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Journal articles on the topic 'Backbone Modification'

Author: Grafiati

Published: 6 September 2023

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1

Servatius, Phil, Lukas Junk, and Uli Kazmaier. "Peptide Modifications: Versatile Tools in Peptide and Natural Product Syntheses." Synlett 30, no. 11 (April 2, 2019): 1289–302. http://dx.doi.org/10.1055/s-0037-1612417.

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Peptide modifications via C–C bond formation have emerged as valuable tools for the preparation and alteration of non-proteinogenic amino acids and the corresponding peptides. Modification of glycine subunits in peptides allows for the incorporation of unusual side chains, often in a highly stereoselective manner, orchestrated by the chiral peptide backbone. Moreover, modifications of peptides are not limited to the peptidic backbone. Many side-chain modifications, not only by variation of existing functional groups, but also by C–H functionalization, have been developed over the past decade. This account highlights the synthetic contributions made by our group and others to the field of peptide modifications and their application in natural product syntheses.1 Introduction2 Peptide Backbone Modifications via Peptide Enolates2.1 Chelate Enolate Claisen Rearrangements2.2 Allylic Alkylations2.3 Miscellaneous Modifications3 Side-Chain Modifications3.1 C–H Activation3.1.1 Functionalization via Csp3–H Bond Activation3.2.2 Functionalization via Csp2–H Bond Activation3.2 On Peptide Tryptophan Syntheses4 Conclusion

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2

Rehpenn, Andreas, Alexandra Walter, and Golo Storch. "Molecular Editing of Flavins for Catalysis." Synthesis 53, no. 15 (March 22, 2021): 2583–93. http://dx.doi.org/10.1055/a-1458-2419.

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AbstractThe diverse activity of flavoenzymes in organic transformations has fascinated researchers for a long time. However, when applied outside an enzyme environment, the isolated flavin cofactor only shows largely reduced activity. This highlights the importance of embedding the reactive isoalloxazine core of flavins in defined surroundings. The latter include crucial non-covalent interactions with amino acid side chains or backbone as well as controlled access to reactants such as molecular oxygen. Nevertheless, molecular flavins are increasingly applied in the organic laboratory as valuable organocatalysts. Chemical modification of the parent isoalloxazine structure is of particular interest in this context in order to achieve reactivity and selectivity in transformations, which are so far only known with flavoenzymes or even unprecedented. This review aims to give a systematic overview of the reported designed flavin catalysts and highlights the impact of each structural alteration. It is intended to serve as a source of information when comparing the performance of known catalysts, but also when designing new flavins. Over the last few decades, molecular flavin catalysis has emerged from proof-of-concept reactions to increasingly sophisticated transformations. This stimulates anticipating new flavin catalyst designs for solving contemporary challenges in organic synthesis.1 Introduction2 N1-Modification3 N3-Modification4 N5-Modification5 C6–C9-Modification6 N10-Modification7 Conclusion

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3

Schmidtgall, Boris, Claudia Höbartner, and Christian Ducho. "NAA-modified DNA oligonucleotides with zwitterionic backbones: stereoselective synthesis of A–T phosphoramidite building blocks." Beilstein Journal of Organic Chemistry 11 (January 13, 2015): 50–60. http://dx.doi.org/10.3762/bjoc.11.8.

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Modifications of the nucleic acid backbone are essential for the development of oligonucleotide-derived bioactive agents. The NAA-modification represents a novel artificial internucleotide linkage which enables the site-specific introduction of positive charges into the otherwise polyanionic backbone of DNA oligonucleotides. Following initial studies with the introduction of the NAA-linkage at T–T sites, it is now envisioned to prepare NAA-modified oligonucleotides bearing the modification at X–T motifs (X = A, C, G). We have therefore developed the efficient and stereoselective synthesis of NAA-linked 'dimeric' A–T phosphoramidite building blocks for automated DNA synthesis. Both the (S)- and the (R)-configured NAA-motifs were constructed with high diastereoselectivities to furnish two different phosphoramidite reagents, which were employed for the solid phase-supported automated synthesis of two NAA-modified DNA oligonucleotides. This represents a significant step to further establish the NAA-linkage as a useful addition to the existing 'toolbox' of backbone modifications for the design of bioactive oligonucleotide analogues.

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4

Meng, Melissa, Boris Schmidtgall, and Christian Ducho. "Enhanced Stability of DNA Oligonucleotides with Partially Zwitterionic Backbone Structures in Biological Media." Molecules 23, no. 11 (November 10, 2018): 2941. http://dx.doi.org/10.3390/molecules23112941.

