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Article ; Online: Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection).

López-Tena, Miguel / Farrera-Soler, Lluc / Barluenga, Sofia / Winssinger, Nicolas

JACS Au

2023 Volume 3, Issue 2, Page(s) 449–458

Abstract: Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo- ... ...

Abstract	Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, U
Language	English
Publishing date	2023-02-01
Publishing country	United States
Document type	Journal Article
ISSN	2691-3704
ISSN (online)	2691-3704
DOI	10.1021/jacsau.2c00588
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Experimental Identification of Immuno- dominant B-cell Epitopes from SARS-CoV-2.

Farrera-Soler, Lluc / Daguer, Jean-Pierre / Barluenga, Sofia / Winssinger, Nicolas

Chimia

2021 Volume 75, Issue 4, Page(s) 276–284

Abstract: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current public health crisis with devastating consequences to our societies. This COVID-19 pandemic has become the most serious threat to global public health in recent ... ...

Abstract	Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current public health crisis with devastating consequences to our societies. This COVID-19 pandemic has become the most serious threat to global public health in recent history. Given the unprecedented economic and social impact that it is causing, identification of immunodominant epitopes from SARS-CoV-2 is of great interest, not only to gain better insight into the adaptive immune response, but also for the development of vaccines, treatments and diagnostic tools. In this review, we summarize the already published or preprinted reports on the experimental identification of B-cell linear epitopes of SARS-CoV-2 proteins. Six different epitopes leading to neutralizing antibodies have been identified. Moreover, a summary of peptide candidates to be used for diagnostic tools is also included.
MeSH term(s)	B-Lymphocytes ; COVID-19 ; Epitopes, B-Lymphocyte ; Humans ; Immunodominant Epitopes ; Pandemics ; SARS-CoV-2
Chemical Substances	Epitopes, B-Lymphocyte ; Immunodominant Epitopes
Language	English
Publishing date	2021-01-20
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	1516-7
ISSN	0009-4293
ISSN	0009-4293
DOI	10.2533/chimia.2021.276
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Article ; Online: Combining recombinase polymerase amplification and DNA-templated reaction for SARS-CoV-2 sensing with dual fluorescence and lateral flow assay output.

Farrera-Soler, Lluc / Gonse, Arthur / Kim, Ki Tae / Barluenga, Sofia / Winssinger, Nicolas

Biopolymers

2022 Volume 113, Issue 4, Page(s) e23485

Abstract: The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission ... ...

Abstract	The early phase of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was exacerbated by a diagnostic challenge of unprecedented magnitude. In the absence of effective therapeutics or vaccines, breaking the chain of transmission through early disease detection and patient isolation was the only means to control the growing pandemic. While polymerase chain reaction (PCR)-based methods and rapid-antigen tests rose to the occasion, the analytical challenge of rapid and sequence-specific nucleic acid-sensing at a point-of-care or home setting stimulated intense developments. Herein we report a method that combines recombinase polymerase amplification and a DNA-templated reaction to achieve a dual readout with either fluorescence (microtiter plate) or naked eye (lateral flow assay: LFA) detection. The nucleic acid templated reaction is based on an S
MeSH term(s)	COVID-19/diagnosis ; DNA ; Humans ; Nucleic Acid Amplification Techniques/methods ; Nucleic Acids ; Recombinases/genetics ; SARS-CoV-2/genetics
Chemical Substances	Nucleic Acids ; Recombinases ; DNA (9007-49-2)
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	1123-x
ISSN	1097-0282 ; 0006-3525
ISSN (online)	1097-0282
ISSN	0006-3525
DOI	10.1002/bip.23485
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Article ; Online: High-affinity peptides developed against calprotectin and their application as synthetic ligands in diagnostic assays.

Díaz-Perlas, Cristina / Ricken, Benjamin / Farrera-Soler, Lluc / Guschin, Dmitrii / Pojer, Florence / Lau, Kelvin / Gerhold, Christian-Benedikt / Heinis, Christian

Nature communications

2023 Volume 14, Issue 1, Page(s) 2774

Abstract: Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type ... ...

