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Zarandi MA, Pathak P, Beltrami N, Walker JN, Zhang F, Brodbelt JS, Schmehl R, Jayawickramarajah J. Heteromeric guanosine (G)-quadruplex derived antenna modules with directional energy transfer. NANOSCALE 2023; 15:19069-19073. [PMID: 37990645 PMCID: PMC11398286 DOI: 10.1039/d3nr04086k] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
A heteromeric guanosine (G)-quadruplex centered self-assembly approach is developed to prepare compact light-harvesting antenna modules featuring multiple donor dyes and a single toehold region. Due to the mix-and-match nature of our approach, the number and placement of donor dyes can be readily fine-tuned via quadruplex assembly. Moreover, hybridization of the toehold with an acceptor containing sequence results in directional energy transfer ensembles with effective absorption coefficients in the 105 M-1 cm-1 range. These compact antennas exhibit system efficiencies that are comparable to much larger and elaborate DNA architectures containing numerous DNA strands.
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Affiliation(s)
| | - Pravin Pathak
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Noah Beltrami
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jada N Walker
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Fengqi Zhang
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Russell Schmehl
- Department of Chemistry, Tulane University, New Orleans, LA, 70118, USA.
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2
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Panda SK, Rai A, Singh AK. Study of paraCEST response on six-coordinated Co(II) and Ni(II) complexes of a pyridine-tetraamide-based ligand. Dalton Trans 2023. [PMID: 38009007 DOI: 10.1039/d3dt02283h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
This study highlights the successful synthesis of a potential ligand, 2,2',2'',2'''-((pyridine-2,6-diylbis(methylene))bis(azanetriyl))tetraacetamide (PATA), along with its corresponding Co(II) and Ni(II) complexes for paraCEST-based agents. X-ray diffraction data confirmed that both the complexes are six coordinated with distorted octahedral geometries, but only the [Co(PATA)]2+ complex has a good structural feature to show paraCEST activity. After a thorough characterization of the ligand and both of its complexes, various studies, including solution-state magnetic properties, redox properties, temperature, and pH variation studies, were carried out. [Co(PATA)]2+ remained inert in the presence of competing ions, under acidic conditions, at high temperatures, and in the physiological pH range. The paraCEST response of [Co(PATA)]2+ has been measured in the presence of HEPES buffer medium, and a high paraCEST feature was discovered at both 37 and 25 °C. The pH variation paraCEST studies were carried out and the exchange rate constant of the probe at 37 and 25 °C was also determined. However, due to the fast exchange of water protons, the [Ni(PATA)(OH2)]2+ complex remained inactive in the CEST process.
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Affiliation(s)
- Suvam Kumar Panda
- Indian Institute of Technology Bhubaneswar, Khordha, Odisha, 752050, India.
| | - Ankit Rai
- Indian Institute of Technology Bhubaneswar, Khordha, Odisha, 752050, India.
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3
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Shi B, Zhou Y, Li X. Recent advances in DNA-encoded dynamic libraries. RSC Chem Biol 2022; 3:407-419. [PMID: 35441147 PMCID: PMC8985084 DOI: 10.1039/d2cb00007e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/16/2022] [Indexed: 11/21/2022] Open
Abstract
The DNA-encoded chemical library (DEL) has emerged as a powerful technology platform in drug discovery and is also gaining momentum in academic research. The rapid development of DNA-/DEL-compatible chemistries has greatly expanded the chemical space accessible to DELs. DEL technology has been widely adopted in the pharmaceutical industry and a number of clinical drug candidates have been identified from DEL selections. Recent innovations have combined DELs with other legacy and emerging techniques. Among them, the DNA-encoded dynamic library (DEDL) introduces DNA encoding into the classic dynamic combinatorial libraries (DCLs) and also integrates the principle of fragment-based drug discovery (FBDD), making DEDL a novel approach with distinct features from static DELs. In this Review, we provide a summary of the recently developed DEDL methods and their applications. Future developments in DEDLs are expected to extend the application scope of DELs to complex biological systems with unique ligand-discovery capabilities.
