1
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Kim MJ, Park H, Jung R, Won C, Ohk S, Kim H, Roh N, Yi K. High-resolution 3-D scanning electron microscopy (SEM) images of DOT TM polynucleotides (PN): Unique scaffold characteristics and potential applications in biomedicine. Skin Res Technol 2024; 30:e13667. [PMID: 38558437 PMCID: PMC10982675 DOI: 10.1111/srt.13667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024]
Abstract
INTRODUCTION Polynucleotides (PN) are becoming more prominent in aesthetic medicine. However, the structural characteristics of PN have not been published and PN from different companies may have different structural characteristics. This study aimed to elucidate the structural attributes of DOT™ PN and distinguish differences with polydeoxyribonucleotides (PDRN) using high-resolution scanning electron microscopy (SEM) imaging. MATERIALS AND METHODS DOT™ PN was examined using a Quanta 3-D field emission gun (FEG) Scanning Electron Microscope (SEM). Sample preparation involved cryogenic cooling, cleavage, etching, and metal coating to facilitate high-resolution imaging. Cryo-FIB/SEM techniques were employed for in-depth structural analysis. RESULTS PDRN exhibited an amorphous structure without distinct features. In contrast, DOT™ PN displayed well-defined polyhedral shapes with smooth, uniformly thick walls. These cells were empty, with diameters ranging from 3 to 8 micrometers, forming a seamless tessellation pattern. DISCUSSION DOT™ PN's distinct geometric tessellation design conforms to the principles of biotensegrity, providing both structural reinforcement and integrity. The presence of delicate partitions and vacant compartments hints at possible uses in the field of pharmaceutical delivery systems. Within the realms of beauty enhancement and regenerative medicine, DOT™ PN's capacity to bolster cell growth and tissue mending could potentially transform approaches to rejuvenation treatments. Its adaptability becomes apparent when considering its contributions to drug administration and surgical procedures. CONCLUSION This study unveils the intricate structural scaffold features of DOT™ PN for the first time, setting it apart from PDRN and inspiring innovation in biomedicine and materials science. DOT™ PN's unique attributes open doors to potential applications across healthcare and beyond.
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Affiliation(s)
| | | | - Rae‐Jun Jung
- Pharmaresearch Co., Ltd. Integrated R&D CenterSungnamSouth Korea
| | - Chee‐Youb Won
- Pharmaresearch Co., Ltd. Integrated R&D CenterSungnamSouth Korea
| | - Seul‐Ong Ohk
- Pharmaresearch Co., Ltd. Integrated R&D CenterSungnamSouth Korea
| | - Hong‐Taek Kim
- Pharmaresearch Co., Ltd. Integrated R&D CenterSungnamSouth Korea
| | - Nark‐Kyung Roh
- Leaders Aesthetic Laser and Cosmetic Surgery CenterSeoulSouth Korea
| | - Kyu‐Ho Yi
- Maylin Clinic (Apgujeong)SeoulSouth Korea
- Division in Anatomy and Developmental BiologyDepartment of Oral BiologyHuman Identification Research InstituteBK21 FOUR ProjectYonsei University College of DentistrySeoulSouth Korea
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2
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Alam I, Boonkoom T, Pitakjakpipop H, Boonbanjong P, Loha K, Saeyang T, Vanichtanankul J, Japrung D. Single-Molecule Analysis of SARS-CoV-2 Double-Stranded Polynucleotides Using Solid-State Nanopore with AI-Assisted Detection and Classification: Implications for Understanding Disease Severity. ACS Appl Bio Mater 2024; 7:1017-1027. [PMID: 38194666 DOI: 10.1021/acsabm.3c00998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
This study utilized solid-state nanopores, combined with artificial intelligence (AI), to analyze the double-stranded polynucleotides encoding angiotensin-converting enzyme 2, receptor-binding domain, and N protein, important parts of SARS-CoV-2 infection. By examining ionic current signals during DNA translocation, we revealed the dynamic interactions and structural characteristics of these nucleotide sequences and also quantified their abundance. Nanopores of sizes 3 and 10 nm were efficiently fabricated and characterized, ensuring an optimal experimental approach. Our results showed a clear relationship between DNA capture rates and concentration, proving our method's effectiveness. Notably, longer DNA sequences had higher capture rates, suggesting their importance for potential disease marker analysis. The 3 nm nanopore demonstrated superior performance in our DNA analysis. Using dwell time measurements and excluded currents, we were able to distinguish the longer DNA fragments, paving the way for a DNA length-based analysis. Overall, our research underscores the potential of nanopore technology, enhanced with AI, in analyzing COVID-19-related DNA and its implications for understanding disease severity. This provides insight into innovative diagnostic and treatment strategies.
