scholarly journals Orthogonal coiled coils enable rapid covalent labelling of two distinct membrane proteins with peptide nucleic acid barcodes

2021 ◽  
Author(s):  
Georgina C Gavins ◽  
Katharina Gröger ◽  
Marc Reimann ◽  
Michael D. Bartoschek ◽  
Sebastian Bultmann ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Membrane Proteins ◽  
Peptide Nucleic Acid ◽  
Coiled Coils ◽  
Amide Bond ◽  
Bond Forming ◽  
Bond Forming Reactions ◽  
Distinct Membrane

Templated chemistry offers the prospect of addressing specificity challenges occurring in bioconjugation reactions. Here, we show two peptide-templated amide-bond forming reactions that enable the concurrent labelling of two different membrane...

scholarly journals Minimizing HCN in DIC/Oxyma-Mediated Amide Bond-Forming Reactions

2020 ◽  
Vol 24 (7) ◽  
pp. 1341-1349 ◽  
Author(s):  
Marion Erny ◽  
Marika Lundqvist ◽  
Jon H. Rasmussen ◽  
Olivier Ludemann-Hombourger ◽  
Frédéric Bihel ◽  
...  
Keyword(s):  
Amide Bond ◽  
Bond Forming ◽  
Bond Forming Reactions

Are Aminomethyl Thioesters Viable Intermediates in Native Chemical Ligation Type Amide Bond Forming Reactions?

2018 ◽  
Vol 71 (9) ◽  
pp. 697
Author(s):  
Carlie L. Charron ◽  
Jade M. Cottam Jones ◽  
Craig A. Hutton
Keyword(s):  
Amide Bond ◽  
Native Chemical Ligation ◽  
Direct Reaction ◽  
Chemical Ligation ◽  
Bond Forming ◽  
Type Process ◽  
Bond Forming Reactions ◽  
Subsequent Conversion ◽  
Three Component Coupling

The condensation of N-mercaptomethyl amines and thioesters is a potential route to amides, via aminomethyl thioester intermediates, in a native chemical ligation type process followed by self-cleavage of the ‘mercaptomethyl’ auxiliary. This paper describes investigations towards the preparation of aminomethyl thioesters, and subsequent conversion into amides, from a three-component coupling of formaldehyde, a thioacid, and an amine. Our studies suggest that while such intermediates may be formed en route to amides, no advantages are offered over the direct reaction of the amine and thioacid precursors.

Metal-catalyzed amide bond forming reactions in an environmentally friendly aqueous medium: nitrile hydrations and beyond

2013 ◽  
Vol 15 (1) ◽  
pp. 46-66 ◽  
Author(s):  
Rocío García-Álvarez ◽  
Pascale Crochet ◽  
Victorio Cadierno
Keyword(s):  
Aqueous Medium ◽  
Environmentally Friendly ◽  
Amide Bond ◽  
Bond Forming ◽  
Bond Forming Reactions ◽  
Metal Catalyzed

Nucleophilic reactivity of peptides toward 2-acyloxy-N-ethylbenzamides. Utility of free peptides as nucleophiles in amide bond forming reactions

1974 ◽  
Vol 39 (19) ◽  
pp. 2831-2835 ◽  
Author(s):  
D. S. Kemp ◽  
Zmira W. Bernstein ◽  
George N. McNeil
Keyword(s):  
Amide Bond ◽  
Bond Forming ◽  
Bond Forming Reactions ◽  
Nucleophilic Reactivity

ChemInform Abstract: Metal-Catalyzed Amide Bond Forming Reactions in an Environmentally Friendly Aqueous Medium: Nitrile Hydrations and Beyond

ChemInform ◽  
2013 ◽  
Vol 44 (16) ◽  
pp. no-no
Author(s):  
Rocio Garcia-Alvarez ◽  
Pascale Crochet ◽  
Victorio Cadierno
Keyword(s):  
Aqueous Medium ◽  
Environmentally Friendly ◽  
Amide Bond ◽  
Bond Forming ◽  
Bond Forming Reactions ◽  
Metal Catalyzed

scholarly journals Minimizing HCN in DIC/Oxyma Mediated Amide Bond Forming Reactions

2020 ◽  
Author(s):  
Marion Erny ◽  
Marika Lundqvist ◽  
Jon H. Rasmussen ◽  
Olivier Ludemann-Hombouger ◽  
Frédéric Bihel ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Peptide Synthesis ◽  
Hydrogen Cyanide ◽  
Reaction Rate ◽  
Solid Support ◽  
Amide Bond ◽  
Prussic Acid ◽  
Bond Forming ◽  
H Nmr ◽  
Bond Forming Reactions

