz spectrum were also observed, which we associate with the release of hydration water in the temperature-dependent formation of guanine quadruplexes. Using a state-of-the-art THz calorimetry approach correlating spectroscopic to thermodynamic changes, we propose a molecular mechanism of hydrophilic hydration driving GMP self-assembly as a function of temperature. The free energy contribution of hydrophilic hydration is shown as a decisive factor in guanine-quadruplex formation. Our findings spotlight the role of hydration in the formation of macromolecular structures and suggest the potential of hydration tuning for regulating DNA transcription and replication.
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Affiliation(s)
- Yu Heng Tao
- Department of Physics, The University of Western Australia, Crawley, WA, Australia
| | - Simon Schulke
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Gareth L Nealon
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia; Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, WA, Australia
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Stuart I Hodgetts
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Alan R Harvey
- School of Human Sciences, The University of Western Australia, Crawley, WA, Australia; Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Vincent P Wallace
- Department of Physics, The University of Western Australia, Crawley, WA, Australia.
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Suresh PS, Kumari S, Sahal D, Sharma U. Innate functions of natural products: A promising path for the identification of novel therapeutics. Eur J Med Chem 2023; 260:115748. [PMID: 37666044 DOI: 10.1016/j.ejmech.2023.115748] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
In the course of evolution, living organisms have become well equipped with diverse natural products that serve important functions, including defence from biotic and abiotic stress, growth regulation, reproduction, metabolism, and epigenetic regulation. It seems to be the organism's ecological niche that influences the natural product's structural and functional diversity. Indeed, natural products constitute the nuts and bolts of molecular co-evolution and ecological relationships among different life forms. Since natural products in the form of specialized secondary metabolites exhibit biological functions via interactions with specific target proteins, they can provide a simultaneous glimpse of both new therapeutics and therapeutic targets in humans as well. In this review, we have discussed the innate role of natural products in the ecosystem and how this intrinsic role provides a futuristic opportunity to identify new drugs and therapeutic targets rapidly.
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Affiliation(s)
- Patil Shivprasad Suresh
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Surekha Kumari
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Dinkar Sahal
- Malaria Drug Discovery Laboratory, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Upendra Sharma
- C-H Activation & Phytochemistry Lab, Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
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5
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Derewenda ZS. C-H Groups as Donors in Hydrogen Bonds: A Historical Overview and Occurrence in Proteins and Nucleic Acids. Int J Mol Sci 2023; 24:13165. [PMID: 37685972 PMCID: PMC10488043 DOI: 10.3390/ijms241713165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Hydrogen bonds constitute a unique type of non-covalent interaction, with a critical role in biology. Until fairly recently, the canonical view held that these bonds occur between electronegative atoms, typically O and N, and that they are mostly electrostatic in nature. However, it is now understood that polarized C-H groups may also act as hydrogen bond donors in many systems, including biological macromolecules. First recognized from physical chemistry studies, C-H…X bonds were visualized with X-ray crystallography sixty years ago, although their true significance has only been recognized in the last few decades. This review traces the origins of the field and describes the occurrence and significance of the most important C-H…O bonds in proteins and nucleic acids.
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Affiliation(s)
- Zygmunt Stanislaw Derewenda
- Department of Molecular Physiology and Biological Physics, School of Medicine, University of Virginia, Charlottesville, VA 22903-2628, USA
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6
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Lv SL, Zeng C, Yu Z, Zheng JF, Wang YH, Shao Y, Zhou XS. Recent Advances in Single-Molecule Sensors Based on STM Break Junction Measurements. BIOSENSORS 2022; 12:bios12080565. [PMID: 35892462 PMCID: PMC9329744 DOI: 10.3390/bios12080565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 12/04/2022]
Abstract
Single-molecule recognition and detection with the highest resolution measurement has been one of the ultimate goals in science and engineering. Break junction techniques, originally developed to measure single-molecule conductance, recently have also been proven to have the capacity for the label-free exploration of single-molecule physics and chemistry, which paves a new way for single-molecule detection with high temporal resolution. In this review, we outline the primary advances and potential of the STM break junction technique for qualitative identification and quantitative detection at a single-molecule level. The principles of operation of these single-molecule electrical sensing mainly in three regimes, ion, environmental pH and genetic material detection, are summarized. It clearly proves that the single-molecule electrical measurements with break junction techniques show a promising perspective for designing a simple, label-free and nondestructive electrical sensor with ultrahigh sensitivity and excellent selectivity.
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Salve M, Amreen K, Pattnaik PK, Goel S. Integrated Microfluidic Device with Carbon-Thread Microelectrodes for Electrochemical DNA Elemental Analysis. IEEE Trans Nanobioscience 2021; 21:322-329. [PMID: 34673493 DOI: 10.1109/tnb.2021.3121659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Evidently, any alternation in the concentration of the essential DNA elements, adenine (A), guanine (G), cytosine (C), and thymine (T), leads to several deformities in the physiological process causing various disorders. So, to realize a simple and precise technique for simultaneous determination of the DNA elements continue to remain a challenge. Microfluidic devices offer numerous advantage, such as low volume consumption, rapid response, highly sensitive and accurate real time analysis, for point of care testing (POCT). Herein, a microfluidic electrochemical device has been developed with three electrodes fabricated using a carbon-thread microelectrode (CTME) for DNA elemental detection. CTME, functionalized with graphitize mesoporous carbon (GMC), worked as a working electrode, bare CTME functioned as an auxiliary electrode while CTME coated with Ag/AgCl ink performed as a reference electrode. The developed device was used for evaluating individual DNA elemental base pairs simultaneously using various electrochemical techniques. The anodic peak current obtained for the DNA bases were 0.56 ± 0.04 V (G), 0.92 ± 0.02 V (A), 1.09 ± 0.05 V (T) and 1.24 ± 0.04 V (C) in a potential window of 0.2 V to 1.5 V. The device was corroborated for simultaneous sensing, and detection limits were found to be 36.73 μM (G), 20 μM (A), 22 μM (T) and 19.78 μM (C) in the linear range of 50 μM - 500 μM. Finally, the device was successfully used for instantaneous determination of DNA bases in the human blood serum sample. Overall, this work demonstrates the use of a simple microfluidic device with CTMEs for electrochemical determination of DNA bases amenable for POCT.