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Affiliation(s)
- Bingbing Shi
- Department of Biochemistry and Molecular Biology, College of Basic Medicine, Jining Medical University Jining Shandong 272067 P. R. China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong Pokfulam Road Hong Kong SAR China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Health@InnoHK, Innovation and Technology Commission Units 1503-1511 15/F. Building 17W Hong Kong SAR China
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4
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Seo H, Ma KY, Tuttle EE, Calderon IAC, Buskermolen AD, Flask CA, Clark HA. A DNA-Based MRI Contrast Agent for Quantitative pH Measurement. ACS Sens 2021; 6:727-732. [PMID: 33625209 PMCID: PMC9489053 DOI: 10.1021/acssensors.1c00296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Extracellular pH is important in clinical measurements due to its correlation to cell metabolism and disease progression. In MRI, T1/T2 ratiometric analysis and other methods have been previously applied to quantify pH using conventional pulse sequences. However, for nanoparticle-based approaches, heterogeneity in size and surface functionalization tends toward qualitative rather than quantitative results. To address this limitation, we developed a novel DNA-based MRI contrast agent, pH-DMRCA, which utilizes a highly programmable and reproducible nanostructure. The pH-DMRCA is a dendritic DNA scaffold that is functionalized with a pH-responsive MRI-sensitive construct, Gd(NP-DO3A), at the end of each DNA arm. We first evaluated the r1 and r2 response of our pH-DMRCA over a range of pH values (pH = 5-9) to establish a relaxometric model of pH. These MRI-based assessments of pH were validated in a separate set of samples using a pH electrode (n = 18) and resulted in a good linear correlation (R2 = 0.99, slope = 0.98, intercept = 0). A Bland-Altman analysis of the results also showed reasonable agreement between the calculated pH and measured pH. Moreover, these pH comparisons were consistent across three different pH-DMRCA concentrations, demonstrating concentration-independence of the method. This MRI-based pH quantification methodology was further verified in human blood plasma. Given the versatility of the DNA-based nanostructures, the contrast agent has a potential to be applied to a wide variety of imaging applications where extracellular pH is important including cancer, stroke, cardiovascular disease, and other important diseases.
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Affiliation(s)
- Hyewon Seo
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Kristine Y Ma
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Erin E Tuttle
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Isen Andrew C Calderon
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Alissa D Buskermolen
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Chris A Flask
- Departments of Radiology, Biomedical Engineering, and Pediatrics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Heather A Clark
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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5
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Cancer Therapy and Imaging Through Functionalized Carbon Nanotubes Decorated with Magnetite and Gold Nanoparticles as a Multimodal Tool. Appl Biochem Biotechnol 2020; 191:1280-1293. [PMID: 32086708 DOI: 10.1007/s12010-020-03280-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023]
Abstract
Pharmacotherapy and imaging are two critical facets of cancer therapy. Carbon nanotubes and their modified species such as magnetic or gold nanoparticle conjugated ones they have been introduced as good candidates for both purposes. Gold nanoparticles enhance effects of X-rays during radiotherapy. Nanomaterial-mediated radiofrequency (RF) hyperthermia refers to using RF to heat tumors treated with nanomaterials for cancer therapy. The combination of hyperthermia and radiotherapy, synergistically, causes a significant reduction in X-ray doses. The present study was conducted to investigate the ability and efficiency of the multi-walled carbon nanotubes functionalized with magnetic Fe3O4 and gold nanoparticles (mf-MWCNT/AuNPs) for imaging and cancer therapy. The mf-MWCNT/AuNPs were utilized for imaging approaches such as ultrasounds, CT scan, and MRI. They were also examined in thermotherapy and radiotherapy. The MCF-7 cell line was used as an in vitro model to study thermotherapy and radiotherapy. The mf-MWCNT/AuNPs are beneficial as a contrast agent in imaging by ultrasounds, CT scan, and MRI. They are also radio waves and X-rays absorbent and enhance the efficiency of thermotherapy and radiotherapy in the elimination of cancer cells. The valuable properties of mf-MWCNT/AuNPs in radio- and thermotherapies and imaging strategies make them a good candidate as a multimodal tool in cancer therapy. Graphical Abstract The mf-MWCNT/AuNPs are beneficial as a contrast agent in imaging by US (ultrasounds), CT scan, and MRI. They are also radio waves and X-rays absorbent and enhance the efficiency of thermotherapy and radiotherapy in the elimination of cancer cells. The valuable properties of the mf-MWCNT/AuNPs in radio- and thermotherapies and imaging strategies make them a good candidate as a multimodal tool in cancer therapy.