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Affiliation(s)
- Ibrar Alam
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Thitikorn Boonkoom
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Harit Pitakjakpipop
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Poramin Boonbanjong
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Kawin Loha
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Thanaya Saeyang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Jarunee Vanichtanankul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Pathumthani 12120, Thailand
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3
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Wang S, Lin PA, DeLuca M, Zauscher S, Arya G, Ke Y. Controlling Silicification on DNA Origami with Polynucleotide Brushes. J Am Chem Soc 2024; 146:358-367. [PMID: 38117542 PMCID: PMC10785815 DOI: 10.1021/jacs.3c09310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023]
Abstract
DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.
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Affiliation(s)
- Shuang Wang
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Po-An Lin
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Marcello DeLuca
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Stefan Zauscher
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Gaurav Arya
- Department
of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
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4
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Deshpande S, Yang Y, Zauscher S, Chilkoti A. Enzymatic Synthesis of Aptamer-Polynucleotide Nanoparticles with High Anticancer Drug Loading for Targeted Delivery. Biomacromolecules 2024; 25:155-164. [PMID: 38051194 DOI: 10.1021/acs.biomac.3c00888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
We report a targeted prodrug delivery platform that can deliver a cytostatic nucleobase analog with high drug loading. We chose fluorouracil (5FU), a drug used to treat various cancers, whose active metabolite 5-fluorodeoxyuridine monophosphate (5-FdUMP) is the antineoplastic agent. We use terminal deoxynucleotidyl transferase (TdT) to polymerize 5-fluorodeoxyuridine triphosphate (5-FdUTP) onto the 3'-end of an aptamer. We find that (i) addition of hydrophobic, unnatural nucleotides at the 3'-end of the 5-FdU polynucleotide by TdT leads to their spontaneous self-assembly into nuclease resistant micelles, (ii) aptamers presented on the micelle corona retain specificity for their cognate receptor on tumor cells, and (iii) the micelles deliver 5FU to tumor cells and exhibit greater cytotoxicity than the free drug. The modular design of our platform, consisting of a targeting moiety, a polynucleotide drug, and a self-assembly domain, can be adapted to encompass a range of polymerizable therapeutic nucleotides and targeting units.
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Affiliation(s)
- Sonal Deshpande
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Stefan Zauscher
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
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5
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Yang Y, Lu Q, Chen Y, DeLuca M, Arya G, Ke Y, Zauscher S. Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures. Angew Chem Int Ed Engl 2023; 62:e202311727. [PMID: 37820028 DOI: 10.1002/anie.202311727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site-specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to "smart" functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.
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Affiliation(s)
- Yunqi Yang
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Qinyi Lu
- Department of Chemistry, Emory University, Atlanta, GA 30322, USA
| | - Yu Chen
- University Program in Materials Science and Engineering, Duke University, Durham, NC 27708, USA
| | - Marcello DeLuca
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, USA
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Yonggang Ke
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30322, USA
| | - Stefan Zauscher
- Department of Mechanical Engineering and Materials Science, Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
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Sviben I, Glavaš M, Erben A, Bachelart T, Pavlović Saftić D, Piantanida I, Basarić N. Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides. Molecules 2023; 28:7533. [PMID: 38005255 PMCID: PMC10672942 DOI: 10.3390/molecules28227533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.
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Affiliation(s)
| | | | | | | | | | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
| | - Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia; (I.S.); (M.G.); (A.E.); (T.B.); (D.P.S.)