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Wang L, Zhao H, He D, Wu Y, Jin L, Li G, Su N, Li H, Xing XH. Insights into the molecular-level effects of atmospheric and room-temperature plasma on mononucleotides and single-stranded homo- and hetero-oligonucleotides. Sci Rep 2020; 10:14298. [PMID: 32868795 PMCID: PMC7459345 DOI: 10.1038/s41598-020-71152-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/09/2020] [Indexed: 01/18/2023] Open
Abstract
Atmospheric and room-temperature plasma (ARTP) has been successfully developed as a useful mutation tool for mutation breeding of various microbes and plants as well animals by genetic alterations. However, understanding of the molecular mechanisms underlying the biological responses to ARTP irradiation is still limited. Therefore, to gain a molecular understanding of how irradiation with ARTP damages DNA, we irradiated the artificially synthesized mononucleotides of dATP, dTTP, dGTP, and dCTP, and the oligonucleotides of dA8, dT8, dG8, dC8, and dA2dT2dG2dC2 as chemical building blocks of DNA with ARTP for 1-4 min, identified the mononucleotide products using 31P- and 1H-nuclear magnetic resonance spectroscopy (NMR), and identified the oligonucleotide products using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) during ARTP treatment. The observed 31P-and 1H-NMR spectrum signals for the plasma-treated and untreated mononucleotides indicated that dATP was less stable to plasma irradiation than the other mononucleotides. The oligonucleotides after treatment with ARTP were found to have been broken into small fragments as shown by mass spectrometry, with the cleaved bonds and produced fragments identified according to their expected spectral m/z values or molecular weights derived from their m/z values. The stabilities of the oligonucleotides differed to ARTP irradiation, with dT8 being the most stable and was more beneficial to stabilizing single-stranded oligonucleotide structures compared to the other base groups (A, G, and C). This was consistent with the average potential energy level obtained by the molecular dynamic simulation of the oligonucleotides, i.e., dT8 > dC8 > dA8 > dG8 > dA2dT2dG2dC2. In summary, we found that ARTP treatment caused various structural changes to the oligonucleotides that may account for the wide and successful applications reported for ARTP-induced mutation breeding of various organisms.
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Affiliation(s)
- Liyan Wang
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
- Biobreeding Center, Wuxi Research Institute of Applied Technologies, Tsinghua University, Wuxi, 214072, People's Republic of China
- TmaxTree Biotechnology Co. Ltd., Luoyang, 471023, People's Republic of China
| | - Hongxin Zhao
- Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
| | - Dong He
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Yinan Wu
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Lihua Jin
- College of Bioengineering, Beijing Polytechnic, Beijing, 100176, People's Republic of China
| | - Guo Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Nan Su
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China
| | - Heping Li
- Department of Engineering Physics, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
| | - Xin-Hui Xing
- MOE Key Laboratory for Industrial Biocatalysis, Department of Chemical Engineering, Center for Synthetic and Systems Biology, Tsinghua University, Haidian District, Beijing, 100084, People's Republic of China.
- Center for Synthetic and System Biology, Tsinghua University, Beijing, People's Republic of China.
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, People's Republic of China.
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Byun WS, Kim WK, Yoon JS, Jarhad DB, Jeong LS, Lee SK. Antiproliferative and Antimigration Activities of Fluoro-Neplanocin A via Inhibition of Histone H3 Methylation in Triple-Negative Breast Cancer. Biomolecules 2020; 10:biom10040530. [PMID: 32244385 PMCID: PMC7226301 DOI: 10.3390/biom10040530] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/30/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is among the most aggressive and potentially metastatic malignancies. Most affected patients have poor clinical outcomes due to the lack of specific molecular targets on tumor cells. The upregulated expression of disruptor of telomeric silencing 1-like (DOT1L), a histone methyltransferase specific for the histone H3 lysine 79 residue (H3K79), is strongly correlated with TNBC cell aggressiveness. Therefore, DOT1L is considered a potential molecular target in TNBC. Fluoro-neplanocin A (F-NepA), an inhibitor of S-adenosylhomocysteine hydrolase, exhibited potent antiproliferative activity against various types of cancer cells, including breast cancers. However, the molecular mechanism underlying the anticancer activity of F-NepA in TNBC cells remains to be elucidated. We determined that F-NepA exhibited a higher growth-inhibitory activity against TNBC cells relative to non-TNBC breast cancer and normal breast epithelial cells. Moreover, F-NepA effectively downregulated the level of H3K79me2 in MDA-MB-231 TNBC cells by inhibiting DOT1L activity. F-NepA also significantly inhibited TNBC cell migration and invasion. These activities of F-NepA might be associated with the upregulation of E-cadherin and downregulation of N-cadherin and Vimentin in TNBC cells. Taken together, these data highlight F-NepA as a strong potential candidate for the targeted treatment of high-DOT1L-expressing TNBC.
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Affiliation(s)
- Woong Sub Byun
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea; (W.S.B.); (W.K.K.)
| | - Won Kyung Kim
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea; (W.S.B.); (W.K.K.)
| | - Ji-seong Yoon
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (J.-s.Y.); (D.B.J.); (L.S.J.)
| | - Dnyandev B. Jarhad
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (J.-s.Y.); (D.B.J.); (L.S.J.)
| | - Lak Shin Jeong
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (J.-s.Y.); (D.B.J.); (L.S.J.)
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute, Seoul National University, Seoul 08826, Korea; (W.S.B.); (W.K.K.)
- Correspondence: ; Tel.: +82-2-880-2475
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Graphene Oxide Nanoribbons in Chitosan for Simultaneous Electrochemical Detection of Guanine, Adenine, Thymine and Cytosine. BIOSENSORS-BASEL 2020; 10:bios10040030. [PMID: 32230779 PMCID: PMC7236021 DOI: 10.3390/bios10040030] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 12/19/2022]
Abstract
Herein, graphene oxide nanoribbons (GONRs) were obtained from the oxidative unzipping of multi-walled carbon nanotubes. Covalent coupling reaction of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC) and N-hydroxy succinimide (NHS) with amine functional groups (-NH2) of the chitosan natural polymer (CH) was used for entrapping GONRs on the activated glassy carbon electrode (GCE/GONRs-CH). The nanocomposite was characterized by high-resolution transmission electron microscopy (HRTEM), and field-emission scanning electron microscopy (FESEM). In addition, the modification steps were monitored using FTIR. The nanocomposite-modified electrode was used for the simultaneous electrochemical determination of four DNA bases; guanine (G), adenine (A), thymine (T) and cytosine (C). The nanocomposite-modified GCE displayed a strong, stable and continuous four oxidation peaks during electrochemistry detection at potentials 0.63, 0.89, 1.13 and 1.27 V for G, A, T and C, respectively. The calibration curves were linear up to 256, 172, 855 and 342 μM with detection limits of 0.002, 0.023, 1.330 and 0.641 μM for G, A, T and C, respectively. The analytical performance of the GCE/GONRs-CH has been used for the determination of G, A, T and C in real samples and obtained a recovery percentage from 91.1%-104.7%. Our preliminary results demonstrated that GCE/GONRs-CH provided a promising platform to detect all four DNA bases for future studies on DNA damage and mutations.