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Deficient stability towards nuclease-mediated degradation is one of the most relevant tasks in the development of oligonucleotide-derived biomedical agents. This hurdle can be overcome through modifications to the native oligonucleotide backbone structure, with the goal of simultaneously retaining the unique hybridization properties of nucleic acids. The nucleosyl amino acid (NAA)-modification is a recently introduced artificial cationic backbone linkage. Partially zwitterionic NAA-modified oligonucleotides had previously shown hybridization with DNA strands with retained base-pairing fidelity. In this study, we report the significantly enhanced stability of NAA-modified oligonucleotides towards 3′- and 5′-exonuclease-mediated degradation as well as in complex biological media such as human plasma and whole cell lysate. This demonstrates the potential versatility of the NAA-motif as a backbone modification for the development of biomedically active oligonucleotide analogues.

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5

Chang, Chi-Fon, and Micheal H. Zehfus. "Effects of backbone modification on helical peptides: The reduced carbonyl modification." Biopolymers 46, no. 3 (September 1998): 181–93. http://dx.doi.org/10.1002/(sici)1097-0282(199809)46:3<181::aid-bip5>3.0.co;2-h.

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6

Dawson, Philip E., Gangamani Beligere, and Liang Yan. "Modification of the polypeptide backbone using chemical synthesis." Journal of Molecular Graphics and Modelling 18, no. 4-5 (2000): 550. http://dx.doi.org/10.1016/s1093-3263(00)80112-6.

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7

Shaykhutdinova, Polina, and Martin Oestreich. "Further Structural Modification of Sulfur-Stabilized Silicon Cations with Binaphthyl Backbones." Synthesis 51, no. 10 (March 11, 2019): 2221–29. http://dx.doi.org/10.1055/s-0037-1610697.

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The synthesis and spectroscopic characterization of two novel cationic silicon–sulfur Lewis pairs with a chiral 4,4′-disubstituted binaphthyl silepine backbone are described. Both Lewis acids induce significant enantioselectivity in the model Diels–Alder reaction of cyclohexa-1,3-diene and chalcone but additional substitution of the binaphthyl backbone exerts a minimal effect on enantioinduction compared to previously reported Lewis acids. Another silicon cation with a chiral spirocyclic backbone induces enantioselectivity in the same range but its synthesis is laborious.

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8

Fan, Linmeng, Min Du, Lichun Kong, Yan Cai, and Xiaobo Hu. "Recognition Site Modifiable Macrocycle: Synthesis, Functional Group Variation and Structural Inspection." Molecules 28, no. 3 (January 31, 2023): 1338. http://dx.doi.org/10.3390/molecules28031338.

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Traditional macrocyclic molecules encode recognition sites in their structural backbones, which limits the variation of the recognition sites and thus, would restrict the adjustment of recognition properties. Here, we report a new oligoamide-based macrocycle capable of varying the recognition functional groups by post-synthesis modification on its structural backbone. Through six steps of common reactions, the parent macrocycle (9) can be produced in gram scale with an overall yield of 31%. The post-synthesis modification of 9 to vary the recognition sites are demonstrated by producing four different macrocycles (10–13) with distinct functional groups, 2-methoxyethoxyl (10), hydroxyl (11), carboxyl (12) and amide (13), respectively. The 1H NMR study suggests that the structure of these macrocycles is consistent with our design, i.e., forming hydrogen bonding network at both rims of the macrocyclic backbone. The 1H-1H NOESY NMR study indicates the recognition functional groups are located inside the cavity of macrocycles. At last, a preliminary molecular recognition study shows 10 can recognize n-octyl-β-D-glucopyranoside (14) in chloroform.

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9

Mazo, Nuria, Claudio D. Navo, Jesús M. Peregrina, Jesús H. Busto, and Gonzalo Jiménez-Osés. "Selective modification of sulfamidate-containing peptides." Organic & Biomolecular Chemistry 18, no. 32 (2020): 6265–75. http://dx.doi.org/10.1039/d0ob01061h.

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Hybrid peptides whose N-terminal residues are activated in the form of α-methylisoserine cyclic sulfamidates exhibit rich reactivity as electrophiles, allowing site- and stereoselective modifications at different backbone and side chain positions.

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10

Strąkowska, Anna, Anna Kosmalska, and Marian Zaborski. "Silsesquioxanes as Modifying Agents of Methylvinylsilicone Rubber." Materials Science Forum 714 (March 2012): 183–89. http://dx.doi.org/10.4028/www.scientific.net/msf.714.183.

