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Article ; Online: Characterization of t-loop formation by TRF2.

Timashev, Leonid A / De Lange, Titia

2020 Volume 11, Issue 1, Page(s) 164–177

Abstract: T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin ... ...

Abstract	T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin proteins can form t-loops. Mouse and human cells contain two isoforms of TRF2, one of which is uncharacterized. We show that both isoforms protect telomeres and form t-loops. The isoforms are not cell cycle regulated and t-loops are present in G1, S, and G2. Using the DNA wrapping deficient TRF2 Topless mutant, we confirm its inability to form t-loops and repress ATM. However, since the mutant is also defective in repression of NHEJ and telomeric localization, the role of topological changes in telomere protection remains unclear. Finally, we show that Rad51 does not affect t-loop frequencies or telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
MeSH term(s)	Animals ; CRISPR-Cas Systems/genetics ; Cell Line ; Mice ; Mice, Knockout ; Proteomics ; Rad51 Recombinase/genetics ; Rad51 Recombinase/metabolism ; Telomeric Repeat Binding Protein 2/genetics ; Telomeric Repeat Binding Protein 2/metabolism
Chemical Substances	TRF2 protein, mouse ; Telomeric Repeat Binding Protein 2 ; Rad51 Recombinase (EC 2.7.7.-) ; Rad51 protein, mouse (EC 2.7.7.-)
Language	English
Publishing date	2020-06-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2020.1783782
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Article: Characterization of t-loop formation by TRF2

Timashev, Leonid A / De Lange, Titia

Nucleus. 2020 Jan. 01, v. 11, no. 1

2020

Abstract	T-loops are thought to hide telomeres from DNA damage signaling and DSB repair pathways. T-loop formation requires the shelterin component TRF2, which represses ATM signaling and NHEJ. Here we establish that TRF2 alone, in the absence of other shelterin proteins can form t-loops. Mouse and human cells contain two isoforms of TRF2, one of which is uncharacterized. We show that both isoforms protect telomeres and form t-loops. The isoforms are not cell cycle regulated and t-loops are present in G1, S, and G2. Using the DNA wrapping deficient TRF2 Topless mutant, we confirm its inability to form t-loops and repress ATM. However, since the mutant is also defective in repression of NHEJ and telomeric localization, the role of topological changes in telomere protection remains unclear. Finally, we show that Rad51 does not affect t-loop frequencies or telomere protection. Therefore, alternative models for how TRF2 forms t-loops should be explored.
Keywords	DNA ; DNA damage ; DNA repair ; cell cycle ; humans ; mice ; mutants ; telomeres ; topology
Language	English
Dates of publication	2020-0101
Size	p. 164-177.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2619626-8
ISSN	1949-1042 ; 1949-1034
ISSN (online)	1949-1042
ISSN	1949-1034
DOI	10.1080/19491034.2020.1783782
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Article ; Online: The DDR at telomeres lacking intact shelterin does not require substantial chromatin decompaction.

Timashev, Leonid A / Babcock, Hazen / Zhuang, Xiaowei / de Lange, Titia

Genes & development

2017 Volume 31, Issue 6, Page(s) 578–589

Abstract: Telomeres are protected by shelterin, a six-subunit protein complex that represses the DNA damage response (DDR) at chromosome ends. Extensive data suggest that TRF2 in shelterin remodels telomeres into the t-loop structure, thereby hiding telomere ends ... ...