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Banuelos-Sanchez G, Franco-Montalban F, Tamayo JA. NMR studies of pyrimidinic nucleosides derived from 2,3-dideoxy-d-ribose with inhibitory activity on LINE-1 mobility. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:118-125. [PMID: 31691341 DOI: 10.1002/mrc.4942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Guillermo Banuelos-Sanchez
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Francisco Franco-Montalban
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Juan A Tamayo
- Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
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12
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Hosseini M, Roy P, Sissler M, Zirbel CL, Westhof E, Leontis N. How to fold and protect mitochondrial ribosomal RNA with fewer guanines. Nucleic Acids Res 2019; 46:10946-10968. [PMID: 30215760 PMCID: PMC6237812 DOI: 10.1093/nar/gky762] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/06/2018] [Indexed: 01/25/2023] Open
Abstract
Mammalian mitochondrial ribosomes evolved from bacterial ribosomes by reduction of ribosomal RNAs, increase of ribosomal protein content, and loss of guanine nucleotides. Guanine is the base most sensitive to oxidative damage. By systematically comparing high-quality, small ribosomal subunit RNA sequence alignments and solved 3D ribosome structures from mammalian mitochondria and bacteria, we deduce rules for folding a complex RNA with the remaining guanines shielded from solvent. Almost all conserved guanines in both bacterial and mammalian mitochondrial ribosomal RNA form guanine-specific, local or long-range, RNA–RNA or RNA–protein interactions. Many solvent-exposed guanines conserved in bacteria are replaced in mammalian mitochondria by bases less sensitive to oxidation. New guanines, conserved only in the mitochondrial alignment, are strategically positioned at solvent inaccessible sites to stabilize the ribosomal RNA structure. New mitochondrial proteins substitute for truncated RNA helices, maintain mutual spatial orientations of helices, compensate for lost RNA–RNA interactions, reduce solvent accessibility of bases, and replace guanines conserved in bacteria by forming specific amino acid–RNA interactions.
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Affiliation(s)
- Maryam Hosseini
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Poorna Roy
- Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Marie Sissler
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Craig L Zirbel
- Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg France
| | - Neocles Leontis
- Department of Chemistry, Bowling Green State University, Bowling Green, OH 43403, USA
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Liao R, Yang P, Wu W, Luo D, Yang D. A DNA Tracer System for Hydrological Environment Investigations. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1695-1703. [PMID: 29361228 DOI: 10.1021/acs.est.7b02928] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To monitor and manage hydrological pollution effectively, tracing sources of pollutants is of great importance and also is in urgent need. A variety of tracers have been developed such as isotopes, silica, bromide, and dyes; however, practical limitations of these traditional tracers still exist such as lack of multiplexed, multipoint tracing and interference of background noise. To overcome these limitations, a new tracing system based on DNA nanomaterials, namely DNA tracer, has already been developed. DNA tracers possess remarkable advantages including sufficient species, specificity, environmental friendly, stable migration, and high sensitivity as well as allowing for multipoints tracing. In this review article, we introduce the molecular design, synthesis, protection and signal readout strategies of DNA tracers, compare the advantages and disadvantages of DNA tracer with traditional tracers, and summarize the-state-of-art applications in hydrological environment investigations. In the end, we provide our perspective on the future development of DNA tracers.
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Affiliation(s)
- Renkuan Liao
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research , Beijing 100048, P. R. China
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072, P. R. China
| | - Peiling Yang
- College of Water Conservancy and Civil Engineering, China Agricultural University , Beijing 100083, P. R. China
| | - Wenyong Wu
- State Key Laboratory of Simulation and Regulation of Water Cycles in River Basins, China Institute of Water Resources and Hydropower Research , Beijing 100048, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University , Ithaca, New York 14853, United States
- Kavli Institute at Cornell for Nanoscale Science, Cornell University , Ithaca, New York 14853, United States
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences , Suzhou 215123, P.R. China
| | - Dayong Yang
- School of Chemical Engineering and Technology, Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University , Tianjin 300072, P. R. China
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Sato H, Wada T, Inoue Y. Synthesis and Conformation Control of Peptide Ribonucleic Acid (PRNA) Containing 5′-Amino-5′-deoxyribopyrimidine and 5′-Amino-5′-deoxyribopurinenucleosides. J BIOACT COMPAT POL 2016. [DOI: 10.1177/0883911504042640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel nucleic acid model, a peptide ribonucleic acid (PRNA) tethering 5′-amino-5′-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, was designed and synthesized. It was demonstrated that the recognition behavior of PRNA could be controlled externally through switching the orientation of the pyrimidine nucleobase of PRNA induced by added borates. We extended this methodology of controlling the nucleobase orientation and recognition behavior of novel mono- and oligomeric PRNAs containing not only 5′-amino-5′-deoxypyrimidinenucleosides but also 5′-amino-5′-deoxypurinenucleosides. In the case of PRNA oligomer containing pyrimidine-purine mixed sequence, efficient orientation switching of nucleobases induced by added borates was also observed.
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Affiliation(s)
- Hirofumi Sato
- Department of Molecular Chemistry Osaka University 2-1 Yamada-oka, Suita 565-0871, Japan
| | - Takehiko Wada
- Department of Molecular Chemistry Osaka University 2-1 Yamada-oka, Suita 565-0871, Japan, Presto, Jst
| | - Yoshihisa Inoue
- Department of Molecular Chemistry Osaka University 2-1 Yamada-oka, Suita 565-0871, Japan, Entropy Control Project ICORP, JST, 4-6-3 Kamishinden Toyonaka 565-0085, Japan
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Che X, Zhang J, Zhu Y, Yang L, Quan H, Gao YQ. Structural Flexibility and Conformation Features of Cyclic Dinucleotides in Aqueous Solutions. J Phys Chem B 2016; 120:2670-80. [PMID: 26878265 DOI: 10.1021/acs.jpcb.5b11531] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cyclic dinucleotides are able to trigger the innate immune system by activating STING. It was found that the binding affinity of asymmetric 2'3'-cGAMP to symmetric dimer of STING is 3 orders of magnitude higher than that of the symmetric 3'3'-cyclic dinucleotides. Such a phenomenon has not been understood yet. Here we show that the subtle changes in phosphodiester linkage of CDNs lead to their distinct structural properties which correspond to the varied binding affinities. 2'-5' and/or 3'-5' linked CDNs adopt specific while different types of ribose puckers and backbone conformations. That ribose conformations and base types have different propensities for anti or syn glycosidic conformations further affects the overall flexibility of CDNs. The counterbalance between backbone ring tension and electrostatic repulsion, both affected by the ring size, also contributes to the different flexibility of CDNs. Our calculations reveal that the free energy cost for 2'3'-cGAMP to adopt the STING-bound structure is smaller than that for 3'3'-cGAMP and cyclic-di-GMP. These findings may serve as a reference for design of CDN-analogues as vaccine adjuvants. Moreover, the cyclization pattern of CDNs closely related to their physiological roles suggests the importance of understanding structural properties in the study of protein-ligand interactions.