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7
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Metelev VG, Baulin EF, Bogdanov AA. Multiple Non-Canonical Base-Stacking Interactions as One of the Major Determinants of RNA Tertiary Structure Organization. Biochemistry (Mosc) 2023; 88:792-800. [PMID: 37748875 DOI: 10.1134/s000629792306007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 09/27/2023]
Abstract
Stacking interactions of heterocyclic bases of ribonucleotides are one of the most important factors in the organization of RNA secondary and tertiary structure. Most of these (canonical) interactions are formed between adjacent residues in RNA polynucleotide chains. However, with the accumulation of data on the atomic tertiary structures of various RNAs and their complexes with proteins, it has become clear that nucleotide residues that are not adjacent in the polynucleotide chains and are sometimes separated in the RNA primary structure by tens or hundreds of nucleotides can interact via (non-canonical) base stacking. This paper presents an exhaustive database of such nonadjacent base-stacking elements (NA-BSEs) and their environment in the macromolecules of natural and synthetic RNAs. Analysis of these data showed that NA-BSE-forming nucleotides, on average, account for about a quarter of all nucleotides in a particular RNA and, therefore, should be considered as bona fide motifs of the RNA tertiary structure. We also classified NA-BSEs by their location in RNA macromolecules. It was shown that the structure-forming role of NA-BSEs involves compact folding of single-stranded RNA loops, transformation of double-stranded bulges into imperfect helices, and binding of RNA regions distant in the primary and secondary RNA structure.
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Affiliation(s)
- Valeriy G Metelev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene F Baulin
- Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexey A Bogdanov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
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8
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Norris V, Demongeot J. The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry. Int J Mol Sci 2022; 23:ijms232112915. [PMID: 36361702 PMCID: PMC9657125 DOI: 10.3390/ijms232112915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/20/2022] [Accepted: 10/23/2022] [Indexed: 11/27/2022] Open
Abstract
It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a ‘view from here’ that we term the Circlet hypothesis as part of a broader Ring World. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution to the fundamental problems probably confronting both the earliest cells and the most recent ones.
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Affiliation(s)
- Victor Norris
- Laboratory of Communication Bactérienne et Stratégies Anti-infectieuses UR4312, Université de Rouen, CEDEX, 76821 Mont-Saint-Aignan, France
- Correspondence:
| | - Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France
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Casabona G, Kaye K. Effects of Polynucleotide Dermal Filler in the Correction of Crow's Feet Using an Antera Three-Dimensional Camera. Aesthetic Plast Surg 2022; 46:1910-1912. [PMID: 35482064 DOI: 10.1007/s00266-022-02891-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Gabriela Casabona
- Scientific Director at Ocean Clinic, Av Ramon y Cajal 7, Marbella, Spain.
| | - Kai Kaye
- Medical Director at Ocean Clinic, Marbella, Spain
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Kim JH, Kim ES, Kim SW, Hong SP, Kim J. Effects of Polynucleotide Dermal Filler in the Correction of Crow's Feet Using an Antera Three-Dimensional Camera. Aesthetic Plast Surg 2022; 46:1902-1909. [PMID: 35357558 DOI: 10.1007/s00266-022-02832-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/24/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Dermal fillers are gaining interest for tissue enlargement and skin improvement. Among them, polynucleotides have demonstrated multiple skin beneficial effects. The effects of polynucleotide fillers were objectively evaluated using an Antera 3D camera, subjectively evaluated by participants and investigators. METHODS Thirty subjects with crow's feet were enrolled in the study. The subjects received polynucleotide filler for crow's feet. Crow's feet grading score (CFGS), global esthetic improvement scale (GAIS), and Antera 3D imaging results were evaluated. RESULTS Twenty-eight subjects (93.3%) completed the study. An improvement in CFGS compared with that at baseline (p < 0.001) was observed 18 weeks after the first injection of polynucleotides. Additionally, at the final visit, there were improvements in wrinkle, texture, pore, depression, and Hb values compared with those at baseline (p < 0.05). However, no significant difference in melanin level was detected between the initial and final visits. CONCLUSIONS Improvements in wrinkles, pores, texture, depression, and Hb level after polynucleotide filler injection were verified by objective and subjective evaluations. To the best of our knowledge, this is the first report on the objective evaluation of polynucleotide fillers in crow's feet using the Antera 3D camera. LEVEL OF EVIDENCE IV This journal requires that authors assign a level of evidence to each article. For a full description of these Evidence-Based Medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .