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The idea and methods of methylvinylsilicone rubber modification are present. Polyhedral oligomeric silsesquioxanes (POSS) functionalized by vinyl-, carboxyl or amino-organic groups were used with the goal of modifying the rubber matrix. Additionally, oxazoline derivative and itaconic acid were used as the coupling agents. Generally, the process of modification contributed to increasing of rubber-filler interactions, however the useful properties of composites depended on a kind of active groups and way of modifications. It has been shown how grafting of POSS molecules to silicone backbone affects the cross-link density, rheometrical and mechanical properties, hysteresis and relaxation rates of the methylvinylsilicone rubber vulcanizates. Moreover, both the presence of silsesquioxanes and the way of composites preparing affect the improvement of filler dispersion degree in the rubber matrix, as indicated by SEM images. The most significant effect was observed for vinylisobutyl-POSS grafting to the silicone backbone which resulted in the considerably improved mechanical properties of the resulting network.

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11

Mesibov, Robert. ""Look what they've done to our data!" — How Aggregators Change Data Items in Collection Records." Biodiversity Information Science and Standards 2 (June 15, 2018): e25906. http://dx.doi.org/10.3897/biss.2.25906.

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Aggregators such as the Atlas of Living Australia (ALA) and the Global Biodiversity Information Facility (GBIF) have recently been criticised for imposing "backbone taxonomies" on records provided by museums, herbaria and other sources. Taxon names may be changed to suit the backbone, with the result that the taxon rank of the record may change and the originally provided name may no longer be searchable online through the aggregator. Aggregators may also delete data items, either by omitting entire fields or rejecting data items not conforming to aggregator-specific data standards. Modifications are more common than deletions and are particularly worrying in geospatial, date and recorder data fields. It can be difficult to locate originally provided data on aggregator websites, even for individual records, and bulk downloads from aggregators typically mask the changes made. In this presentation I document the loss and modification of biodiversity data items by aggregators and suggest strategies for museums and herbaria to counter data loss and modification.

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12

Sester, David P., Shalin Naik, Shannon J. Beasley, David A. Hume, and Katryn J. Stacey. "Phosphorothioate Backbone Modification Modulates Macrophage Activation by CpG DNA." Journal of Immunology 165, no. 8 (October 15, 2000): 4165–73. http://dx.doi.org/10.4049/jimmunol.165.8.4165.

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13

Wang, Xiaoyan, Mengli Feng, Lu Xiao, Aijun Tong, and Yu Xiang. "Postsynthetic Modification of DNA Phosphodiester Backbone for Photocaged DNAzyme." ACS Chemical Biology 11, no. 2 (December 16, 2015): 444–51. http://dx.doi.org/10.1021/acschembio.5b00867.

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14

Murahashi, Shun-Ichi, Akira Mitani, and Kyuuhei Kitao. "Ruthenium-catalyzed glycine-selective oxidative backbone modification of peptides." Tetrahedron Letters 41, no. 52 (December 2000): 10245–49. http://dx.doi.org/10.1016/s0040-4039(00)01823-2.

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15

Abkowitz, M. A., M. Stolka, R. J. Weagley, K. McGrane, and F. E. Knier. "Chemical modification of charge transport in silicon backbone polymers." Synthetic Metals 28, no. 1-2 (January 1989): 553–58. http://dx.doi.org/10.1016/0379-6779(89)90573-0.

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16

Darapaneni, Chandra Mohan, Prathap Jeya Kaniraj, and Galia Maayan. "Water soluble hydrophobic peptoids via a minor backbone modification." Organic & Biomolecular Chemistry 16, no. 9 (2018): 1480–88. http://dx.doi.org/10.1039/c7ob02928d.

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17

Mahanta, Nilkamal, Andi Liu, Shihui Dong, Satish K. Nair, and Douglas A. Mitchell. "Enzymatic reconstitution of ribosomal peptide backbone thioamidation." Proceedings of the National Academy of Sciences 115, no. 12 (March 5, 2018): 3030–35. http://dx.doi.org/10.1073/pnas.1722324115.