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Affiliation(s)
- Xing Che
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Jun Zhang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Yanyu Zhu
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Lijiang Yang
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Hui Quan
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, and Biodynamic Optical Imaging Center, Peking University , Beijing 100871, China
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16
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Arteta MY, Berti D, Montis C, Campbell RA, Eriksson C, Clifton LA, Skoda MWA, Soltwedel O, Koutsioubas A, Baglioni P, Nylander T. On the formation of dendrimer/nucleolipids surface films for directed self-assembly. SOFT MATTER 2015; 11:1973-1990. [PMID: 25626114 DOI: 10.1039/c4sm02712d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe the formation and structure of nucleolipid/dendrimer multilayer films controlled by non-covalent interactions to obtain biomaterials that exhibit molecular recognition of nucleic acids. Layers of cationic poly(amidoamine) (PAMAM) dendrimers of generation 4 and the anionic nucleolipids 1,2-dilauroyl-sn-glycero-3-phosphatidylnucleosides (DLPNs) based on uridine (DLPU) and adenosine (DLPA) were first formed at the silica-water interface. The PAMAM/DLPN layers were then exposed to short oligonucleotides, polynucleotides and single stranded DNA (ssDNA). The interfacial properties were characterized using quartz crystal microbalance with dissipation monitoring, attenuated total reflection Fourier transform infrared spectroscopy and neutron reflectometry. Both types of DLPN were found to adsorb as aggregates to preadsorbed PAMAM monolayers with a similar interfacial structure and composition before rinsing with pure aqueous solution. Nucleic acids were found to interact with PAMAM/DLPA layers due to base pairing interactions, while the PAMAM/DLPU layers did not have the same capability. This was attributed to the structure of the DLPA layer, which is formed by aggregates that extend from the interface towards the bulk after rinsing with pure solvent, while the DLPU layer forms compact structures. In complementary experiments using a different protocol, premixed PAMAM/DLPN samples adsorbed to hydrophilic silica only when the mixtures contained positively charged aggregates, which is rationalized in terms of electrostatic forces. The PAMAM/DLPA layers formed from the adsorption of these mixtures also bind ssDNA although in this case the adsorption is mediated by the opposite charges of the film and the nucleic acid rather than specific base pairing. The observed molecular recognition of nucleic acids by dendrimers functionalized via non-covalent interactions with nucleolipids is discussed in terms of biomedical applications such as gene vectors and biosensors.
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Affiliation(s)
- Marianna Yanez Arteta
- Physical Chemistry, Department of Chemistry, Lund University, P. O. Box 124, S-221 00 Lund, Sweden.
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Nayak A, Sahu PK, Song J, Lee SK, Jeong LS. Regio- and stereoselective synthesis of 2′-β-substituted-fluoroneplanocin A analogues as potential anticancer agents. Org Biomol Chem 2015. [DOI: 10.1039/c5ob01348h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Regio- and stereoselective synthesis of a series of 2′-β-substituted-6′-fluoro-cyclopentenyl-pyrimidines and -purines 8 and 9 as potential anticancer agents is described.
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Affiliation(s)
- Akshata Nayak
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Pramod K. Sahu
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Jayoung Song
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Sang Kook Lee
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
| | - Lak Shin Jeong
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 151-742
- Korea
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Achrainer F, Emel'yanenko VN, Tantawy W, Verevkin SP, Zipse H. Transfer hydrogenation as a redox process in nucleotides. J Phys Chem B 2014; 118:10426-9. [PMID: 25111787 DOI: 10.1021/jp507855k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a combined theoretical and experimental strategy, the heats of hydrogenation of the nucleotide bases uracil, thymine, cytosine, adenine, and guanine have been determined. The most easily hydrogenated base is uracil, followed by thymine and cytosine. Comparison of these hydrogenation enthalpies with those of ketones and aldehydes derived from sugar models indicates the possibility of near-thermoneutral hydrogen transfer between uracil and the sugar phosphate backbone in oligonucleotides.
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Affiliation(s)
- Florian Achrainer
- Department of Chemistry, LMU München , Butenandtstrasse 5-13, D-81377 München, Germany
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19
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Groves P, Strzelecka-Kiliszek A, Sekrecka-Belniak A, Canales A, Jiménez-Barbero J, Bandorowicz-Pikula J, Pikula S, Cañada FJ. Exploring NMR methods as a tool to select suitable fluorescent nucleotide analogues. Org Biomol Chem 2014; 11:5332-8. [PMID: 23842795 DOI: 10.1039/c3ob40159f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Fluorescent analogues provide important tools for biochemical/biophysical research. However, the analogues contain chemical modifications much larger than those known to affect ligand-binding, such as the inversion of a carbon centre or substitution of an atom. We lack experimental tools and protocols to select the most appropriate fluorescent analogue. Herein, we use several NMR spectroscopy methods, including Saturation Transfer Difference (STD), STD competition and transferred nuclear Overhauser effect spectroscopy (Tr-NOESY), as tools to select appropriate fluorescent probes. Annexin A6 (AnxA6) is a ubiquitous protein that forms in vitro GTP-induced ion channels. We used this protein as a model and screened guanosine triphosphate (GTP) and four fluorescent analogues against AnxA6. STD reported that the GTP moiety of all ligands made similar contacts with the protein, despite additional interactions between the fluorescent tags and AnxA6. Competition STD experiments verified that the analogues and GTP bind to the same site. Tr-NOESY indicated that the bound conformation of the base relative to ribose is altered for some analogues compared to GTP. MANT-GTP or the BODIPY thioester of guanosine 5'-O-(3-thiotriphosphate) are the most suitable fluorescent analogues for AnxA6, according to NMR. These results reveal NMR as a useful technique to select and design proper fluorescent tags for biochemical/biophysical assays.
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Affiliation(s)
- Patrick Groves
- Chemical Biology Division, Instituto de Tecnologia Química e Biológica (ITQB-UNL), Oeiras, Portugal.