Abstract	Common inflammatory disorders such as ulcerative colitis and Crohn's disease are non-invasively diagnosed or monitored by the biomarker calprotectin. However, current quantitative tests for calprotectin are antibody-based and vary depending on the type of antibody and assay used. Additionally, the binding epitopes of applied antibodies are not characterized by structures and for most antibodies it is unclear if they detect calprotectin dimer, tetramer, or both. Herein, we develop calprotectin ligands based on peptides, that offer advantages such as homogenous chemical composition, heat-stability, site-directed immobilization, and chemical synthesis at high purity and at low cost. By screening a 100-billion peptide phage display library against calprotectin, we identified a high-affinity peptide (K
MeSH term(s)	Humans ; Leukocyte L1 Antigen Complex/analysis ; Crohn Disease/diagnosis ; Colitis, Ulcerative/diagnosis ; Peptides/metabolism ; Biomarkers/analysis ; Antibodies/metabolism ; Feces/chemistry
Chemical Substances	Leukocyte L1 Antigen Complex ; Peptides ; Biomarkers ; Antibodies
Language	English
Publishing date	2023-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-38075-7
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Article ; Online: Dual Bcl-X

Daguer, Jean-Pierre / Gonse, Arthur / Shchukin, Yevhenii / Farrera-Soler, Lluc / Barluenga, Sofia / Winssinger, Nicolas

Bioorganic & medicinal chemistry

2021 Volume 44, Page(s) 116282

Abstract: A dual Bcl- ... ...

Abstract	A dual Bcl-X
MeSH term(s)	Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Antineoplastic Agents/pharmacology ; Cell Proliferation/drug effects ; Cell Survival/drug effects ; DNA/chemistry ; Dose-Response Relationship, Drug ; Drug Discovery ; Drug Screening Assays, Antitumor ; Humans ; K562 Cells ; Molecular Structure ; Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors ; Small Molecule Libraries/chemical synthesis ; Small Molecule Libraries/chemistry ; Small Molecule Libraries/pharmacology ; Structure-Activity Relationship ; bcl-X Protein/antagonists & inhibitors
Chemical Substances	Antineoplastic Agents ; BCL2 protein, human ; BCL2L1 protein, human ; Proto-Oncogene Proteins c-bcl-2 ; Small Molecule Libraries ; bcl-X Protein ; DNA (9007-49-2)
Language	English
Publishing date	2021-06-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2021.116282
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ab Jg. 2022: Lesesaal (EG)

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Article ; Online: A mating mechanism to generate diversity for the Darwinian selection of DNA-encoded synthetic molecules.

Vummidi, Balayeshwanth R / Farrera-Soler, Lluc / Daguer, Jean-Pierre / Dockerill, Millicent / Barluenga, Sofia / Winssinger, Nicolas

Nature chemistry

2021 Volume 14, Issue 2, Page(s) 141–152

Abstract: DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to ... ...

Abstract	DNA-encoded library technologies enable the screening of synthetic molecules but have thus far not tapped into the power of Darwinian selection with iterative cycles of selection, amplification and diversification. Here we report a simple strategy to rapidly assemble libraries of conformationally constrained peptides that are paired in a combinatorial fashion (suprabodies). We demonstrate that the pairing can be shuffled after each amplification cycle in a process similar to DNA shuffling or mating to regenerate diversity. Using simulations, we show the benefits of this recombination in yielding a more accurate correlation of selection fitness with affinity after multiple rounds of selection, particularly if the starting library is heterogeneous in the concentration of its members. The method was validated with selections against streptavidin and applied to the discovery of PD-L1 binders. We further demonstrate that the binding of self-assembled suprabodies can be recapitulated by smaller (∼7 kDa) synthetic products that maintain the conformational constraint of the peptides.
MeSH term(s)	B7-H1 Antigen/chemistry ; DNA/chemistry ; DNA/genetics ; Drug Discovery/methods ; Evolution, Chemical ; Evolution, Molecular ; Ligands ; Peptide Nucleic Acids/chemistry ; Recombination, Genetic ; Reproducibility of Results ; Small Molecule Libraries/chemistry ; Synthetic Biology
Chemical Substances	B7-H1 Antigen ; Ligands ; Peptide Nucleic Acids ; Small Molecule Libraries ; DNA (9007-49-2)
Language	English
Publishing date	2021-12-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2464596-5
ISSN	1755-4349 ; 1755-4330
ISSN (online)	1755-4349
ISSN	1755-4330
DOI	10.1038/s41557-021-00829-5
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Article ; Online: PNA-Based Dynamic Combinatorial Libraries (PDCL) and screening of lectins.

Farrera-Soler, Lluc / Daguer, Jean-Pierre / Raunft, Patrick / Barluenga, Sofia / Imberty, Anne / Winssinger, Nicolas

Bioorganic & medicinal chemistry

2020 Volume 28, Issue 10, Page(s) 115458

Abstract: Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used ... ...