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Chan MS, Leung HM, Wong SW, Lin Z, Gao Q, Chang TJH, Lai KWC, Lo PK. Reversible reconfiguration of high-order DNA nanostructures by employing G-quartet toeholds as adhesive units. NANOSCALE 2020; 12:2464-2471. [PMID: 31915778 DOI: 10.1039/c9nr08070h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
G-quadruplex structures are becoming useful alternative interaction modules for the assembly of DNA nanomaterials because of their unique inducibility by cations. In this study, we demonstrated a new strategy for the assembly of polymeric DNA nanoarchitectures in the presence of cations, such as K+ and Na+, by employing G-quartet toeholds at the edges of discrete mini-square DNA building blocks as adhesive units. In comparison with the Watson-Crick base-paired duplex linkers, G-quadruplex arrays embedded in the self-assembled DNA system exhibit higher thermal stability. The morphology of these doughnut-shaped or spherical-shaped DNA nanostructures is highly regulated by the orientation of the folded G-quadruplexes either in parallel or antiparallel orientation in response to different cations. Furthermore, this G-quadruplex-mediated assembly strategy is able to manipulate the cycling of DNA assemblies between discrete and polymeric states by means of introducing cations and chelating agents sequentially. This property enables the reversible manipulation of the DNA-based nanosystems for at least 4 cycles. The G-quadruplex array embedded in this self-assembled DNA system can become a scaffold for functional molecules, as a number of organic molecules and proteins exhibit specific binding to these G-quadruplex structures. Besides, embedded G-quadruplexes are also considered as functional components of nanoscale electronic materials due to their electron transport through the stacked orientation of the G-quartet. Therefore, this work is an important step towards obtaining reversible, responsive G-quadruplex-induced DNA-based nanomaterials with versatile functionalities which will be highly useful in further electronic, biomedical and drug-delivery applications.
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Affiliation(s)
- Miu Shan Chan
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Hoi Man Leung
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Sze Wing Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Zihong Lin
- Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Qi Gao
- Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Tristan Juin Han Chang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - King Wai Chiu Lai
- Department of Biomedical Engineering, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China and Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China.
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7
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Corbin BA, Pollard AC, Allen MJ, Pagel MD. Summary of Imaging in 2020: Visualizing the Future of Healthcare with MR Imaging. Mol Imaging Biol 2019; 21:193-199. [PMID: 30680525 PMCID: PMC6450763 DOI: 10.1007/s11307-019-01315-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Imaging in 2020 meeting convenes biannually to discuss innovations in medical imaging. The 2018 meeting, titled "Visualizing the Future of Healthcare with MR Imaging," sought to encourage discussions of the future goals of MRI research, feature important discoveries, and foster scientific discourse between scientists from a variety of fields of expertise. Here, we highlight presented research and resulting discussions of the meeting.
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Affiliation(s)
- Brooke A Corbin
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, USA
| | - Alyssa C Pollard
- Department of Chemistry, Rice University, 6100 S Main Street, Houston, TX, USA
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX, USA
| | - Matthew J Allen
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI, USA.
| | - Mark D Pagel
- Department of Chemistry, Rice University, 6100 S Main Street, Houston, TX, USA.
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, 1881 East Road, Houston, TX, USA.
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8
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Abstract
DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.