Abstract	Telomeres are protected by shelterin, a six-subunit protein complex that represses the DNA damage response (DDR) at chromosome ends. Extensive data suggest that TRF2 in shelterin remodels telomeres into the t-loop structure, thereby hiding telomere ends from double-stranded break repair and ATM signaling, whereas POT1 represses ATR signaling by excluding RPA. An alternative protection mechanism was suggested recently by which shelterin subunits TRF1, TRF2, and TIN2 mediate telomeric chromatin compaction, which was proposed to minimize access of DDR factors. We performed superresolution imaging of telomeres in mouse cells after conditional deletion of TRF1, TRF2, or both, the latter of which results in the complete loss of shelterin. Upon removal of TRF1 or TRF2, we observed only minor changes in the telomere volume in most of our experiments. Upon codeletion of TRF1 and TRF2, the telomere volume increased by varying amounts, but even those samples exhibiting small changes in telomere volume showed DDR at nearly all telomeres. Upon shelterin removal, telomeres underwent 53BP1-dependent clustering, potentially explaining at least in part the apparent increase in telomere volume. Furthermore, chromatin accessibility, as determined by ATAC-seq (assay for transposase-accessible chromatin [ATAC] with high-throughput sequencing), was not substantially altered by shelterin removal. These results suggest that the DDR induced by shelterin removal does not require substantial telomere decompaction.
MeSH term(s)	Animals ; Cells, Cultured ; Chromatin/physiology ; DNA Damage ; Mice ; Microscopy, Fluorescence ; Telomere/ultrastructure ; Telomeric Repeat Binding Protein 1/physiology ; Telomeric Repeat Binding Protein 2/physiology ; Tumor Suppressor p53-Binding Protein 1/physiology
Chemical Substances	Chromatin ; TRF2 protein, mouse ; Telomeric Repeat Binding Protein 1 ; Telomeric Repeat Binding Protein 2 ; Trp53bp1 protein, mouse ; Tumor Suppressor p53-Binding Protein 1
Language	English
Publishing date	2017-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, N.I.H., Extramural
ZDB-ID	806684-x
ISSN	1549-5477 ; 0890-9369
ISSN (online)	1549-5477
ISSN	0890-9369
DOI	10.1101/gad.294108.116
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Zs.A 2292: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Mammalian Pericardium-Based Bioprosthetic Materials in Xenotransplantation and Tissue Engineering.

Grebenik, Ekaterina A / Gafarova, Elvira R / Istranov, Leonid P / Istranova, Elena V / Ma, Xiaowei / Xu, Jing / Guo, Weisheng / Atala, Anthony / Timashev, Peter S

Biotechnology journal

2020 Volume 15, Issue 8, Page(s) e1900334

Abstract: Bioprosthetic materials based on mammalian pericardium tissue are the gold standard in reconstructive surgery. Their application range covers repair of rectovaginal septum defects, abdominoplastics, urethroplasty, duraplastics, maxillofacial, ophthalmic, ...

Abstract	Bioprosthetic materials based on mammalian pericardium tissue are the gold standard in reconstructive surgery. Their application range covers repair of rectovaginal septum defects, abdominoplastics, urethroplasty, duraplastics, maxillofacial, ophthalmic, thoracic and cardiovascular reconstruction, etc. However, a number of factors contribute to the success of their integration into the host tissue including structural organization, mechanical strength, biocompatibility, immunogenicity, surface chemistry, and biodegradability. In order to improve the material's properties, various strategies are developed, such as decellularization, crosslinking, and detoxification. In this review, the existing issues and long-term achievements in the development of bioprosthetic materials based on the mammalian pericardium tissue, aimed at a wide-spectrum application in reconstructive surgery are analyzed. The basic technical approaches to preparation of biocompatible forms providing continuous functioning, optimization of biomechanical and functional properties, and clinical applicability are described.
MeSH term(s)	Animals ; Biocompatible Materials ; Humans ; Mammals ; Pericardium ; Prostheses and Implants/standards ; Tissue Engineering ; Transplantation, Heterologous
Chemical Substances	Biocompatible Materials
Language	English
Publishing date	2020-03-04
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2221885-3
ISSN	1860-7314 ; 1860-6768
ISSN (online)	1860-7314
ISSN	1860-6768
DOI	10.1002/biot.201900334
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Zs.A 6349: Show issues

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Article ; Online: Chemical cross-linking of xenopericardial biomeshes: A bottom-up study of structural and functional correlations.

Grebenik, Ekaterina A / Istranov, Leonid P / Istranova, Elena V / Churbanov, Semyon N / Shavkuta, Boris S / Dmitriev, Ruslan I / Veryasova, Nadezhda N / Kotova, Svetlana L / Kurkov, Alexander V / Shekhter, Anatoly B / Timashev, Peter S

Xenotransplantation

2019 Volume 26, Issue 3, Page(s) e12506

Abstract: Decellularized bovine pericardium (DBP)-based biomeshes are the gold standard in reconstructive surgery. In order to prolong their stability after the transplantation, various chemical cross-linking strategies are employed. However, structural and ... ...