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Affiliation(s)
- Jeong Ho Kim
- Department of Plastic and Reconstructive Surgery, Wonju Severance Christian Hospital, Wonju College of Medicine, Yonsei University, Wonju, Republic of Korea
| | - Eon Su Kim
- Department of Plastic and Reconstructive Surgery, Wonju Severance Christian Hospital, Wonju College of Medicine, Yonsei University, Wonju, Republic of Korea
| | - Sug Won Kim
- Department of Plastic and Reconstructive Surgery, Wonju Severance Christian Hospital, Wonju College of Medicine, Yonsei University, Wonju, Republic of Korea
| | - Seung Phil Hong
- Department of Dermatology, Wonju Severance Christian Hospital, Wonju College of Medicine, Yonsei University, Wonju, Republic of Korea
| | - Jiye Kim
- Department of Plastic and Reconstructive Surgery, Wonju Severance Christian Hospital, Wonju College of Medicine, Yonsei University, Wonju, Republic of Korea.
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Macii F, Cupellini L, Stifano M, Santolaya J, Pérez-Arnaiz C, Pucci A, Barone G, García B, Busto N, Biver T. Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes. Spectrochim Acta A Mol Biomol Spectrosc 2021; 260:119914. [PMID: 34015745 DOI: 10.1016/j.saa.2021.119914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/23/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
We present here a combined spectroscopic and theoretical analysis of the binding of N,N'-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggregates disruption and monomers intercalation. Oppositely, for RNAs, no intercalation but groove binding with the formation of supramolecular aggregates is observed. Among all the tested biosubstrates, the affinity of PZPERY towards DNA G-quadruplexes (G4) is the greatest one with a preference for human telomeric G4s. Focusing on hybrid G4 forms, either sitting-atop ("tetrad-parallel") or lateral ("groove-parallel") binding modes were considered in the discussion of the experimental results and molecular dynamics (MD) simulations. Both turned out to be possible concurrently, in agreement also with the experimental binding stoichiometries higher than 2:1.
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Affiliation(s)
- Francesca Macii
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Mariassunta Stifano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Javier Santolaya
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Cristina Pérez-Arnaiz
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Andrea Pucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Begoña García
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain
| | - Natalia Busto
- Department of Chemistry, University of Burgos, Pza. Misael Bañuelos s/n, 09001 Burgos, Spain.
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy; Department of Pharmacy, University of Pisa, Via Bonanno Pisano 6, 56126 Pisa, Italy.
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12
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DeLorenzi C. Invited Discussion on: Comparative Evaluation of Safety and Efficacy of a Novel Hyaluronic Acid Polynucleotide/Poly-L-Lactic Acid Composite Dermal Filler. Aesthetic Plast Surg 2021; 45:1802-1803. [PMID: 34089080 DOI: 10.1007/s00266-021-02361-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
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14
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Goozner M. Back to the future in la la land. Mod Healthc 2014; 44:26. [PMID: 25318297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
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16
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Abstract
OBJECTIVE A theory of fuzzy polynucleotides, including an n-dimensional metric fuzzy polynucleotide space, has been previously introduced by the present author for fuzzy-theoretical analysis of nucleic acids [Sadegh-Zadeh K. Fuzzy genomes. Artif Intell Med 2000;18:1-28; Sadegh-Zadeh K. Ein Verfahren zur Fuzzydecodierung und Fuzzydechiffrierung von Informationen. Offenlegungsschrift DE 199 36 925 A 1. Deutsches Patent- und Markenamt; 2001]. The conceptual framework of that theory has been used by Nieto et al. [Nieto JJ, Torres A, Vázquez-Trasande MM. A metric space to study differences between polynucleotides. Appl Math Lett 2003;16:1289-94; Nieto JJ, Torres A, Georgiou DN, Karakasidis TE. Fuzzy polynucleotide spaces and metrics. Bull Math Biol 2006;68:703-25] and Torres et al. [Torres A, Nieto JJ. The fuzzy polynucleotide space: basic properties. Bioinformatics 2003;19:587-92; Torres A, Nieto JJ. Fuzzy logic in medicine and bioinformatics. J Biomed Biotechnol 2006;1-7 [Article ID 91908]] to create a completely different, 12-dimensional metric space which they have also called 'the fuzzy polynucleotide space'. In the present paper both spaces are compared. MATERIAL AND METHOD Both metric spaces are briefly outlined. Similarity and dissimilarity relationships between polynucleotide strings are measured in both spaces to compare their performance. RESULTS Nieto et al.'s and Torres et al.'s metric space measures the relationships between polynucleotide chains incorrectly. Structurally highly different polynucleotide sequences are misclassified as highly similar ones, and completely different sequences are misclassified as identical ones. For this reason their construct is to be considered as a device of misdiagnosis that bears "fuzzy polynucleotide space" as a misnomer.