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Methyl-coenzyme M reductase (MCR) is an essential enzyme found strictly in methanogenic and methanotrophic archaea. MCR catalyzes a reversible reaction involved in the production and consumption of the potent greenhouse gas methane. The α-subunit of this enzyme (McrA) contains several unusual posttranslational modifications, including the only known naturally occurring example of protein thioamidation. We have recently demonstrated by genetic deletion and mass spectrometry that the tfuA and ycaO genes of Methanosarcina acetivorans are involved in thioamidation of Gly465 in the MCR active site. Modification to thioGly has been postulated to stabilize the active site structure of MCR. Herein, we report the in vitro reconstitution of ribosomal peptide thioamidation using heterologously expressed and purified YcaO and TfuA proteins from M. acetivorans. Like other reported YcaO proteins, this reaction is ATP-dependent but requires an external sulfide source. We also reconstitute the thioamidation activity of two TfuA-independent YcaOs from the hyperthermophilic methanogenic archaea Methanopyrus kandleri and Methanocaldococcus jannaschii. Using these proteins, we demonstrate the basis for substrate recognition and regioselectivity of thioamide formation based on extensive mutagenesis, biochemical, and binding studies. Finally, we report nucleotide-free and nucleotide-bound crystal structures for the YcaO proteins from M. kandleri. Sequence and structure-guided mutagenesis with subsequent biochemical evaluation have allowed us to assign roles for residues involved in thioamidation and confirm that the reaction proceeds via backbone O-phosphorylation. These data assign a new biochemical reaction to the YcaO superfamily and paves the way for further characterization of additional peptide backbone posttranslational modifications.

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18

Zhu, Sucheng, Tao Zheng, Lingxin Kong, Jinli Li, Bo Cao, Michael S. DeMott, Yihua Sun, et al. "Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications." Biomolecules 10, no. 11 (October 28, 2020): 1491. http://dx.doi.org/10.3390/biom10111491.

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DNA phosphorothioate (PT) modification is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and serves as a constitute element of bacterial restriction–modification (R–M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions. This work describes three detailed methods derived from iodine-induced specific cleavage-an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq)-for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained. Here, we provide time-saving and less labor-consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will offer great potential for better understanding the biology of the PT modifications and open the door to future further systematical study.

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19

Yang, Weiwei, Alexey Fomenkov, Dan Heiter, Shuang-yong Xu, and Laurence Ettwiller. "High-throughput sequencing of EcoWI restriction fragments maps the genome-wide landscape of phosphorothioate modification at base resolution." PLOS Genetics 18, no. 9 (September 19, 2022): e1010389. http://dx.doi.org/10.1371/journal.pgen.1010389.

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Phosphorothioation (PT), in which a non-bridging oxygen is replaced by a sulfur, is one of the rare modifications discovered in bacteria and archaea that occurs on the sugar-phosphate backbone as opposed to the nucleobase moiety of DNA. While PT modification is widespread in the prokaryotic kingdom, how PT modifications are distributed in the genomes and their exact roles in the cell remain to be defined. In this study, we developed a simple and convenient technique called EcoWI-seq based on a modification-dependent restriction endonuclease to identify genomic positions of PT modifications. EcoWI-seq shows similar performance than other PT modification detection techniques and additionally, is easily scalable while requiring little starting material. As a proof of principle, we applied EcoWI-seq to map the PT modifications at base resolution in the genomes of both the Salmonella enterica cerro 87 and E. coli expressing the dnd+ gene cluster. Specifically, we address whether the partial establishment of modified PT positions is a stochastic or deterministic process. EcoWI-seq reveals a systematic usage of the same subset of target sites in clones for which the PT modification has been independently established.

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20

Liu, Shi, Ross W. Cheloha, Tomoyuki Watanabe, Thomas J. Gardella, and Samuel H. Gellman. "Receptor selectivity from minimal backbone modification of a polypeptide agonist." Proceedings of the National Academy of Sciences 115, no. 49 (November 15, 2018): 12383–88. http://dx.doi.org/10.1073/pnas.1815294115.

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Human parathyroid hormone (PTH) and N-terminal fragments thereof activate two receptors, hPTHR1 and hPTHR2, which share ∼51% sequence similarity. A peptide comprising the first 34 residues of PTH is fully active at both receptors and is used to treat osteoporosis. We have used this system to explore the hypothesis that backbone modification of a promiscuous peptidic agonist can provide novel receptor-selective agonists. We tested this hypothesis by preparing a set of variants of PTH(1–34)-NH2 that contained a single β-amino-acid residue replacement at each of the first eight positions. These homologs, each containing one additional backbone methylene unit relative to PTH(1–34)-NH2 itself, displayed a wide range of potencies in cell-based assays for PTHR1 or PTHR2 activation. The β-scan series allowed us to identify two homologs, each containing two α→β replacements, that were highly selective, one for PTHR1 and the other for PTHR2. These findings suggest that backbone modification of peptides may provide a general strategy for achieving activation selectivity among polypeptide-modulated receptors, and that success requires consideration of both β2- and β3-residues, which differ in terms of side-chain location.

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21

Rozners, Eriks. "Recent Advances in Chemical Modification of Peptide Nucleic Acids." Journal of Nucleic Acids 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/518162.

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Peptide nucleic acid (PNA) has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.