Abstract	Decellularized bovine pericardium (DBP)-based biomeshes are the gold standard in reconstructive surgery. In order to prolong their stability after the transplantation, various chemical cross-linking strategies are employed. However, structural and functional properties of the biomeshes differ in dependence on the cross-linker used. Here, we performed a bottom-up study of structural and functional alterations of DBP-based biomeshes following cross-linking with hexamethylene diisocyanate (HMDC), ethylene glycol diglycidyl ether (EGDE), 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and genipin. The in vitro cytotoxicity tests supported their clinical applicability. Their structural differences (eg roughness, fibre thickness, pore morphology) were evaluated using the two-photon confocal laser scanning, atomic force, scanning electron and polarized light microscopies. HMDC and EDC samples appeared to be the roughest. Complex mechanical trials indicated the tendency to reduced Young's Modulus and mechanical anisotropy values of DBP upon cross-linking. The lowest mechanical anisotropy was found in EDC and genipin sample groups. In vitro collagenase susceptibility was the highest for EDC samples and the lowest for EGDE samples. The comparative analysis of the results allowed us to recognize the strengths and weaknesses of each cross-linker in relation to a particular clinical application.
MeSH term(s)	Animals ; Cattle ; Cross-Linking Reagents ; Iridoids/pharmacology ; Materials Testing/methods ; Pericardium/surgery ; Tissue Engineering/methods ; Transplantation, Heterologous
Chemical Substances	Cross-Linking Reagents ; Iridoids ; genipin (A3V2NE52YG)
Language	English
Publishing date	2019-01-22
Publishing country	Denmark
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1236298-0
ISSN	1399-3089 ; 0908-665X
ISSN (online)	1399-3089
ISSN	0908-665X
DOI	10.1111/xen.12506
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Zs.A 4514: Show issues

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Article ; Online: Template switching during break-induced replication is promoted by the Mph1 helicase in Saccharomyces cerevisiae.

Stafa, Anamarija / Donnianni, Roberto A / Timashev, Leonid A / Lam, Alicia F / Symington, Lorraine S

Genetics

2014 Volume 196, Issue 4, Page(s) 1017–1028

Abstract: Chromosomal double-strand breaks (DSBs) that have only one end with homology to a donor duplex undergo repair by strand invasion followed by replication to the chromosome terminus (break-induced replication, BIR). Using a transformation-based assay ... ...

Abstract	Chromosomal double-strand breaks (DSBs) that have only one end with homology to a donor duplex undergo repair by strand invasion followed by replication to the chromosome terminus (break-induced replication, BIR). Using a transformation-based assay system, it was previously shown that BIR could occur by several rounds of strand invasion, DNA synthesis, and dissociation. Here we describe a modification of the transformation-based assay to facilitate detection of switching between donor templates during BIR by genetic selection in diploid yeast. In addition to the expected recovery of template switch products, we found a high frequency of recombination between chromosome homologs during BIR, suggesting transfer of the DSB from the transforming linear DNA to the donor chromosome, initiating secondary recombination events. The frequency of BIR increased in the mph1Δ mutant, but the percentage of template switch events was significantly decreased, revealing an important role for Mph1 in promoting BIR-associated template switching. In addition, we show that the Mus81, Rad1, and Yen1 structure-selective nucleases act redundantly to facilitate BIR.
MeSH term(s)	Chromosome Breakage ; Chromosomes, Fungal/genetics ; Chromosomes, Fungal/metabolism ; DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; DNA Breaks, Double-Stranded ; DNA Helicases/metabolism ; DNA Repair Enzymes/metabolism ; DNA Replication ; DNA, Fungal/metabolism ; DNA-Binding Proteins/metabolism ; Endonucleases/metabolism ; Holliday Junction Resolvases/metabolism ; Recombinational DNA Repair ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Templates, Genetic ; Translocation, Genetic
Chemical Substances	DNA, Fungal ; DNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Endonucleases (EC 3.1.-) ; MUS81 protein, S cerevisiae (EC 3.1.-) ; RAD1 protein, S cerevisiae (EC 3.1.-) ; Holliday Junction Resolvases (EC 3.1.21.-) ; Yen1 protein, S cerevisiae (EC 3.1.21.-) ; MPH1 protein, S cerevisiae (EC 3.6.1.-) ; PIF1 protein, S cerevisiae (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-) ; DEAD-box RNA Helicases (EC 3.6.4.13) ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2014-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2167-2
ISSN	1943-2631 ; 0016-6731
ISSN (online)	1943-2631
ISSN	0016-6731
DOI	10.1534/genetics.114.162297
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Article ; Online: Sae2 promotes DNA damage resistance by removing the Mre11-Rad50-Xrs2 complex from DNA and attenuating Rad53 signaling.