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20
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De Leeuw HPM, Haasnoot CAG, Altona C. Empirical Correlations Between Conformational Parameters in β-D-Furanoside Fragments Derived from a Statistical Survey of Crystal Structures of Nucleic Acid Constituents Full Description of Nucleoside Molecular Geometries in Terms of Four Parameters. Isr J Chem 2013. [DOI: 10.1002/ijch.198000059] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shigdar S, Macdonald J, O'Connor M, Wang T, Xiang D, Al.Shamaileh H, Qiao L, Wei M, Zhou SF, Zhu Y, Kong L, Bhattacharya S, Li C, Duan W. Aptamers as theranostic agents: modifications, serum stability and functionalisation. SENSORS 2013; 13:13624-37. [PMID: 24152925 PMCID: PMC3859083 DOI: 10.3390/s131013624] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 02/07/2023]
Abstract
Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selection procedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents.
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Affiliation(s)
- Sarah Shigdar
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
| | - Joanna Macdonald
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Michael O'Connor
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Tao Wang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Dongxi Xiang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Hadi Al.Shamaileh
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Liang Qiao
- Storr Liver Unit, at the Westmead Millennium Institute, The University of Sydney at the Westmead Hospital, Westmead NSW 2145, Australia; E-Mail:
| | - Ming Wei
- School of Medical Science and Griffith Health Institute, Griffith University, Gold Coast Campus, Southport 4222, Australia; E-Mail:
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA; E-Mail:
| | - Yimin Zhu
- Suzhou Key Laboratory of Nanobiomedicine, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China; E-Mail:
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria 3217, Australia; E-Mail:
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India; E-Mail:
| | - ChunGuang Li
- Centre for Complimentary Medicine Research, National Institute of Complementary Medicine, University of Western Sydney, Campbelltown Campus, Penrith, NSW 2751, Australia; E-Mail:
| | - Wei Duan
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
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22
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Luschtinetz R, Gemming S, Seifert G. Theoretical study on the CH⋯NC hydrogen bond interaction in thiophene-based molecules. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Stegemann B, Klebe G. Cofactor-binding sites in proteins of deviating sequence: comparative analysis and clustering in torsion angle, cavity, and fold space. Proteins 2011; 80:626-48. [PMID: 22095739 DOI: 10.1002/prot.23226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/29/2011] [Accepted: 10/10/2011] [Indexed: 12/13/2022]
Abstract
Small molecules are recognized in protein-binding pockets through surface-exposed physicochemical properties. To optimize binding, they have to adopt a conformation corresponding to a local energy minimum within the formed protein-ligand complex. However, their conformational flexibility makes them competent to bind not only to homologous proteins of the same family but also to proteins of remote similarity with respect to the shape of the binding pockets and folding pattern. Considering drug action, such observations can give rise to unexpected and undesired cross reactivity. In this study, datasets of six different cofactors (ADP, ATP, NAD(P)(H), FAD, and acetyl CoA, sharing an adenosine diphosphate moiety as common substructure), observed in multiple crystal structures of protein-cofactor complexes exhibiting sequence identity below 25%, have been analyzed for the conformational properties of the bound ligands, the distribution of physicochemical properties in the accommodating protein-binding pockets, and the local folding patterns next to the cofactor-binding site. State-of-the-art clustering techniques have been applied to group the different protein-cofactor complexes in the different spaces. Interestingly, clustering in cavity (Cavbase) and fold space (DALI) reveals virtually the same data structuring. Remarkable relationships can be found among the different spaces. They provide information on how conformations are conserved across the host proteins and which distinct local cavity and fold motifs recognize the different portions of the cofactors. In those cases, where different cofactors are found to be accommodated in a similar fashion to the same fold motifs, only a commonly shared substructure of the cofactors is used for the recognition process.
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Affiliation(s)
- Björn Stegemann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
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Beingessner RL, Diaz JA, Hemraz UD, Fenniri H. Synthesis of a β-glycoside functionalized GΛC motif for self-assembly into rosette nanotubes with predefined length. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2010.11.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Sinkeldam RW, Wheat AJ, Boyaci H, Tor Y. Emissive nucleosides as molecular rotors. Chemphyschem 2010; 12:567-70. [PMID: 21344595 DOI: 10.1002/cphc.201001002] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Renatus W Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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Tsuchiya H, Uchiyama M, Hara K, Nakatsu Y, Tsuzuki T, Inoue H, Harashima H, Kamiya H. Improved gene correction efficiency with a tailed duplex DNA fragment. Biochemistry 2008; 47:8754-9. [PMID: 18642931 DOI: 10.1021/bi800588k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A 606-base single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, corrects a hygromycin resistance and enhanced green fluorescent protein (Hyg-EGFP) fusion gene more efficiently than a PCR fragment, which is the conventional type of DNA fragment used in gene correction. Here, a tailed duplex, obtained by annealing an oligonucleotide to the ss DNA fragment, was used in the correction. The tailed duplex may be a good substrate for the RAD51 protein, an important enzyme in homologous recombination, which could be the gene correction pathway. The annealing of the oligonucleotides enhanced the correction efficiency of the Hyg-EGFP gene, especially when annealed in the 3'-region of the ss DNA fragment. Both the length and backbone structure of the oligonucleotides affected the gene correction efficiency. This type of gene correction device was also effective for another target gene, the rpsL gene. The results obtained in this study indicate that tailed duplex DNA fragments are effective nucleic acids for gene correction.
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Affiliation(s)
- Hiroyuki Tsuchiya
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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IUPAC-IUB joint commission on biochemical nomenclature abbreviations and symbols for the description of conformations of polynucleotide chains. ACTA ACUST UNITED AC 2008; Appendix 1:Appendix 1C. [PMID: 18428807 DOI: 10.1002/0471142700.nca01cs00] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This appendix presents nomenclature rules that are as close as possible to the originally published version and are reproduced here with permission from the European Journal of Biochemistry. A web-based version prepared by G.P. Moss is also available.
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Baldelli Bombelli F, Berti D, Milani S, Lagi M, Barbaro P, Karlsson G, Brandt A, Baglioni P. Collective headgroup conformational transition in twisted micellar superstructures. SOFT MATTER 2008; 4:1102-1113. [PMID: 32907145 DOI: 10.1039/b800210j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Predictions on amphiphilic self-assemblies traditionally rely on considerations on molecular shape and charge of the surfactant. In the case of functional surfactants a more sophisticated toolbox becomes necessary to design amphiphiles encoding chemical functionalities that provide additional responsive properties to their self-assemblies. Here we report on a comprehensive and combined structural-spectroscopic characterization of 1,2-dilauroyl-phosphatidyl-adenosine (DLPA) micelles in phosphate buffer. The temperature dependence, more precisely the thermal history of the sample, is explicitly taken into account. The experimental data, supplemented with MD simulations, indicate the presence of two possible states at room temperature, characterized by distinctly different structural properties that depend on the thermal history of the sample. The twisted superstructures, produced by aging DLPA micelles through intermicellar assembly of locally cylindrical aggregates at room temperature, collapse upon warming at 35 °C, yielding aligned filaments and/or wormlike structures. The initial superstructures cannot be recovered by thermal inversion. The reason for this behaviour is that the thermal activation causes a redistribution of syn-anti conformations of adenosine headgroups, as indicated by spectroscopic results (NMR, CD, FTIR), which is then collectively frozen thanks to molecular constraints present in the aggregate.