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Affiliation(s)
- Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering , Nanjing University , Nanjing 210023 , China.,ARNA Laboratory , Université de Bordeaux, Inserm U 1212, CNRS UMR5320, IECB , Pessac 33600 , France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135 , 612 65 Brno , Czech Republic
| | - Dipankar Sen
- Department of Molecular Biology & Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada
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9
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Lee H, Sung D, Kim J, Kim BT, Wang T, An SSA, Seo SW, Yi DK. Silica nanoparticle-based dual imaging colloidal hybrids: cancer cell imaging and biodistribution. Int J Nanomedicine 2015; 10 Spec Iss:215-25. [PMID: 26357472 PMCID: PMC4559254 DOI: 10.2147/ijn.s88311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this study, fluorescent dye-conjugated magnetic resonance (MR) imaging agents were investigated in T mode. Gadolinium-conjugated silica nanoparticles were successfully synthesized for both MR imaging and fluorescence diagnostics. Polyamine and polycarboxyl functional groups were modified chemically on the surface of the silica nanoparticles for efficient conjugation of gadolinium ions. The derived gadolinium-conjugated silica nanoparticles were investigated by zeta potential analysis, transmission electron microscopy, inductively coupled plasma mass spectrometry, and energy dispersive x-ray spectroscopy. MR equipment was used to investigate their use as contrast-enhancing agents in T1 mode under a 9.4 T magnetic field. In addition, we tracked the distribution of the gadolinium-conjugated nanoparticles in both lung cancer cells and organs in mice.
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Affiliation(s)
- Haisung Lee
- Molecular Diagnostics, In Vitro Diagnostics Unit, New Business Division, SK Telecom, Republic of Korea
| | - Dongkyung Sung
- Department of Life Sciences, Graduate School of Korea University, Seoul, Republic of Korea
| | - Jinhoon Kim
- Interdisciplinary Graduate Program of Biomedical Engineering, School of Medicine, Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Byung-Tae Kim
- Interdisciplinary Graduate Program of Biomedical Engineering, School of Medicine, Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Tuntun Wang
- Department of Chemistry, Myongji University, Seoul, Republic of Korea
| | - Seong Soo A An
- Department of Bionanotechnology, Gachon Medical Research Institute, Gachon University, Seongnam, Republic of Korea
| | - Soo-Won Seo
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Dong Kee Yi
- Department of Chemistry, Myongji University, Seoul, Republic of Korea
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10
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Li G, Zheng W, Liu Y, Li X. Novel encoding methods for DNA-templated chemical libraries. Curr Opin Chem Biol 2015; 26:25-33. [PMID: 25635927 DOI: 10.1016/j.cbpa.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 12/12/2022]
Abstract
Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.
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Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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11
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Sengar A, Heddi B, Phan AT. Formation of G-quadruplexes in poly-G sequences: structure of a propeller-type parallel-stranded G-quadruplex formed by a G₁₅ stretch. Biochemistry 2014; 53:7718-23. [PMID: 25375976 DOI: 10.1021/bi500990v] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Poly-G sequences are found in different genomes including human and have the potential to form higher-order structures with various applications. Previously, long poly-G sequences were thought to lead to multiple possible ways of G-quadruplex folding, rendering their structural characterization challenging. Here we investigate the structure of G-quadruplexes formed by poly-G sequences d(TTG(n)T), where n = 12 to 19. Our data show the presence of multiple and/or higher-order G-quadruplex structures in most sequences. Strikingly, NMR spectra of the TTG₁₅T sequence containing a stretch of 15 continuous guanines are exceptionally well-resolved and indicate the formation of a well-defined G-quadruplex structure. The NMR solution structure of this sequence revealed a propeller-type parallel-stranded G-quadruplex containing three G-tetrad layers and three single-guanine propeller loops. The same structure can potentially form anywhere along a long G(n) stretch, making it unique for molecular recognition by other cellular molecules.
