Dataset Information

Direct Observation and Analysis of the Halo-Amino-Nitro Alkane Functional Group.

ABSTRACT: Conventional amide synthesis is a mainstay in discipline-spanning applications, and it is a reaction type that historically developed as a singular paradigm when considering the carbon-nitrogen bond-forming step. Umpolung amide synthesis (UmAS) exploits the unique properties of an ?-halo nitroalkane in its reaction with an amine to produce an amide. The "umpolung" moniker reflects its paradigm-breaking C-N bond formation on the basis of evidence that the nucleophilic nitronate carbon and electrophilic nitrogen engage to form a tetrahedral intermediate (TI) that is an unprecedented functional group, a 1,1,1-halo-amino-nitro alkane (HANA). Studies probing HANA transience have failed to capture this (presumably) highly reactive intermediate. We report here the direct observation of a HANA, its conversion thermally to an amide functionality, and quantitative analysis of this process using computational techniques. These findings validate the HANA as a functional group common to UmAS and diverted UmAS, opening the door to its targeted use and creative manipulation.

SUBMITTER: Crocker MS

PROVIDER: S-EPMC7405871 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Direct Observation and Analysis of the Halo-Amino-Nitro Alkane Functional Group.

Crocker Michael S MS Foy Hayden H Tokumaru Kazuyuki K Dudding Travis T Pink Maren M Johnston Jeffrey N JN

Chem 20190328 5

Conventional amide synthesis is a mainstay in discipline-spanning applications, and it is a reaction type that historically developed as a singular paradigm when considering the carbon-nitrogen bond-forming step. Umpolung amide synthesis (UmAS) exploits the unique properties of an α-halo nitroalkane in its reaction with an amine to produce an amide. The "umpolung" moniker reflects its paradigm-breaking C-N bond formation on the basis of evidence that the nucleophilic nitronate carbon and electro ...[more]

PMID: 32766460

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Project description:BackgroundIt has been an abiding belief among geneticists that multicellular organisms' genomes can be analyzed under the assumption that a single individual has a uniform genome in all its cells. Despite some evidence to the contrary, this belief has been used as an axiomatic assumption in most genome analysis software packages. In this paper we present observations in human whole genome data, human whole exome data and in mouse whole genome data to challenge this assumption. We show that heterogeneity is in fact ubiquitous and readily observable in ordinary Next Generation Sequencing (NGS) data.ResultsStarting with the assumption that a single NGS read (or read pair) must come from one haplotype, we built a procedure for directly observing haplotypes at a local level by examining 2 or 3 adjacent single nucleotide polymorphisms (SNPs) which are close enough on the genome to be spanned by individual reads. We applied this procedure to NGS data from three different sources: whole genome of a Central European trio from the 1000 genomes project, whole genome data from laboratory-bred strains of mouse, and whole exome data from a set of patients of head and neck tumors. Thousands of loci were found in each genome where reads spanning 2 or 3 SNPs displayed more than two haplotypes, indicating that the locus is heterogeneous. We show that such loci are ubiquitous in the genome and cannot be explained by segmental duplications. We explain them on the basis of cellular heterogeneity at the genomic level. Such heterogeneous loci were found in all normal and tumor genomes examined.ConclusionsOur results highlight the need for new methods to analyze genomic variation because existing ones do not systematically consider local haplotypes. Identification of cancer somatic mutations is complicated because of tumor heterogeneity. It is further complicated if, as we show, normal tissues are also heterogeneous. Methods for biomarker discovery must consider contextual haplotype information rather than just whether a variant "is present".

Dataset Information

Direct Observation and Analysis of the Halo-Amino-Nitro Alkane Functional Group.

Publications

Direct Observation and Analysis of the Halo-Amino-Nitro Alkane Functional Group.

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