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22

Micklefield, Jason. "Backbone Modification of Nucleic Acids: Synthesis, Structure and Therapeutic Applications." Current Medicinal Chemistry 8, no. 10 (August 1, 2001): 1157–79. http://dx.doi.org/10.2174/0929867013372391.

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23

Li, Cong, Ling Zhu, Zhi Zhu, Hao Fu, Gareth Jenkins, Chunming Wang, Yuan Zou, Xin Lu, and Chaoyong James Yang. "Backbone modification promotes peroxidase activity of G-quadruplex-based DNAzyme." Chemical Communications 48, no. 67 (2012): 8347. http://dx.doi.org/10.1039/c2cc32919k.

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24

Ranganathan, Darshan, Narendra K. Vaish, and Kavita Shah. "Protein Backbone Modification by Novel C.alpha.-C Side-Chain Scission." Journal of the American Chemical Society 116, no. 15 (July 1994): 6545–57. http://dx.doi.org/10.1021/ja00094a008.

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25

Zanda, Matteo. "Trifluoromethyl group: an effective xenobiotic function for peptide backbone modification." New Journal of Chemistry 28, no. 12 (2004): 1401. http://dx.doi.org/10.1039/b405955g.

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26

Zuo, Chao, Shan Tang, Yan-Yan Si, Zhipeng A. Wang, Chang-Lin Tian, and Ji-Shen Zheng. "Efficient synthesis of longer Aβ peptides via removable backbone modification." Organic & Biomolecular Chemistry 14, no. 22 (2016): 5012–18. http://dx.doi.org/10.1039/c6ob00712k.

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27

De Mesmaeker, Alain, Adrian Waldner, Jacques Lebreton, Pascale Hoffmann, Valérie Fritsch, Romain M. Wolf, and Susan M. Freier. "Amides as a New Type of Backbone Modification in Oligonucleotides." Angewandte Chemie International Edition in English 33, no. 2 (February 1, 1994): 226–29. http://dx.doi.org/10.1002/anie.199402261.

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28

Zaini, Mahirah, Rohah A. Majid, and Hossein Nikbakht. "Modification of Montmorillonite with Diamine Surfactants." Applied Mechanics and Materials 695 (November 2014): 224–27. http://dx.doi.org/10.4028/www.scientific.net/amm.695.224.

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Sodium montmorillonite (Na-MMT) was modified with various type of diamine surfactants. The modification imparts hydrophobic characters of MMT, thus enhancing its compatibility and dispersibility in polymer matrix. In this research, pristine MMT was modified with three types of diamine surfactants, namely, 1,3 diaminopropane (DAP), 1,8 diamino octane (DAO) and 1,5 diamino-2-Methyl pentane (DAMP). These diamines have different molecular structures where DAP has a short linear structure, DAO has eight carbons while DAMP has a methyl branch on its backbone. The modification was carried via cationic exchange process. X-ray diffraction (XRD) analysis showed the enhancement of d-spacing of MMT galleries and the formation of intercalated structure with the incorporation of diamines. Overall, type of diamines did not give significant effect on the d-spacing values with DAMP-MMT exhibited a slightly higher d-spacing at 13. 36 Å. The presence of methyl branch on the DAMP backbone was thought provide more spacing for the diamine to intercalate through the MMT gallery. Meanwhile, the detection of –NH bending amine group at 1470 cm-1 on the Fourier infrared (FTIR) spectra, corresponding to the free surfactant tail, had confirmed the successfulness of cationic exchange reaction between the diamines and MMT surface.

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29

Scully, Conor C. G., Christopher J. White, and Andrei K. Yudin. "The effect of backbone flexibility on site-selective modification of macrocycles." Organic & Biomolecular Chemistry 14, no. 43 (2016): 10230–37. http://dx.doi.org/10.1039/c6ob01778a.

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Li, Yuxiang, Minseok Kim, Ziang Wu, Changyeon Lee, Young Woong Lee, Jin-Woo Lee, Young Jun Lee, Ergang Wang, Bumjoon J. Kim, and Han Young Woo. "Influence of backbone modification of difluoroquinoxaline-based copolymers on the interchain packing, blend morphology and photovoltaic properties of nonfullerene organic solar cells." Journal of Materials Chemistry C 7, no. 6 (2019): 1681–89. http://dx.doi.org/10.1039/c8tc06206d.

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Shan, Junwen, Thomas Böck, Thorsten Keller, Leonard Forster, Torsten Blunk, Jürgen Groll, and Jörg Teßmar. "TEMPO/TCC as a Chemo Selective Alternative for the Oxidation of Hyaluronic Acid." Molecules 26, no. 19 (October 1, 2021): 5963. http://dx.doi.org/10.3390/molecules26195963.