<p>Aiming at advancing protocols for safer, environmentally sensible peptide synthesis we report our findings with regards to the occurrence of hydrogen cyanide (HCN, prussic acid) in amide bond forming reactions mediated by diisopropylcarbodiimide (DIC) and ethyl (hydroxyimino)cyanoacetate (Oxyma). We have determined that HCN is always formed in amide bond forming reactions on solid support in N,N-dimethylformamide (DMF) when employing DIC/Oxyma. In an attempt to minimize the formation of prussic acid by means of preventing the linear DIC/Oxyma adduct <b>2</b> from cyclizing to oxadiazole <b>3</b> and in turn releasing HCN, we evaluated a series of greener solvents such as N-butylpyrrolidinone (NBP), NBP/ethyl acetate (EtOAc, 1:1), methyl 5-(dimethylamino)-2-methyl-5-oxopentanoate (PolarClean, PC), and PC/EtOAc (1:1). We found that the ratio between <b>2</b> and <b>3</b> greatly depends on the solvent used and consequently, we further examined DMF, NBP, NBP/EtOAc (1:1) and NBP/EtOAc (1:4) as solvents for DIC/Oxyma mediated amidations on solid support and in solution. We found that using carboxylic acid/Oxyma/DIC in a 1:1:1 ratio the rate of HCN formation decreases in the following order DMF>NBP>NBP/EtOAc (1:1)>NBP/EtOAc (1:4) while the reaction rate increases in order of DMF~NBPin situ scavenging of the HCN formed. We carried out DIC/Oxyma mediated amidation of Fmoc-Gly-OH + (S)-(-)-1-phenylethylamine in DMF-d<sub>7</sub> with 0, 5 and 10 equiv of dimethyl trisulfide (DMTS) as HCN scavenger. The formation of HCN and rate of amidation was monitored by <sup>1</sup>H NMR, revealing that DMTS scavenges HCN without inhibiting the rate of amidation. DIC/Oxyma mediated amidations of Fmoc‑Ser(<i>t</i>‑Bu)‑OH with (S)-(‑)-1-phenylethylamine in DMF and NBP/EtOAc (1:4) with and without 10 equiv of DMTS were carried out and found to be comparable.</p>

Development of thiol-responsive amide bond cleavage device and its application for peptide nucleic acid-based DNA releasing system

2010 ◽  
Vol 51 (18) ◽  
pp. 2525-2528 ◽  
Author(s):  
Akira Shigenaga ◽  
Jun Yamamoto ◽  
Hiroko Hirakawa ◽  
Keiji Ogura ◽  
Nami Maeda ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Peptide Nucleic Acid ◽  
Bond Cleavage ◽  
Amide Bond ◽  
Amide Bond Cleavage

scholarly journals Minimizing HCN in DIC/Oxyma Mediated Amide Bond Forming Reactions

2020 ◽  
Author(s):  
Marion Erny ◽  
Marika Lundqvist ◽  
Jon H. Rasmussen ◽  
Olivier Ludemann-Hombouger ◽  
Frédéric Bihel ◽  
...  
Keyword(s):  
Carboxylic Acid ◽  
Peptide Synthesis ◽  
Hydrogen Cyanide ◽  
Reaction Rate ◽  
Solid Support ◽  
Amide Bond ◽  
Prussic Acid ◽  
Bond Forming ◽  
H Nmr ◽  
Bond Forming Reactions

<p>Aiming at advancing protocols for safer, environmentally sensible peptide synthesis we report our findings with regards to the occurrence of hydrogen cyanide (HCN, prussic acid) in amide bond forming reactions mediated by diisopropylcarbodiimide (DIC) and ethyl (hydroxyimino)cyanoacetate (Oxyma). We have determined that HCN is always formed in amide bond forming reactions on solid support in N,N-dimethylformamide (DMF) when employing DIC/Oxyma. In an attempt to minimize the formation of prussic acid by means of preventing the linear DIC/Oxyma adduct <b>2</b> from cyclizing to oxadiazole <b>3</b> and in turn releasing HCN, we evaluated a series of greener solvents such as N-butylpyrrolidinone (NBP), NBP/ethyl acetate (EtOAc, 1:1), methyl 5-(dimethylamino)-2-methyl-5-oxopentanoate (PolarClean, PC), and PC/EtOAc (1:1). We found that the ratio between <b>2</b> and <b>3</b> greatly depends on the solvent used and consequently, we further examined DMF, NBP, NBP/EtOAc (1:1) and NBP/EtOAc (1:4) as solvents for DIC/Oxyma mediated amidations on solid support and in solution. We found that using carboxylic acid/Oxyma/DIC in a 1:1:1 ratio the rate of HCN formation decreases in the following order DMF>NBP>NBP/EtOAc (1:1)>NBP/EtOAc (1:4) while the reaction rate increases in order of DMF~NBPin situ scavenging of the HCN formed. We carried out DIC/Oxyma mediated amidation of Fmoc-Gly-OH + (S)-(-)-1-phenylethylamine in DMF-d<sub>7</sub> with 0, 5 and 10 equiv of dimethyl trisulfide (DMTS) as HCN scavenger. The formation of HCN and rate of amidation was monitored by <sup>1</sup>H NMR, revealing that DMTS scavenges HCN without inhibiting the rate of amidation. DIC/Oxyma mediated amidations of Fmoc‑Ser(<i>t</i>‑Bu)‑OH with (S)-(‑)-1-phenylethylamine in DMF and NBP/EtOAc (1:4) with and without 10 equiv of DMTS were carried out and found to be comparable.</p>

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

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