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Affiliation(s)
| | - Debora Berti
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence, Italy.
| | - Silvia Milani
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence, Italy.
| | - Marco Lagi
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence, Italy.
| | | | - Göran Karlsson
- Department of Physical and Analytical Chemistry, Uppsala University, Sweden
| | | | - Piero Baglioni
- Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, Florence, Italy.
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31
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Anbarasu A, Anand S, Rao S. Investigations on unconventional hydrogen bonds in RNA binding proteins: The role of CH⋯OC interactions. Biosystems 2007; 90:792-801. [PMID: 17555865 DOI: 10.1016/j.biosystems.2007.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 04/16/2007] [Accepted: 04/18/2007] [Indexed: 11/16/2022]
Abstract
We have investigated the roles played by C-H...O=C interactions in RNA binding proteins. There was an average of 78 CH...O=C interactions per protein and also there was an average of one significant CH...O=C interactions for every 6 residues in the 59 RNA binding proteins studied. Main chain-Main chain (MM) CH...O=C interactions are the predominant type of interactions in RNA binding proteins. The donor atom contribution to CH...O=C interactions was mainly from aliphatic residues. The acceptor atom contribution for MM CH...O=C interactions was mainly from Val, Phe, Leu, Ile, Arg and Ala. The secondary structure preference analysis of CH...O=C interacting residues showed that, Arg, Gln, Glu and Tyr preferred to be in helix, while Ala, Asp, Cys, Gly, Ile, Leu, Lys, Met, Phe, Trp and Val preferred to be in strand conformation. Most of the CH...O=C interacting polar amino acid residues were solvent exposed while, majority of the CH...O=C interacting non polar residues were excluded from the solvent. Long and medium-range CH...O=C interactions are the predominant type of interactions in RNA binding proteins. More than 50% of CH...O=C interacting residues had a higher conservation score. Significant percentage of CH...O=C interacting residues had one or more stabilization centers. Sixty-six percent of the theoretically predicted stabilizing residues were also involved in CH...O=C interactions and hence these residues may also contribute additional stability to RNA binding proteins.
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Affiliation(s)
- Anand Anbarasu
- School of Bio-Technology, Chemical and Bio-Medical Engineering, VIT University, Vellore 632014, India
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Foloppe N, Nilsson L. Toward a full characterization of nucleic acid components in aqueous solution: simulations of nucleosides. J Phys Chem B 2007; 109:9119-31. [PMID: 16852085 DOI: 10.1021/jp044513u] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The eight nucleoside constituents of nucleic acids were simulated for 50 ns in explicit water with molecular dynamics. This provides equilibrium populations of the torsional degrees of freedom, their kinetics of interconversion, their couplings, and how they are influenced by water. This is important, given that a full and quantitative characterization of the nucleosides in aqueous solution by experimental means has been elusive, despite immense efforts in that direction. It is with the anti/syn equilibrium that the simulations are most complementary to experiment, by accessing directly the influence of the sugar type, sugar pucker, and base on the anti/syn populations. The glycosidic torsion distributions in the anti conformation are strongly affected by water and depart from the corresponding X-ray modal values and the associated energy minima in vacuo. Water also preferentially stabilizes some sugar conformations, showing that potential energies in vacuo are not sufficient to understand the nucleosides. Deoxythymidine (but not other pyrimidines) significantly populates the syn orientation. Guanine favors the syn orientation more than adenine. The ribose favors the syn orientation significantly more than the deoxyribose. The NORTH pucker coexists with the syn conformers. A hydrogen bond is frequently formed between the 5'-OH group and the syn bases, despite competition by water. The rate of the anti/syn transitions with purines is on the nanosecond time scale, confirming a long held assumption underpinning the interpretation of ultrasonic relaxation studies. Therefore, our knowledge of the structure and dynamics of nucleosides in solvent is only limited by the accuracy of the potential used to simulate them, and it is shown that such simulations provide a distinct and unique test of nucleic acid force fields. This confirmed that the widely distributed CHARMM27 force field is, overall, well-balanced with a particularly good representation of the ribose. Specific improvements, however, are suggested for the deoxyribose and torsion gamma.
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Affiliation(s)
- Nicolas Foloppe
- Center for Structural Biochemistry, Department of Biosciences, Karolinska Institutet, S-141 57 Huddinge, Sweden
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Bombelli FB, Berti D, Almgren M, Karlsson G, Baglioni P. Light Scattering and Cryo-Transmission Electron Microscopy Investigation of the Self-Assembling Behavior of Di-C12P-Nucleosides in Solution. J Phys Chem B 2006; 110:17627-37. [PMID: 16942108 DOI: 10.1021/jp060594d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aggregates formed from freshly prepared and annealed samples of dilauroyl-phosphatidyl-adenosine, dilauroyl-phosphatidyl-uridine, and their 1:1 mixture have been investigated by dynamic light scattering, cryo-transmission electron microscopy (cryo-TEM) observations, and circular dichroism. The two surfactants differ only for the nucleoside at the phospholipid polar headgroup and self-assemble in solution to form supramolecular structures that behave dissimilarly. The uridine derivative forms long wormlike aggregates that are invariant with the aging of the solution, while the wormlike aggregate of the adenosine derivative undergoes, as the sample ages, a subsequent self-assembling process forming giant helicoidal aggregates that coexist with the smaller wormlike aggregates. Dynamic light scattering and cryo-TEM show that the large helicoidal structures are formed at the expense of the small wormlike micelles. The 1:1 mixture behaves as the adenosine derivative and evolves to form giant superstructures for all the lipid concentrations investigated. Circular dichroism measurements suggest that the formation of the supramolecular helicoidal structure might not be driven by a purely chiral effect, but rather stacking and hydrogen bonding, present at the phospholipid headgroups of the self-assembled nucleosides, contribute to the final supramolecular structure.