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Hyaluronic acid (HA)-based hydrogels are very commonly applied as cell carriers for different approaches in regenerative medicine. HA itself is a well-studied biomolecule that originates from the physiological extracellular matrix (ECM) of mammalians and, due to its acidic polysaccharide structure, offers many different possibilities for suitable chemical modifications which are necessary to control, for example, network formation. Most of these chemical modifications are performed using the free acid function of the polymer and, additionally, lead to an undesirable breakdown of the biopolymer’s backbone. An alternative modification of the vicinal diol of the glucuronic acid is oxidation with sodium periodate to generate dialdehydes via a ring opening mechanism that can subsequently be further modified or crosslinked via Schiff base chemistry. Since this oxidation causes a structural destruction of the polysaccharide backbone, it was our intention to study a novel synthesis protocol frequently applied to selectively oxidize the C6 hydroxyl group of saccharides. On the basis of this TEMPO/TCC oxidation, we studied an alternative hydrogel platform based on oxidized HA crosslinked using adipic acid dihydrazide as the crosslinker.

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Max, J. B., D. V. Pergushov, L. V. Sigolaeva, and F. H. Schacher. "Polyampholytic graft copolymers based on polydehydroalanine (PDha) – synthesis, solution behavior and application as dispersants for carbon nanotubes." Polymer Chemistry 10, no. 23 (2019): 3006–19. http://dx.doi.org/10.1039/c8py01390j.

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We herein introduce a versatile platform of graft copolymers featuring a polyampholytic backbone and side chains of varying length and polarity using post-polymerization modification of polydehydroalanine (PDha).

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33

Handelmann, Jens, Chatla Naga Babu, Henning Steinert, Christopher Schwarz, Thorsten Scherpf, Alexander Kroll, and Viktoria H. Gessner. "Towards the rational design of ylide-substituted phosphines for gold(i)-catalysis: from inactive to ppm-level catalysis." Chemical Science 12, no. 12 (2021): 4329–37. http://dx.doi.org/10.1039/d1sc00105a.

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Modification of the backbone in ylide-substituted phosphines allowed a remarkable boost in the catalytic activity, thus enabling a series of gold catalyzed transformations at very low catalyst loadings.

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34

Yi, Zhengran, Lanchao Ma, Ping Li, Long Xu, Xiaowei Zhan, Jingui Qin, Xingguo Chen, Yunqi Liu, and Shuai Wang. "Enhancing the organic thin-film transistor performance of diketopyrrolopyrrole–benzodithiophene copolymers via the modification of both conjugated backbone and side chain." Polymer Chemistry 6, no. 30 (2015): 5369–75. http://dx.doi.org/10.1039/c5py00704f.

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35

Tang, Shan, Chao Zuo, Dong-Liang Huang, Xiao-Ying Cai, Long-Hua Zhang, Chang-Lin Tian, Ji-Shen Zheng, and Lei Liu. "Chemical synthesis of membrane proteins by the removable backbone modification method." Nature Protocols 12, no. 12 (November 16, 2017): 2554–69. http://dx.doi.org/10.1038/nprot.2017.129.

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36

Cheloha, Ross W., Tomoyuki Watanabe, Thomas Dean, Samuel H. Gellman, and Thomas J. Gardella. "Backbone Modification of a Parathyroid Hormone Receptor-1 Antagonist/Inverse Agonist." ACS Chemical Biology 11, no. 10 (August 17, 2016): 2752–62. http://dx.doi.org/10.1021/acschembio.6b00404.

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37

Li, Jia-Bin, Shan Tang, Ji-Shen Zheng, Chang-Lin Tian, and Lei Liu. "Removable Backbone Modification Method for the Chemical Synthesis of Membrane Proteins." Accounts of Chemical Research 50, no. 5 (April 4, 2017): 1143–53. http://dx.doi.org/10.1021/acs.accounts.7b00001.

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38

Kuwahara, M., S. Minezaki, J. i. Nagashima, H. Ozaki, and H. Sawai. "Effect of backbone-modification of oligodeoxyribonucleic acid on primer extension reactions." Nucleic Acids Symposium Series 52, no. 1 (September 1, 2008): 453–54. http://dx.doi.org/10.1093/nass/nrn230.

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Kato, Kazuaki, Tomoya Ise, and Kohzo Ito. "Crystal structure transition of polyrotaxanes attributable to competing rings and backbone induced by in situ modification of the backbone." Polymer 55, no. 6 (March 2014): 1514–19. http://dx.doi.org/10.1016/j.polymer.2014.01.044.