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HILMOE RJ. THE EFFECT OF END GROUPS AND THE INITIAL SITE OF ATTACK ON POLYNUCLEOTIDES BY POLYNUCLEOTIDE PHOSPHORYLASE AND CERTAIN PHOSPHODIESTERASES. Ann N Y Acad Sci 2006; 81:660-74. [PMID: 14401822 DOI: 10.1111/j.1749-6632.1959.tb49347.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Le Pecq JB. Use of ethidium bromide for separation and determination of nucleic acids of various conformational forms and measurement of their associated enzymes. Methods Biochem Anal 2006; 20:41-86. [PMID: 4947800 DOI: 10.1002/9780470110393.ch2] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Abstract
The binding of manganese(III)-tetra(4-N-methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA-dT)2, poly(dI-dC)2, and poly(dG-dC)2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD spectra, which changed greatly depending on the porphyrin to DNA base-pair molar ratio (r), were normalized with respect to DNA concentration and deconvoluted. Three independent component binding modes (named mode 1, 2, and 3 in the order of increasing r values) were identified, which successfully simulated the observed CD spectra with negligibly small residuals for a wide range of r values. In the case of poly(dA-dT)2, poly (dI-dC)2, and CT DNA, all the three modes appeared, whereas in the case of poly(dG-dC)2 DNA, only modes 1 and 3 appeared in the r range studied. The r dependence of each binding mode, i.e., its relative affinity toward DNA, has been revealed by this analysis. Mode 1, which appeared as a single binding mode at very low r values (r < or = ca. 0.05), was inhibited by the addition of methyl green, a drug that preferentially binds to the major groove of poly (dA-dT)2 DNA. Berenil, a known minor groove binder to poly(dA-dT)2 or poly(dI-dC)2 DNA, inhibited modes 2 and 3. From these inhibition experiments as well as comparison of the component spectra for DNAs of different sequence, a binding site on DNA was proposed for each component binding mode. The number of DNA base pairs covered by a single molecule of porphyrin was estimated.
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Affiliation(s)
- Y Nitta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902 Japan
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Meyer U, Nyffeler M, Engler A, Urwyler A, Schedlowski M, Knuesel I, Yee BK, Feldon J. The time of prenatal immune challenge determines the specificity of inflammation-mediated brain and behavioral pathology. J Neurosci 2006; 26:4752-62. [PMID: 16672647 PMCID: PMC6674174 DOI: 10.1523/jneurosci.0099-06.2006] [Citation(s) in RCA: 576] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Disturbance to early brain development is implicated in several neuropsychiatric disorders including autism, schizophrenia, and mental retardation. Epidemiological studies have indicated that the risk of developing these disorders is enhanced by prenatal maternal infection, presumably as a result of neurodevelopmental defects triggered by cytokine-related inflammatory events. Here, we demonstrate that the effects of maternal immune challenge between middle and late gestation periods in mice are dissociable in terms of fetal brain cytokine responses to maternal inflammation and the pathological consequences in brain and behavior. Specifically, the relative expression of pro- and anti-inflammatory cytokines in the fetal brains in response to maternal immune challenge may be an important determinant among other developmental factors for the precise pathological profile emerging in later life. Thus, the middle and late gestation periods correspond to two windows with differing vulnerability to adult behavioral dysfunction, brain neuropathology in early adolescence, and of the acute cytokine responses in the fetal brain.