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Schlimme E, Boos KS, Bojanovski D, Lüstorff J. Untersuchungen der mitochondrialen Adeninnucleotid-Translokation mit Nucleotidanaloga. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.19770891007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Monajjemi M, Sajadi MS, Sayadia R, Kia M, Ghasemi G. Structural Studies and Investigation of NMR Shielding Tensors in Coordination Of Magnesium Hydrate to Purine Nucleotide 5'-Monophosphates (AMP, GMP,IMP). MAIN GROUP METAL CHEMISTRY 2005. [DOI: 10.1515/mgmc.2005.28.2.71] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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36
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Wada T, Sato H, Inoue Y. External reversible control of recognition behavior of alpha-peptide ribonucleic acid (alpha-PRNA) through anti-syn orientational switching of the nucleobase induced by borate esterification of the cis-2',3'-diol. Biopolymers 2004; 76:15-20. [PMID: 14997470 DOI: 10.1002/bip.10563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A novel nucleic acid model using peptide ribonucleic acid (PRNA), which contains 5'-amino-5'-deoxypyrimidine ribonucleoside as a recognition site for nucleic acids, has been designed, synthesized and applied to the external reversible control of recognition behavior of the complementary polynucleotide through the orientational switching of the nucleobase induced by borate.
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37
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Lin W, Li K, Moore BM, Doughty MB. Conformational properties of nucleotide-based template-competitive HIV-1 reverse transcriptase inhibitors: analysis of enzyme binding modes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2003; 22:283-97. [PMID: 12816387 DOI: 10.1081/ncn-120021428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Nucleotides 2-(4-azidophenacyl)thio-1,N6-etheno-2'-deoxyadenosine 5'-triphosphate 1 and its tetrafluoro analog 2 inhibit HIV-1 reverse transcriptase (RT) competitively relative to template. These template-competitive RT inhibitors (TCRTIs) were analyzed for conformational properties by molecular modeling and NMR analysis. Both inhibitors prefer sugar conformations of C2'-endo/C3'-exo with a high-anti glycosidic bond rotation and +sc/ap phosphate conformation (gamma). The major effect of the etheno group is to favor an extended, fully staggered anti conformation in the N1-C2-S-CH2 psi1 side chain rotation, and NMR analysis detects a long range sugar H4' to side chain phenyl meta-H NOE, a result consistent with this compact structure as an important contributor to the solution structure. The binding model generated places the phenyl side chain in a lipophilic pocket in the template grip region of the RT polymerase domain with the Mg-triphosphate complexed to active site carboxylates. The structures of the TCRTIs are compared with that of the template-competitive DNA polymerase inhibitor 2-(4-azidophenacyl)thio-2'-deoxyadenosine 5'-triphosphate 3, and a theoretical model for selectivity is proposed.
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Affiliation(s)
- Weiying Lin
- Department of Chemistry and Physics, Southeastern Louisiana University, Hammond, Louisiana 70402, USA
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38
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Shi Z, Olson CA, Bell AJ, Kallenbach NR. Non-classical helix-stabilizing interactions: C-H...O H-bonding between Phe and Glu side chains in alpha-helical peptides. Biophys Chem 2002; 101-102:267-79. [PMID: 12488007 DOI: 10.1016/s0301-4622(02)00171-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The classical picture of H-bonds has evolved considerably. In contrast to earlier expectations, C-H...O H-bonds are now known to be prevalent in both small organic and large biological systems. However, there are few reports on the energetic contribution of C-H...O H-bonds in protein or polypeptide systems and we do not know whether such interactions are stabilizing. Here we investigate C-H...O H-bonding interactions between Phe and Glu side chains by determining their effects on the helicity of model alpha-helical peptides using a combination of CD and NMR spectroscopy. The results suggest that Glu/Phe C-H...O H-bonding interactions stabilize helical structure, but only in the orientation Glu --> Phe (N --> C). Each Glu --> Phe (N --> C) interaction can contribute approximately -0.5 kcal mol(-1) to the stability of helical peptide. In the reverse orientation, Phe --> Glu (N --> C) appears to contribute negligibly. pH titrations provide further evidence for the existence of C-H...O H-bonds. The C-H...O H-bonding interactions in these peptides are insensitive to the screening effect of added neutral salt. Our results provide quantitative energetic information on C-H...O H-bonds that should be useful for empirical force-field calibration.
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Affiliation(s)
- Zhengshuang Shi
- Department of Chemistry, New York University, New York, NY 10003, USA
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Wu N, Pai EF. Crystal structures of inhibitor complexes reveal an alternate binding mode in orotidine-5'-monophosphate decarboxylase. J Biol Chem 2002; 277:28080-7. [PMID: 12011084 DOI: 10.1074/jbc.m202362200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structures of the enzyme orotidine-5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with its product UMP and the inhibitors 6-hydroxyuridine 5'-phosphate (BMP), XMP, and CMP are reported. A mutant version of the protein, in which four residues of the flexible phosphate-binding loop (180)Gly-Gly(190) were removed and Arg(203) was replaced by alanine, was also analyzed. The XMP and CMP complexes reveal a ligand-binding mode that is distinct from the one identified previously with the aromatic rings located outside the binding pocket. A potential pathway for ligand binding is discussed.
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Affiliation(s)
- Ning Wu
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
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Fischer BE, Bau R. Coordination sites in nucleotides: x-ray crystal structure of the ternary complex copper(II)-uridine 5'-monophosphate-2,2'-dipyridylamine. Inorg Chem 2002. [DOI: 10.1021/ic50179a007] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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41
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Binding of nucleobases to a dizinc macrocyclic complex. Supramolecular assembling of dinuclear clusters through N–H⋯O and C–H⋯O hydrogen bonding. Inorganica Chim Acta 2001. [DOI: 10.1016/s0020-1693(01)00327-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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42
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Abstract
Although the peptide C(alpha)H group has historically not been thought to form hydrogen bonds within proteins, ab initio quantum calculations show it to be a potent proton donor. Its binding energy to a water molecule lies in the range between 1.9 and 2.5 kcal/mol for nonpolar and polar amino acids; the hydrogen bond (H-bond) involving the charged lysine residue is even stronger than a conventional OH..O interaction. The preferred H-bond lengths are quite uniform, about 3.32 A. Formation of each interaction results in a downfield shift of the bridging hydrogen's chemical shift and a blue shift in the C(alpha)H stretching frequency, potential diagnostics of the presence of such an H-bond within a protein.
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Affiliation(s)
- S Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan 84322-0300, USA.