Chen, Huan / Donnianni, Roberto A / Handa, Naofumi / Deng, Sarah K / Oh, Julyun / Timashev, Leonid A / Kowalczykowski, Stephen C / Symington, Lorraine S

Proceedings of the National Academy of Sciences of the United States of America

2015 Volume 112, Issue 15, Page(s) E1880–7

Abstract: The Mre11-Rad50-Xrs2/NBS1 (MRX/N) nuclease/ATPase complex plays structural and catalytic roles in the repair of DNA double-strand breaks (DSBs) and is the DNA damage sensor for Tel1/ATM kinase activation. Saccharomyces cerevisiae Sae2 can function with ... ...

Abstract	The Mre11-Rad50-Xrs2/NBS1 (MRX/N) nuclease/ATPase complex plays structural and catalytic roles in the repair of DNA double-strand breaks (DSBs) and is the DNA damage sensor for Tel1/ATM kinase activation. Saccharomyces cerevisiae Sae2 can function with MRX to initiate 5'-3' end resection and also plays an important role in attenuation of DNA damage signaling. Here we describe a class of mre11 alleles that suppresses the DNA damage sensitivity of sae2Δ cells by accelerating turnover of Mre11 at DNA ends, shutting off the DNA damage checkpoint and allowing cell cycle progression. The mre11 alleles do not suppress the end resection or hairpin-opening defects of the sae2Δ mutant, indicating that these functions of Sae2 are not responsible for DNA damage resistance. The purified M(P110L)RX complex shows reduced binding to single- and double-stranded DNA in vitro relative to wild-type MRX, consistent with the increased turnover of Mre11 from damaged sites in vivo. Furthermore, overproduction of Mre11 causes DNA damage sensitivity only in the absence of Sae2. Together, these data suggest that it is the failure to remove Mre11 from DNA ends and attenuate Rad53 kinase signaling that causes hypersensitivity of sae2Δ cells to clastogens.
MeSH term(s)	Cell Cycle/genetics ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Checkpoint Kinase 2/genetics ; Checkpoint Kinase 2/metabolism ; DNA Breaks, Double-Stranded ; DNA Damage ; DNA Repair ; DNA, Fungal/genetics ; DNA, Fungal/metabolism ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Endodeoxyribonucleases/genetics ; Endodeoxyribonucleases/metabolism ; Endonucleases/genetics ; Endonucleases/metabolism ; Exodeoxyribonucleases/genetics ; Exodeoxyribonucleases/metabolism ; Microscopy, Fluorescence ; Multiprotein Complexes/genetics ; Multiprotein Complexes/metabolism ; Mutation ; Protein Binding ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Signal Transduction/genetics
Chemical Substances	Cell Cycle Proteins ; DNA, Fungal ; DNA-Binding Proteins ; Multiprotein Complexes ; RAD50 protein, S cerevisiae ; SAE2 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; XRS2 protein, S cerevisiae ; Checkpoint Kinase 2 (EC 2.7.1.11) ; RAD53 protein, S cerevisiae (EC 2.7.12.1) ; Endodeoxyribonucleases (EC 3.1.-) ; Endonucleases (EC 3.1.-) ; Exodeoxyribonucleases (EC 3.1.-) ; MRE11 protein, S cerevisiae (EC 3.1.-)
Language	English
Publishing date	2015-04-14
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1503331112
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Zs.A 1148: Show issues

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Article ; Online: Implantation of Various Cell-Free Matrixes Does Not Contribute to the Restoration of Hyaline Cartilage within Full-Thickness Focal Defects

Shabnam I. Ibragimova / Ekaterina V. Medvedeva / Irina A. Romanova / Leonid P. Istranov / Elena V. Istranova / Aleksey V. Lychagin / Andrey A. Nedorubov / Peter S. Timashev / Vladimir I. Telpukhov / Andrei S. Chagin

International Journal of Molecular Sciences, Vol 23, Iss 292, p

2022 Volume 292

Abstract: Articular cartilage is a highly organized tissue that has a limited ability to heal. Tissue engineering is actively exploited for joint tissue reconstruction in numerous cases of articular cartilage degeneration associated with trauma, arthrosis, ... ...