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Affiliation(s)
- Anjali Sengar
- School of Physical and Mathematical Sciences, Nanyang Technological University , Singapore 637371, Singapore
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12
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Chmielewski MJ, Buhler E, Candau J, Lehn JM. Multivalency by Self-Assembly: Binding of Concanavalin A to Metallosupramolecular Architectures Decorated with Multiple Carbohydrate Groups. Chemistry 2014; 20:6960-77. [DOI: 10.1002/chem.201304511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Indexed: 12/17/2022]
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Affiliation(s)
- Marie C. Heffern
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Lauren M. Matosziuk
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
| | - Thomas J. Meade
- Department of Chemistry, Molecular Biosciences, Neurobiology, Biomedical Engineering, and Radiology, Northwestern University, Evanston, Illinois 60208-3113
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14
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Brückner K, Schwarz K, Beck S, Linscheid MW. DNA Quantification via ICP-MS Using Lanthanide-Labeled Probes and Ligation-Mediated Amplification. Anal Chem 2013; 86:585-91. [DOI: 10.1021/ac402668p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kathrin Brückner
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Kathleen Schwarz
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Sebastian Beck
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
| | - Michael W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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15
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Sapsford KE, Algar WR, Berti L, Gemmill KB, Casey BJ, Oh E, Stewart MH, Medintz IL. Functionalizing nanoparticles with biological molecules: developing chemistries that facilitate nanotechnology. Chem Rev 2013; 113:1904-2074. [PMID: 23432378 DOI: 10.1021/cr300143v] [Citation(s) in RCA: 818] [Impact Index Per Article: 74.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kim E Sapsford
- Division of Biology, Department of Chemistry and Materials Science, Office of Science and Engineering Laboratories, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
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16
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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17
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Abstract
Interlock is a structural element in DNA G-quadruplexes that can be compared with the commonly used complementary binding of ‘sticky ends’ in DNA duplexes. G-quadruplex interlocking can be a basis for the assembly of higher-order structures. In this study, we formulated a rule to engineer (3 + 1) interlocked dimeric G-quadruplexes and established the folding topology of the designed DNA sequences by nuclear magnetic resonance spectroscopy. These interlocked G-quadruplexes are very stable and can serve as compact robust scaffolds for various applications. Different structural elements can be engineered in these robust scaffolds. We demonstrated the anti-HIV inhibition activity of the newly designed DNA sequences.
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Affiliation(s)
- Anh Tuân Phan
- School of Physical and Mathematical Sciences and School of Biological Sciences, Nanyang Technological University, Singapore.
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18
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Do NQ, Phan AT. Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study. Chemistry 2012; 18:14752-9. [PMID: 23019076 DOI: 10.1002/chem.201103295] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Indexed: 01/24/2023]
Abstract
Guanine-rich sequence motifs, which contain tracts of three consecutive guanines connected by single non-guanine nucleotides, are abundant in the human genome and can form a robust G-quadruplex structure with high stability. Herein, by using NMR spectroscopy, we investigate the equilibrium between monomeric and 5'-5' stacked dimeric propeller-type G-quadruplexes that are formed by DNA sequences containing GGGT motifs. We show that the monomer-dimer equilibrium depends on a number of parameters, including the DNA concentration, DNA flanking sequences, the concentration and type of cations, and the temperature. We report on the high-definition structure of a simple monomeric G-quadruplex containing three single-residue loops, which could serve as a reference for propeller-type G-quadruplex structures in solution.
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Affiliation(s)
- Ngoc Quang Do
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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Bernard ED, Beking MA, Rajamanickam K, Tsai EC, Derosa MC. Target binding improves relaxivity in aptamer-gadolinium conjugates. J Biol Inorg Chem 2012; 17:1159-75. [PMID: 22903502 DOI: 10.1007/s00775-012-0930-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Accepted: 07/29/2012] [Indexed: 11/24/2022]
Abstract
MRI contrast agents (CA) have been heavily used over the past several decades to enhance the diagnostic value of the obtained images. From a design perspective, two avenues to improve the efficacy of contrast agents are readily evident: optimization of magnetic properties of the CA, and optimization of the pharmacokinetics and distribution of the CA in the patient. Contrast agents consisting of DNA aptamer-gadolinium(III) conjugates provide a single system in which these factors can be addressed simultaneously. In this proof-of-concept study, the 15mer thrombin aptamer was conjugated to diethylenetriaminepentaacetic (DTPA) dianhydride to form a monoamide derivative of the linear open-chain chelate present in the commonly used contrast agent Magnevist(®). The stability of the conjugated DNA aptamer-DTPA-Gd(III) chelate in a transmetallation study using Zn(II) was found to be similar to that reported for DTPA-Gd(III). Relaxivity enhancements of 35 ± 4 and 20 ± 1 % were observed in the presence of thrombin compared to a control protein at fields of 9.4 and 1.5 T, respectively. The inclusion of spacers between the aptamer and the DTPA to eliminate possible steric effects was also investigated but not found to improve the relaxation enhancement achieved in comparison to the unaltered aptamer conjugate.