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43
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Metzler DE, Metzler CM, Sauke DJ. The Nucleic Acids. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Wada T, Minamimoto N, Inaki Y, Inoue Y. Peptide Ribonucleic Acids (PRNA). 2. A Novel Strategy for Active Control of DNA Recognition through Borate Ester Formation. J Am Chem Soc 2000. [DOI: 10.1021/ja9935456] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takehiko Wada
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Narutoshi Minamimoto
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Yoshiaki Inaki
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
| | - Yoshihisa Inoue
- Contribution from the Department of Molecular Chemistry and Department of Material and Life Science, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan and Inoue Photochirogenesis Project, ERATO, JST, 4-6-3 Kamishinden, Toyonaka 565-0085, Japan
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45
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Kingston RL, Scopes RK, Baker EN. The structure of glucose-fructose oxidoreductase from Zymomonas mobilis: an osmoprotective periplasmic enzyme containing non-dissociable NADP. Structure 1996; 4:1413-28. [PMID: 8994968 DOI: 10.1016/s0969-2126(96)00149-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
BACKGROUND The organism Zymomonas mobilis occurs naturally in sugar-rich environments. To protect the bacterium against osmotic shock, the periplasmic enzyme glucose-fructose oxidoreductase (GFOR) produces the compatible, solute sorbitol by reduction of fructose, coupled with the oxidation of glucose to gluconolactone. Hence, Z mobilis can tolerate high concentrations of sugars and this property may be useful in the development of an efficient microbial process for ethanol production. Each enzyme subunit contains tightly associated NADP which is not released during the catalytic cycle. RESULTS The structure of GFOR was determined by X-ray crystallography at 2.7 A resolution. Each subunit of the tetrameric enzyme comprises two domains, a classical dinucleotide-binding domain, and a C-terminal domain based on a predominantly antiparallel nine-stranded beta sheet. In the tetramer, the subunits associate to form two extended 18-stranded beta sheets, which pack against each other in a face to face fashion, creating an extensive interface at the core of the tetramer. An N-terminal arm from each subunit wraps around the dinucleotide-binding domain of an adjacent subunit, covering the adenine ring of NADP. CONCLUSIONS In GFOR, the NADP is found associated with a classical dinucleotide-binding domain in a conventional fashion. The NADP is effectively buried in the protein-subunit interior as a result of interactions with the N-terminal arm from an adjacent subunit in the tetramer, and with a short helix from the C-terminal domain of the protein. This accounts for NADP's inability to dissociate. The N-terminal arm may also contribute to stabilization of the tetramer. The enzyme has an unexpected structural similarity with the cytoplasmic enzyme glucose-6-phosphate dehydrogenase (G6PD). We hypothesize that both enzymes have diverged from a common ancestor. The mechanism of catalysis is still unclear, but we have identified a conserved structural motif (Glu-Lys-Pro) in the active site of GFOR and G6PD that may be important for catalysis.
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Affiliation(s)
- R L Kingston
- Department of Biochemistry, Massey University, Palmerston North, New Zealand
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46
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Böhm HJ, Klebe G. Was läßt sich aus der molekularen Erkennung in Protein-Ligand-Komplexen für das Design neuer Wirkstoffe lernen? Angew Chem Int Ed Engl 1996. [DOI: 10.1002/ange.19961082205] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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47
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Elia GR, Childs RF, Britten JF, Yang DS, Santarsiero BD. Structure and wavelength modification in retinylidene iminium salts. CAN J CHEM 1996. [DOI: 10.1139/v96-063] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The spectroscopic and structural properties of the perchlorate and triflate salts of N-n-butyl-retinylidene imine, 2 and 3, have been examined in solution and solid phases. In solution these salts were found to exhibit very similar UV and NMR spectroscopic properties. However, in the solid state marked differences in their absorption spectra (2, λmax = 504 nm; 3, λmax = 445 nm) and13C NMR spectra were found. The structures of the two salts were determined by X-ray crystallography. The cations in each of the salts were shown to have very similar conformations, detailed structures, and packing in their crystal lattices. The differences in the spectroscopic properties of the salts in the solid state could not be accounted for on the basis of any structural differences in the cations themselves. In terms of cation–anion interactions, a strong hydrogen bonding interaction was found in each case between the N-H proton and an oxygen atom of the counterion. However, there were significant differences between the two salts in terms of the [Formula: see text] internuclear distances (2, [Formula: see text] and in 3, 2.85(1) Å). The results are strongly suggestive that the wavelength and positive charge delocalization in retinylidène iminium salts are controlled by variation of the distance between the anion and the proton bonded to the Schiff base nitrogen atom. The work reported here represents the first examples of secondary retinylidene iminium salts containing an N-alkyl substituent to be successfully analyzed by X-ray crystallography. The relationship of these observations in the solid state to the spectroscopic properties of the natural visual pigments is explored. Key words: retinylidène iminium salts, iminium salts, cation–anion interactions.
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Schweitzer BA, Kool ET. Aromatic Nonpolar Nucleosides as Hydrophobic Isosteres of Pyrimidine and Purine Nucleosides. J Org Chem 1994; 59:7238-7242. [PMID: 20882116 PMCID: PMC2946157 DOI: 10.1021/jo00103a013] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Described are the design, synthesis, and structures of three nonpolar nucleoside isosteres to be used as probes of noncovalent bonding in DNA and as isosteric replacements for the natural nucleosides in designed nucleic acid structures. Reaction of substituted aryl Grignards with 3',5'-bis-O-toluoyl-α-deoxyibofuranosyl chloride and subsequent deprotection with sodium methoxide in methanol afforded the two β-C-nucleoside pyrimidine analogs 1 and 2. The dimethylindolyl nucleoside 3, a purine isostere, was obtained by a nucleophilic displacement on α-chlorodeoxyribofuranose by the sodium salt of 4,6-dimethylindole, followed by deprotection. Regio- and stereochemistry of the products were established with NOE difference spectra and (1)H NMR splitting patterns. Analogs 1 and 2 are nonpolar isosteres of thymidine, and nucleoside 3 is an isostere of 2-aminodeoxyadenosine, the triply-bonded Watson-Crick partner of thymidine. Semiempirical AM1 calculations were carried out to provide bond length information to assess structural similarities between the isosteres and their natural counterparts.
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49
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Xiong JP, Xia ZX, Wang Y. Crystal structure of trichosanthin-NADPH complex at 1.7 A resolution reveals active-site architecture. NATURE STRUCTURAL BIOLOGY 1994; 1:695-700. [PMID: 7634073 DOI: 10.1038/nsb1094-695] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We describe here the crystal structure of the trichosanthin-NADPH complex determined at a resolution of 1.7 A. The adenine base stacks between Tyr 70 and Tyr 111. Arg 163, Glu 160 and Tyr 70 form hydrogen bonds to N(3), O(3') and, through a water molecule, to N(9) of adenosine, respectively. This is the first high resolution structure of a complex between a ribosome-inactivating protein and a substrate analogue, in which the electron density of the N-glycosidic bond is well defined and the preassociated water, thought to be responsible for hydrolyzing the N-C bond, is also explicitly elucidated.
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Affiliation(s)
- J P Xiong
- Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences
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50
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Dimethyldioxirane oxidations: A new and efficient desulfurization of thiopyrimidine and thiopurine nucleosides. Tetrahedron Lett 1993. [DOI: 10.1016/s0040-4039(00)61566-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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