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Yan A, Wu E, Lennarz WJ. Studies of yeast oligosaccharyl transferase subunits using the split-ubiquitin system: topological features and in vivo interactions. Proc Natl Acad Sci U S A 2005; 102:7121-6. [PMID: 15886282 PMCID: PMC1129144 DOI: 10.1073/pnas.0502669102] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oligosaccharyl transferase (OT) catalyzes the cotranslational N-glycosylation of nascent polypeptides in the endoplasmic reticulum in all eukaryotic systems. Due to the inherent difficulty in characterizing this membrane protein complex, the mode of enzymatic action has not been resolved. Here, we used a membrane protein two-hybrid approach, the split-ubiquitin system, to address two aspects of the enzyme complex in yeast: the topological features, as well as the in vivo interactions of all of the components. We investigated the N- and C-terminal orientation of these proteins and the presence or the absence of a cleavable signal sequence at their N termini. We found that Ost2p and Stt3p have only their N terminus located in the cytosol, whereas Ost3p and Swp1p have only their C terminus oriented in the cytosol. In the case of Ost5p and Ost6p, both their N and C termini are present in the cytosol. These findings also suggested that Ost2p, Stt3p, Ost5p, and Ost6p do not have a cleavable N-terminal signal sequence. The pairwise analysis of in vivo interactions among all of the OT subunits demonstrated that OT subunits display specific interactions with each other in a functional complex. By comparing this interaction pattern with that detected in vitro in a nonfunctional complex, we proposed that a distinct conformation rearrangement takes place when the enzyme complex changes from the nonfunctional state to the activated functional state. This finding is consistent with earlier work by others indicating that OT exhibits allosteric properties.
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Affiliation(s)
- Aixin Yan
- Department of Biochemistry and Cell Biology and Institute for Cell and Developmental Biology, Stony Brook University, Stony Brook, NY 11794, USA
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Abstract
We developed an improved method for cultivation-independent sorting of bacterial cells. The technique is based on labeling the target cells by in situ hybridization with polynucleotide transcript probes. Due to the probes' length, part of the probe remains outside the cell and can subsequently be used to capture the cells. Target cells are immobilized during a second hybridization step in microplates that are coated with DNA that is complementary to the probe sequence. The method was applied successfully to artificial mixtures of cells with polynucleotide probes targeting either rRNA, a plasmid-borne beta-lactamase gene, or a chromosome-borne glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. Cells could be separated based on phylogenetic parameters (using rRNA-targeted probes) as well as on other DNA-encoded traits.
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Affiliation(s)
- K Zwirglmaier
- Lehrstuhl für Mikrobiologie, Technische Universität München, 85350 Freising, Germany
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Abstract
Recent crystallographic studies reveal loops in human AP endonuclease 1 (APE1) that interact with the major and minor grooves of DNA containing apurinic/apyrimidinic (AP) sites. These loops are postulated to stabilize the DNA helix and the flipped out AP residue. The loop alpha8 interacts with the major groove on the 3' side of the AP site. To determine the essentiality of the amino acids that constitute the alpha8 loop, we created a mutant library containing random nucleotides at codons 222-229 that, in wild-type APE1, specify the sequence NPKGNKKN. Upon expression of the library (2 x 10(6) different clones) in Escherichia coli and multiple rounds of selection with the alkylating agent methyl-methane sulfonate (MMS), we obtained approximately 2 x 10(5) active mutants that complemented the MMS sensitivity of AP endonuclease-deficient E. coli. DNA sequencing showed that active mutants tolerated amino acid substitutions at all eight randomized positions. Basic and uncharged polar amino acids together comprised the majority of substitutions, reflecting the positively charged, polar character of the wild-type loop. Asn-222, Asn-226, and Asn-229 exhibited the least mutability, consistent with x-ray data showing that each asparagine contacts a DNA phosphate. Substitutions at residues 226-229, located nearer to the AP site, that reduced basicity or hydrogen bonding potential, increased Km 2- to 6-fold and decreased AP site binding; substitutions at residues 222-225 exhibited lesser effects. This initial mutational analysis of the alpha8 loop supports and extends the conclusion of crystallographic studies that the loop is important for binding of AP.DNA and AP site incision.