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Affiliation(s)
- Elyse D Bernard
- Department of Chemistry, Ottawa-Carleton Chemistry Institute, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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20
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Cassimjee KE, Marín SR, Berglund P. Synthesis of cyclic polyamines by enzymatic generation of an amino aldehyde in situ. Macromol Rapid Commun 2012; 33:1580-3. [PMID: 22761014 DOI: 10.1002/marc.201200347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 06/11/2012] [Indexed: 01/24/2023]
Abstract
Multifunctional polycationic polyamines, for example, used in drug and gene delivery, have product range limitations in their synthesis methods. Here, we synthesize a polyamine by forming a self-assembling amino aldehyde from the corresponding amino alcohol with horse liver alcohol dehydrogenase (HLADH), followed by reduction. Circular polyamines were synthesized from 3-amino-propan-1-ol as starting material, analogous to cyclic polyamines formed from azetidin. The product had an isolated yield of 89.7% or 15.3 g L(-1) . The predicted range of possible polyamine products by this method is broad since many amino alcohols are putative substrates for HLADH. The enzyme also had activity for 2-amino-propan-1-ol and 2-amino-2-phenyl-ethanol, for which the enantioselectivity was 330 (S) and 32 (R), respectively.
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21
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Wang P, Jaganathan H, Ivanisevic A. Multicomponent DNA-templated nanoparticle chains with controllable dimension and composition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:2021-2026. [PMID: 21626683 DOI: 10.1002/smll.201100067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Indexed: 05/30/2023]
Affiliation(s)
- Pengfei Wang
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN 47907-2032, USA
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22
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Franceschin M, Borbone N, Oliviero G, Casagrande V, Scuotto M, Coppola T, Borioni S, Mayol L, Ortaggi G, Bianco A, Amato J, Varra M. Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate. Bioconjug Chem 2011; 22:1309-19. [PMID: 21688831 DOI: 10.1021/bc100526q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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23
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Chang YH, Chen CY, Singh G, Chen HY, Liu GC, Goan YG, Aime S, Wang YM. Synthesis and Physicochemical Characterization of Carbon Backbone Modified [Gd(TTDA)(H2O)]2− Derivatives. Inorg Chem 2011; 50:1275-87. [DOI: 10.1021/ic101799c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Chiao-Yun Chen
- Department of Medical Imaging, Kaohsiung Medical University Hospital
- Department of Radiology
| | - Gyan Singh
- Department of Biological Science and Technology
| | | | - Gin-Chung Liu
- Department of Medical Imaging, Kaohsiung Medical University Hospital
- Department of Radiology
| | - Yih-Gang Goan
- Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- Department of Nursing, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Silvio Aime
- Department of Chemistry IFM and Molecular Imaging Center, University of Torino, Torino, Italy
| | - Yun-Ming Wang
- Department of Biological Science and Technology
- Institute of Molecular Medicine and Bioengineering
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24
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Cavalieri F, Ng SL, Mazzuca C, Jia Z, Bulmus V, Davis TP, Caruso F. Thin multilayer films and microcapsules containing DNA quadruplex motifs. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2011; 7:101-111. [PMID: 21105053 DOI: 10.1002/smll.201001246] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The assembly of multifunctional nanostructures bearing G-quadruplex motifs broadens the prospects of using G-quadruplexes as therapeutic carriers. Herein, we report the synthesis and characterization of an oligodeoxyguanosine, G15-mer polymer conjugate. We demonstrate that G15-mer oligonucleotides grafted to a polymer chain preserve the ability to self-assemble into ordered structures. The G-quadruplex-polymer conjugates were assembled onto a surface via hybridization with 30-mer cytosine strands, C30-mer, using a layer-by-layer approach to form microcapsules. A mechanism for the sequential assembly of the multilayer films and microcapsules is presented. We further investigate the photophysical behavior of porphyrin TMPyP4 bound to multilayer-coated particles. This study shows that the multilayer films bear residual and functional quadruplex moieties that can be used to effectively bind therapeutic agents.