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40

Vorherr, Thomas, Ian Lewis, Joerg Berghausen, Felix Huth, Michael Schaefer, Roman Wille, Jinhai Gao, and Bing Wang. "Pyridyl-Ala Modified Cyclic Hexapeptides: In-Vitro and In-Vivo Profiling for Oral Bioavailability." International Journal of Peptide Research and Therapeutics 26, no. 3 (October 11, 2019): 1383–97. http://dx.doi.org/10.1007/s10989-019-09935-y.

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Abstract We and others have been aiming at modifications to maintain or to enhance solubility while enabling permeability for cyclic hexapeptides. Especially, the 2-pyridyl-Ala modification was investigated, since in this case, the pyridyl-nitrogen is able to form an H-bond to the NH of the same residue. The hypothesis of a backbone side-chain interaction was demonstrated by NMR experiments, and further results obtained on a variety of pyridyl-Ala derivatives, studied systematically in the context of permeability, are presented in this contribution. Thus, this study sheds some more light on the pyridyl-Ala modification, which had been reported earlier. In addition to the in vitro profiling, the extent of oral bioavailability was assessed in rats. In principle, the pyridyl-Ala residue can be considered as an amino acid supporting oral uptake. Graphic Abstract

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41

Su, Yongdong, Maitsetseg Bayarjargal, Tracy K. Hale, and Vyacheslav V. Filichev. "DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies." Beilstein Journal of Organic Chemistry 17 (March 29, 2021): 749–61. http://dx.doi.org/10.3762/bjoc.17.65.

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Two phosphate modifications were introduced into the DNA backbone using the Staudinger reaction between the 3’,5’-dinucleoside β-cyanoethyl phosphite triester formed during DNA synthesis and sulfonyl azides, 4-(azidosulfonyl)-N,N,N-trimethylbutan-1-aminium iodide (N+ azide) or p-toluenesulfonyl (tosyl or Ts) azide, to provide either a zwitterionic phosphoramidate with N+ modification or a negatively charged phosphoramidate for Ts modification in the DNA sequence. The incorporation of these N+ and Ts modifications led to the formation of thermally stable parallel DNA triplexes, regardless of the number of modifications incorporated into the oligodeoxynucleotides (ONs). For both N+ and Ts-modified ONs, the antiparallel duplexes formed with complementary RNA were more stable than those formed with complementary DNA (except for ONs with modification in the middle of the sequence). Additionally, the incorporation of N+ modifications led to the formation of duplexes with a thermal stability that was less dependent on the ionic strength than native DNA duplexes. The thermodynamic analysis of the melting curves revealed that it is the reduction in unfavourable entropy, despite the decrease in favourable enthalpy, which is responsible for the stabilisation of duplexes with N+ modification. N+ONs also demonstrated greater resistance to nuclease digestion by snake venom phosphodiesterase I than the corresponding Ts-ONs. Cell uptake studies showed that Ts-ONs can enter the nucleus of mouse fibroblast NIH3T3 cells without any transfection reagent, whereas, N+ONs remain concentrated in vesicles within the cytoplasm. These results indicate that both N+ and Ts-modified ONs are promising for various in vivo applications.

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Fuchs, Elisabeth, Christoph Falschlunger, Ronald Micura, and Kathrin Breuker. "The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry." Nucleic Acids Research 47, no. 14 (July 5, 2019): 7223–34. http://dx.doi.org/10.1093/nar/gkz574.

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Abstract The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5′-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.

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Rajagopalan, Narayani, and A. S. Khanna. "Effect of Methyltrimethoxy Silane Modification on Yellowing of Epoxy Coating on UV (B) Exposure." Journal of Coatings 2014 (June 11, 2014): 1–7. http://dx.doi.org/10.1155/2014/515470.

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The exterior durability of epoxies is severely affected due to its poor weathering resistance. Epoxies exhibit chalking and discoloration under UV exposure caused as a result of photodegradation. The present work aims at studying the extent to which the color change and yellowing caused due to weathering under accelerated weathering conditions, of DGEBA epoxy, could be lowered by in situ modification of the epoxy polymer backbone with a silane, namely, MTMS. The epoxy resin and silane-modified epoxy resin were formulated into a TiO2-based white coating, applied on mild steel panels, and exposed in a UV (B) weatherometer. The color change (dE) and yellowness index (YI) values of weathered panels were evaluated using a spectrophotometer. The weathered samples were also characterized using FTIR-imaging technique to study the effect of weathering on the structural backbone of the formulated coatings. The silane-modified epoxy coatings showed lowered yellowing by 45% on UV exposure and the enhanced resistance to yellowing of the modified coatings was indicated by lowered dE and YI values. The enhanced resistance to yellowing by the silane-modified epoxy was attributed to the strengthening of the epoxy backbone by introduction of Si–O–C linkage onto the epoxy polymeric chain.