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Affiliation(s)
- Jiang-Cheng Shen
- Department of Pathology, University of Washington, 1959 NE Pacific Avenue, Seattle, WA 98195-7705, USA
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HEPPEL LA, WHITFELD PR, MARKHAM R. Nucleotide exchange reactions catalysed by ribonuclease and spleen phosphodiesterase. II. Synthesis of polynucleotides. Biochem J 2003; 60:8-15. [PMID: 14363175 PMCID: PMC1215643 DOI: 10.1042/bj0600008] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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JACOB TM, KHORANA HG. Studies on Polynucleotides. XXXVII.1 The Synthesis of Specific Deoxyribopolynucleotides.2 Further Examination of the Approach Involving Stepwise Synthesis3. J Am Chem Soc 2002; 87:368-74. [PMID: 14228463 DOI: 10.1021/ja01080a038] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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RALPH RK, SMITH RA, KHORANA HG. Studies on Polynucleotides. XV.* Enzymic Degradation. The Mode of Action of Pancreatic Deoxyribonuclease on Thymidine, Deoxycytidine, and Deoxyadenosine Polynucleotides. Biochemistry 2002; 1:131-7. [PMID: 14490045 DOI: 10.1021/bi00907a020] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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SOELL D, KHORANA HG. Studies on Polynucleotides. XXXV.1 The Specific Synthesis of C3'-C5'-Linked Ribooligonucleotides. VIII.2 The Synthesis of Ribodinucleotides Bearing 3'-Phosphomonoester Groups3. J Am Chem Soc 2002; 87:350-9. [PMID: 14228461 DOI: 10.1021/ja01080a036] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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MILLARD B, CUKIER R, NIRENBERG M. Interaction of Escherichia coli Ribosomal Ribonucleic Acid with Synthetic Polynucleotides. Sedimentation Properties, and Thermal Stability as Measured by Fluroescence Polarization*. Biochemistry 2002; 4:976-85. [PMID: 14337717 DOI: 10.1021/bi00881a026] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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SOELL D, KHORANA HG. Studies on Polynucleotides. XXXVI.1 The Specific Synthesis of C3'-C5'-Linked Ribooligonucleotides. IX.2 The Synthesis of Ribodinucleotides Bearing 3'-Phosphomonoester Groups3. J Am Chem Soc 2002; 87:360-7. [PMID: 14228462 DOI: 10.1021/ja01080a037] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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JACOB TM, KHORANA HG. Studies on Polynucleotides. XLIV.1 The Synthesis of Dodecanucleotides Containing the Repeating Trinucleotide Sequence Thymidylyl- (3'→5') -thymidylyl- (3'→5') -deoxycytidine2,3. J Am Chem Soc 2002; 87:2971-81. [PMID: 14302376 DOI: 10.1021/ja01091a029] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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STRAUS DB, FRESCO JR. Synthesis of N-Benzoyl-2'-O-tetrahydropyranylguanosine-5'-phosphate, an Intermediate in the Chemical Synthesis of Polyriboguanylic Acid1. J Am Chem Soc 2002; 87:1364-74. [PMID: 14293758 DOI: 10.1021/ja01084a035] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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LAMBORG MR, ZAMECNIK PC, LI TK, KAEGI J, VALLEE BL. Anomalous Rotatory Dispersion of Soluble Ribonucleic Acid and Its Relation to Amino Acid Synthetase Recognition*. Biochemistry 2002; 4:63-70. [PMID: 14285246 DOI: 10.1021/bi00877a012] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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OHTSUKA E, MOON MW, KHORANA HG. Studies on Polynucleotides. XLIII.1 The Synthesis of Deoxyribopolynucleotides Containing Repeating Dinucleotide Sequences2,3. J Am Chem Soc 2002; 87:2956-70. [PMID: 14302088 DOI: 10.1021/ja01091a028] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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NARANG SA, JACOB TM, KHORANA HG. Studies on Polynucleotides. XLVI.1 The Synthesis of Hexanucleotides Containing the Repeating Trinucleotide Sequences Deoxycytidylyl-(3'→5')-deoxyadenylyl-(3'→5')-deoxyadenosine and Deoxyguanylyl-(3'→5')-deoxyadenylyl-(3'→5')- deoxyadenosine2. J Am Chem Soc 2002; 87:2988-95. [PMID: 14302090 DOI: 10.1021/ja01091a031] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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KHORANA HG, JACOB TM, MOON MW, NARANG SA, OHTSUKA E. Studies on Polynucleotides. XLII.1 The Synthesis of Deoxyribopolynucleotides Containing Repeating Nucleotide Sequences.2 Introduction and General Considerations3. J Am Chem Soc 2002; 87:2954-6. [PMID: 14302087 DOI: 