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Affiliation(s)
- Francesca Cavalieri
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, 00173 Rome, Italy
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25
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Polyion complex micelle MRI contrast agents from poly(ethylene glycol)-b-poly(l-lysine) block copolymers having Gd-DOTA; preparations and their control of T1-relaxivities and blood circulation characteristics. J Control Release 2010; 148:160-7. [DOI: 10.1016/j.jconrel.2010.08.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/04/2010] [Accepted: 08/12/2010] [Indexed: 11/17/2022]
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Scheuermann J, Neri D. DNA-encoded chemical libraries: a tool for drug discovery and for chemical biology. Chembiochem 2010; 11:931-7. [PMID: 20391457 DOI: 10.1002/cbic.201000066] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Scheuermann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland.
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Jaganathan H, Gieseck RL, Ivanisevic A. Characterizing proton relaxation times for metallic and magnetic layer-by-layer-coated, DNA-templated nanoparticle chains. NANOTECHNOLOGY 2010; 21:245103. [PMID: 20484793 DOI: 10.1088/0957-4484/21/24/245103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Metallic and superparamagnetic DNA-templated nanoparticle (NP) chains are examined as potential imaging agents. Proton relaxation times (T(1) and T(2)) are measured for DNA nanostructures using nuclear magnetic resonance (NMR) spectroscopy. The layer-by-layer (LBL) method was used to encapsulate the DNA-templated NP chains and demonstrated a change in proton relaxation times. Results from this study suggest that LBL-coated, DNA-templated nanostructures can serve as effective imaging agents for magnetic resonance imaging (MRI) applications.
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Affiliation(s)
- Hamsa Jaganathan
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47906, USA
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28
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Shcharbin D, Pedziwiatr E, Blasiak J, Bryszewska M. How to study dendriplexes II: Transfection and cytotoxicity. J Control Release 2009; 141:110-27. [PMID: 19815039 DOI: 10.1016/j.jconrel.2009.09.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/22/2009] [Indexed: 12/23/2022]
Abstract
This paper reviews different techniques for analyzing the transfection efficiencies and cytotoxicities of dendriplexes-complexes of nucleic acids with dendrimers. Analysis shows that three plasmids are mainly used in transfection experiments: plasmid DNA encoding luciferase from the firefly Photinus pyralis, beta-galactosidase, or green fluorescent protein. The effective charge ratio of transfection does not directly correlate with the charge ratio obtained from gel electrophoresis, zeta-potential or ethidium bromide intercalation data. The most popular cells for transfection studies are human embryonic kidney cells (HEK293), mouse embryonic cells (NIH/3T3), SV40 transformed monkey kidney fibroblasts (COS-7) and human epithelioid cervical carcinoma cells (HeLa). Cellular uptake is estimated using fluorescently-labeled dendrimers or nucleic acids. Transfection efficiency is measured by the luciferase reporter assay for luciferase, X-Gal staining or beta-galactosidase assay for beta-galactosidase, and confocal microscopy for green fluorescent protein. Cytotoxicity is determined by the MTT test and lactate dehydrogenase assays. On the basis of the papers reviewed, a standard essential set of techniques for characterizing dendriplexes was constructed: (1) analysis of size and shape of dendriplexes in dried/frozen state by electron or atomic force microscopy; (2) analysis of charge/molar ratio of complexes by gel electrophoresis or ethidium bromide intercalation assay or zeta-potential measurement; (3) analysis of hydrodynamic diameter of dendriplexes in solution by dynamic light scattering. For the evaluation of transfection efficiency the essential techniques are (4) luciferase reporter assay, beta-galactosidase assay or green fluorescent protein microscopy, and (5) cytotoxicity by the MTT test. All these tests allow the transfection efficiencies and cytotoxicities of different kinds of dendrimers to be compared.