Abstract	Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used with small molecules interacting with each other through reversible covalent interaction. However, application of this technology in biomedical research and drug discovery has been limited by the reversibility of covalent exchange and the analytical deconvolution of small molecule fragments. Here we report a supramolecular approach based on the use of a constant short PNA tag to direct the combinatorial pairing of fragment. This PNA tag yields fast exchange kinetics, while still delivering the benefits of cooperativity, and provides favourable properties for analytical deconvolution by MALDI. A selection from >6,000 assemblies of glycans (mono-, di-, tri-saccharides) targeting AFL, a lectin from pathogenic fungus, yielded a 95 nM assembly, nearly three orders of magnitude better in affinity than the corresponding glycan alone (41 µM).
MeSH term(s)	Combinatorial Chemistry Techniques ; Drug Evaluation, Preclinical ; Lectins/analysis ; Molecular Structure ; Peptide Nucleic Acids/chemistry ; Polysaccharides/chemistry
Chemical Substances	Lectins ; Peptide Nucleic Acids ; Polysaccharides
Language	English
Publishing date	2020-03-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1161284-8
ISSN	1464-3391 ; 0968-0896
ISSN (online)	1464-3391
ISSN	0968-0896
DOI	10.1016/j.bmc.2020.115458
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Jg. 1995 - 2021: Lesesall (2.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma.

Farrera-Soler, Lluc / Daguer, Jean-Pierre / Barluenga, Sofia / Vadas, Oscar / Cohen, Patrick / Pagano, Sabrina / Yerly, Sabine / Kaiser, Laurent / Vuilleumier, Nicolas / Winssinger, Nicolas

PloS one

2020 Volume 15, Issue 9, Page(s) e0238089

Abstract: A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from ... ...

Abstract	A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
MeSH term(s)	Amino Acid Sequence ; Antibodies, Viral/blood ; Antibodies, Viral/immunology ; Betacoronavirus/immunology ; Betacoronavirus/isolation & purification ; COVID-19 ; Coronavirus Infections/pathology ; Coronavirus Infections/virology ; Epitope Mapping ; Epitopes/blood ; Epitopes/chemistry ; Epitopes/immunology ; Furin/metabolism ; Humans ; Pandemics ; Peptide Nucleic Acids/chemistry ; Peptides/chemistry ; Pneumonia, Viral/pathology ; Pneumonia, Viral/virology ; Protein Array Analysis ; Protein Structure, Tertiary ; Proteolysis ; Recombinant Proteins/biosynthesis ; Recombinant Proteins/chemistry ; Recombinant Proteins/isolation & purification ; SARS-CoV-2 ; Sequence Alignment ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Antibodies, Viral ; Epitopes ; Peptide Nucleic Acids ; Peptides ; Recombinant Proteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Furin (EC 3.4.21.75)
Keywords	covid19
Language	English
Publishing date	2020-09-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0238089
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Article ; Online: Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma.

Lluc Farrera-Soler / Jean-Pierre Daguer / Sofia Barluenga / Oscar Vadas / Patrick Cohen / Sabrina Pagano / Sabine Yerly / Laurent Kaiser / Nicolas Vuilleumier / Nicolas Winssinger

PLoS ONE, Vol 15, Iss 9, p e

2020 Volume 0238089

Abstract	A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2') known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of immunodominant linear epitopes from SARS-CoV-2 patient plasma

Lluc Farrera-Soler / Jean-Pierre Daguer / Sofia Barluenga / Oscar Vadas / Patrick Cohen / Sabrina Pagano / Sabine Yerly / Laurent Kaiser / Nicolas Vuilleumier / Nicolas Winssinger / Nicholas J. Mantis

PLoS ONE, Vol 15, Iss

2020 Volume 9

Abstract	A novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) is the source of a current pandemic (COVID-19) with devastating consequences in public health and economic stability. Using a peptide array to map the antibody response of plasma from healing patients (12) and heathy patients (6), we identified three immunodominant linear epitopes, two of which correspond to key proteolytic sites on the spike protein (S1/S2 and S2’) known to be critical for cellular entry. We show biochemical evidence that plasma positive for the epitope adjacent to the S1/S2 cleavage site inhibits furin-mediated proteolysis of spike.
Keywords	Medicine ; R ; Science ; Q ; covid19
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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