10.1021/ja01091a027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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NARANG SA, KHORANA HG. Studies on Polynucleotides. XLV.1 The Synthesis of Dodecanucleotides Containing the Repeating Trinucleotide Sequence Thymidylyl- (3'→5') -thymidylyl- (3'→5') -deoxyinosine2. J Am Chem Soc 2002; 87:2981-8. [PMID: 14302089 DOI: 10.1021/ja01091a030] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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MILES HT. Quantitative infrared spectra in D20 of some nucleosides, nucleotides, and polynucleotides; a new measure of polynucleotide interaction. ACTA ACUST UNITED AC 2000; 30:324-8. [PMID: 13607449 DOI: 10.1016/0006-3002(58)90057-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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BEERS RF, HENDLEY DD, STEINER RF. Inhibition and activation of polynucleotide phosphorylase through the formation of complexes between acridine orange and polynucleotides. Nature 2000; 182:242-4. [PMID: 13577797 DOI: 10.1038/182242a0] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
RNA molecules that bind tightly and specifically to a Rex fusion protein have been isolated from a conformationally constrained pool of random sequence RNAs. The anti-Rex aptamers effectively mimic several features of the wild-type Rex-binding element (XBE). The highest-affinity aptamers effectively compete with the wild-type XBE for binding to the RNA-binding domain of Rex, an arginine-rich motif (ARM), but do not bind to the functionally analogous Rev protein or its ARM. However, characteristic sequence and structural motifs found in some of the anti-Rex aptamers may provide insights into how the Rex protein can interact with other viral RNAs, such as the Rev-responsive element. The anti-Rex aptamers can functionally substitute for the XBE in vivo, a result which supports a previously proposed model for mRNA transport in which the viral genome serves as a platform for assembling a nucleoprotein complex that can co-opt the cellular transport apparatus. Overall, these studies suggest that anti-Rex aptamers may serve as RNA decoys of the Rex protein.
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Affiliation(s)
- S Baskerville
- Department of Biology, Indiana University at Bloomington, Bloomington, Indiana, USA
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Government-owned inventions; availability for licensing. National Institutes of Health, Public Health Service, DHHS. Notice. Fed Regist 1999; 64:9338-9. [PMID: 10557591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The inventions listed below are owned by agencies of the U.S. Government and are available for licensing in the U.S. in accordance with 35 U.S.C. 207 to achieve expeditious commercialization of results of federally-funded research and development. Foreign patent applications are filed on selected inventions to extend market coverage for companies and may also be available for licensing.
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Abstract
Yeast Rad27 is a 5'-->3' exonuclease and a flap endo-nuclease. Apn1 is the major apurinic/apyrimidinic (AP) endonuclease in yeast. The rad27 deletion mutants are highly sensitive to methylmethane sulfonate (MMS). By examining the role of Rad27 in different modes of DNA excision repair, we wish to understand why the cytotoxic effect of MMS is dramatically enhanced in the absence of Rad27. Base excision repair (BER) of uracil-containing DNA was deficient in rad27 mutant extracts in that (i) the Apn1 activity was reduced, and (ii) after DNA incision by Apn1, hydrolysis of 1-5 nucleotides 3' to the baseless sugar phosphate was deficient. Thus, some AP sites may lead to unprocessed DNA strand breaks in rad27 mutant cells. The severe MMS sensitivity of rad27 mutants is not caused by a reduction of the Apn1 activity. Surprisingly, we found that Apn1 endonuclease sensitizes rad27 mutant cells to MMS. Deleting the APN1 gene largely restored the resistance of rad27 mutants to MMS. These results suggest that unprocessed DNA strand breaks at AP sites are mainly responsible for the MMS sensitivity of rad27 mutants. In contrast, nucleotide excision repair and BER of oxidative damage were not affected in rad27 mutant extracts, indicating that Rad27 is specifically required for BER of AP sites in DNA.
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Affiliation(s)
- X Wu
- Graduate Center for Toxicology, University of Kentucky, Lexington, KY 40536, USA
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