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44

De Zotti, Marta, Barbara Biondi, Cristina Peggion, Matteo De Poli, Haleh Fathi, Simona Oancea, Claudio Toniolo, and Fernando Formaggio. "Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity." Beilstein Journal of Organic Chemistry 8 (July 24, 2012): 1161–71. http://dx.doi.org/10.3762/bjoc.8.129.

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Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu11-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated. Our results indicate that (i) a thioamide linkage is well tolerated in the overall helical conformation of the [Leu11-OMe] lipopeptide analogue and (ii) this backbone modification is compatible with the preservation of its typical membrane leakage and antibiotic properties, although somewhat attenuated.

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Afsar, Ashfaq, Laurence M. Harwood, Michael J. Hudson, James Westwood, and Andreas Geist. "Effective separation of the actinides Am(iii) and Cm(iii) by electronic modulation of bis-(1,2,4-triazin-3-yl)phenanthrolines." Chemical Communications 51, no. 27 (2015): 5860–63. http://dx.doi.org/10.1039/c5cc00567a.

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It has been shown that modification of the phenanthroline backbone of CyMe₄-BTPhen leads to subtle electronic modulation, permitting differential ligation of Am(iii) and Cm(iii) resulting in separation factors up to 7.

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Purushottam, Landa, Srinivasa Rao Adusumalli, Maheshwerreddy Chilamari, and Vishal Rai. "Chemoselective and site-selective peptide and native protein modification enabled by aldehyde auto-oxidation." Chemical Communications 53, no. 5 (2017): 959–62. http://dx.doi.org/10.1039/c6cc09555k.

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Chemical technology delivers precision engineering of the native protein backbone. A lysine residue undergoes single-site formylation or acylation in a multi-step yet operationally simple one-pot process.

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Phan, Hoang Anh T., Sam G. Giannakoulias, Taylor M. Barrett, Chunxiao Liu, and E. James Petersson. "Rational design of thioamide peptides as selective inhibitors of cysteine protease cathepsin L." Chemical Science 12, no. 32 (2021): 10825–35. http://dx.doi.org/10.1039/d1sc00785h.

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Information on the effects of sidechain and backbone modification on the activity of cathepsin (Cts) L, V, K, S, and B was used to design a thioamide peptide that is inert to all Cts and selectively inhibits Cts L.

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Liu, Baizhen. "Blood Cell Count and Detection Method Based on YOLO." Highlights in Science, Engineering and Technology 27 (December 27, 2022): 594–99. http://dx.doi.org/10.54097/hset.v27i.3822.

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Blood Cell Count and Detection (BCCD) has always been a popular topic in object detection and many researchers have applied and modified the two basic models: Faster RCNN and Yolo. However, it is still difficult to tell which model or modification would perform better on other BCCD datasets. Thus, this paper mainly focuses on finding a better model and modifications to BCCD example datasets containing 364 images of blood cells. Faster RCNN and Yolo v5 were used as the basic two models for the dataset. Through training and comparisons between the two models, the better model was chosen to make further modifications or adjustments to achieve a better maP result possible. The result shows that in this specific dataset, Yolo v5 performs better. The modified Yolo v5 model also has an improvement of 0.6 percent of map 0.5 and 0.5 percent of map 0.95 comparing to the original model, showing that modification of model configuration, model structures including head and backbone would efficiently improve the time taken for training and maP.

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Wang, Chenchen, and Rampi Ramprasad. "Novel Hybrid Polymer Dielectrics Based on Group 14 Chemical Motifs." International Journal of High Speed Electronics and Systems 23, no. 01n02 (March 2014): 1420002. http://dx.doi.org/10.1142/s012915641420002x.

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The present contribution provides a strategy to enhance the dielectric constant of polyethylene by chemical modification while not overly compromising its large band gap. Isolated polyethylene chains are considered and the CH2 motifs in the backbone are allowed to be substituted by a number of Group 14 motifs, including SiF2, SiCl2, GeF2, GeCl2, SnF2, and SnCl2, in a systematic, progressive, and exhaustive combinatorial manner. Our results indicate that consecutive SnF2 or GeF2 motifs in the polyethylene backbone are most desirable, which can lead to systems with dielectric constant as high as 47.

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Cheloha, Ross W., Akira Maeda, Thomas Dean, Thomas J. Gardella, and Samuel H. Gellman. "Backbone modification of a polypeptide drug alters duration of action in vivo." Nature Biotechnology 32, no. 7 (June 15, 2014): 653–55. http://dx.doi.org/10.1038/nbt.2920.

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