Abstract	Articular cartilage is a highly organized tissue that has a limited ability to heal. Tissue engineering is actively exploited for joint tissue reconstruction in numerous cases of articular cartilage degeneration associated with trauma, arthrosis, rheumatoid arthritis, and osteoarthritis. However, the optimal scaffolds for cartilage repair are not yet identified. Here we have directly compared five various scaffolds, namely collagen-I membrane, collagen-II membrane, decellularized cartilage, a cellulose-based implant, and commercially available Chondro-Gide ® (Geistlich Pharma AG, Wolhusen, Switzerland) collagen membrane. The scaffolds were implanted in osteochondral full-thickness defects, formed on adult Wistar rats using a hand-held cutter with a diameter of 2.0 mm and a depth of up to the subchondral bone. The congruence of the articular surface was almost fully restored by decellularized cartilage and collagen type II-based scaffold. The most vivid restoration was observed 4 months after the implantation. The formation of hyaline cartilage was not detected in any of the groups. Despite cellular infiltration into scaffolds being observed in each group except cellulose, neither chondrocytes nor chondro-progenitors were detected. We concluded that for restoration of hyaline cartilage, scaffolds have to be combined either with cellular therapy or morphogens promoting chondrogenic differentiation.
Keywords	articular cartilage ; full-thickness defect ; scaffold ; collagen membrane ; decellularized cartilage ; cellulose ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2022-12-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Implantation of Various Cell-Free Matrixes Does Not Contribute to the Restoration of Hyaline Cartilage within Full-Thickness Focal Defects.

Ibragimova, Shabnam I / Medvedeva, Ekaterina V / Romanova, Irina A / Istranov, Leonid P / Istranova, Elena V / Lychagin, Aleksey V / Nedorubov, Andrey A / Timashev, Peter S / Telpukhov, Vladimir I / Chagin, Andrei S

International journal of molecular sciences

2021 Volume 23, Issue 1

Abstract	Articular cartilage is a highly organized tissue that has a limited ability to heal. Tissue engineering is actively exploited for joint tissue reconstruction in numerous cases of articular cartilage degeneration associated with trauma, arthrosis, rheumatoid arthritis, and osteoarthritis. However, the optimal scaffolds for cartilage repair are not yet identified. Here we have directly compared five various scaffolds, namely collagen-I membrane, collagen-II membrane, decellularized cartilage, a cellulose-based implant, and commercially available Chondro-Gide
MeSH term(s)	Animals ; Fibrillar Collagens/metabolism ; Hyaline Cartilage/pathology ; Knee Joint/pathology ; Male ; Osteogenesis ; Prosthesis Implantation ; Rats, Wistar ; SOX9 Transcription Factor/metabolism ; Tissue Scaffolds/chemistry ; Rats
Chemical Substances	Fibrillar Collagens ; SOX9 Transcription Factor
Language	English
Publishing date	2021-12-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23010292
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Article ; Online: Solvent-free synthesis and characterization of allyl chitosan derivatives.

Akopova, Tatiana A / Demina, Tatiana S / Cherkaev, Georgii V / Khavpachev, Mukhamed A / Bardakova, Kseniya N / Grachev, Andrey V / Vladimirov, Leonid V / Zelenetskii, Alexander N / Timashev, Petr S

RSC advances

2019 Volume 9, Issue 36, Page(s) 20968–20975

Abstract: The solvent-free synthesis of allyl-substituted chitosan derivatives through reactive co-extrusion of chitosan powder with allyl bromide at shear deformation was performed. For the structural characterization, FTIR and NMR methods were employed. The ... ...

Abstract	The solvent-free synthesis of allyl-substituted chitosan derivatives through reactive co-extrusion of chitosan powder with allyl bromide at shear deformation was performed. For the structural characterization, FTIR and NMR methods were employed. The results were confirmed by chemical analysis. The total content of allyl substituents from 5 to 50 per 100 chitosan units as a function of the component ratio in the reactive mixtures was revealed. Carrying out the reaction without any additives leads to the selective formation of
Language	English
Publishing date	2019-07-04
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/c9ra03830b
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