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Affiliation(s)
- Dzmitry Shcharbin
- Institute of Biophysics and Cellular Engineering of NASB, Minsk, Belarus.
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Nwe K, Andolina CM, Huang CH, Morrow JR. PARACEST properties of a dinuclear neodymium(III) complex bound to DNA or carbonate. Bioconjug Chem 2009; 20:1375-82. [PMID: 19555071 DOI: 10.1021/bc900146z] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A dinuclear Nd(III) macrocyclic complex of 1 (1,4-bis[1-(4,7,10-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane]-p-xylene) and mononuclear complexes of 1,4,7-tris-1,4,7,10-tetraazacyclododecane, 2, and 1,4,7-tris[(N-N-diethyl)carbamoylmethyl]-1,4,7,10-tetraazacyclododecane, 3, are prepared. Complexes of 1 and 2 give rise to a PARACEST (paramagnetic chemical exchange saturation transfer) peak from exchangeable amide protons that resonate approximately 12 ppm downfield from the bulk water proton resonance. The dinuclear Nd(III) complex is promising as a PARACEST contrast agent for MRI applications, because it has an optimal pH of 7.5 and the rate constant for amide proton exchange (2700 s(-1)) is nearly as large as it can be within slow exchange conditions with bulk water. Dinuclear Ln(2)(1) complexes (Ln(III) = Nd(III), Eu(III)) bind tightly to anionic ligands including carbonate, diethyl phosphate, and DNA. The CEST amide peak of Nd(2)(1) is enhanced by certain DNA sequences that contain hairpin loops, but decreases in the presence of diethyl phosphate or carbonate. Direct excitation luminescence studies of Eu(2)(1) show that double-stranded and hairpin-loop DNA sequences displace one water ligand on each Eu(III) center. DNA displaces carbonate ion despite the low dissociation constant for the Eu(2)(1) carbonate complex (K(d) = 15 microM). Enhancement of the CEST effect of a lanthanide complex by binding to DNA is a promising step toward the preparation of PARACEST agents containing DNA scaffolds.
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Affiliation(s)
- Kido Nwe
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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Escudier JM, Dupouy C, Fountain MA, del Mundo IMA, Jacklin EM, Morrow JR. Synthesis and luminescence properties of a trinucleotide-europium(III) complex conjugate. Org Biomol Chem 2009; 7:3251-7. [PMID: 19641782 DOI: 10.1039/b902643f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two trinucleotide conjugates of the macrocyclic ligand 1,4,7-tris(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane are prepared. One contains only DNA (1) and the second is a chimeric RNA/DNA conjugate (2). The synthetic methodology used to prepare the trinucleotide macrocyclic ligand conjugates is based on the introduction of a convertible nucleoside which has an electrophilic function to facilitate the attachment of any nucleophilic ligand to the 5-position of the 3-nucleoside unit. The convertible nucleoside is first treated with the macrocyclic ligand, 1,4,7,10-tetraazacyclododecane, followed by alkylation of the three remaining amine groups to give a conjugated macrocyclic ligand with three pendent amide groups. Addition of an equivalent of EuCl3 to trinucleotide (1) or (2) yields the complexes Eu(1) and Eu(2), respectively. Studies using time-resolved and steady state direct excitation luminescence spectroscopy show that Eu(III) binds to the macrocyclic moiety in 1 and in 2. The excitation peak frequency for the 7Fo5Do transition and the unexpectedly low number of water ligands in Eu(1) and Eu(2) are consistent with additional interactions of the Eu(III) macrocycle with one of the phosphate diester groups. Studies show that Eu(2) undergoes cleavage at the uridine nucleotide. The unique point of attachment of the macrocyclic complex will enable the preparation of new lanthanide nucleic acid conjugates with useful properties.
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Affiliation(s)
- Jean-Marc Escudier
- Université Paul Sabatier, 118 Route de Narbonne, 31062 Toulouse Cedex 4, France.
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