Journal: Food Chemistry: Molecular Sciences

Article Title: Real-time PCR to target Hoodia in herbal supplements: a tool for conservation and trade regulation

doi: 10.1016/j.fochms.2026.100367

Figure Lengend Snippet: Oligonucleotides design. (A) Sequence alignment of the 88 bp Hoodia PCR amplicon using all 29 available Hoodia ITS2 region sequences, including 8 from the vascular plant ITS2 database, 8 from the NCBI database and 13 generated in-house (Table S3). The positions of the designed oligonucleotide (Hoodia-F, Hoodia-R and Hoodia-P) are underlined. (B) Sequence alignment at the Hoodia-P probe binding site between the consensus Hoodia PCR amplicon sequence (derived from A) and all observed sequence variations from closely related species (Clusters 1–10) (Table S4). For each variation cluster, the number of associated hits from closely related species is indicated in parentheses (Table S4). All observed single-nucleotide variations (SNVs) are shown in red. SNVs indicated in grey were used to design the two non-Hoodia probes (Non-Hoodia-Pa and Non-Hoodia-Pb). The positions of all designed oligonucleotides are underlined.

Article Snippet: The real-time PCR assay was carried out using oligonucleotides (Eurogentec, Liège, Belgium), 1× SsoAdvanced universal probes supermix (Bio-Rad, Hercules, USA) and CFX Duet Real-Time PCR System (Bio-Rad, Hercules, USA).

Techniques: Sequencing, Amplification, Generated, Binding Assay, Derivative Assay

Journal: Nucleic Acids Research

Article Title: HM-DyadCap – capture and mapping of 5-hydroxymethylcytosine/5-methylcytosine CpG dyads in mammalian DNA

doi: 10.1093/nar/gkag389

Figure Lengend Snippet: Comparison of MECP2 wt and HM maps with MeDIP and hMeDIP maps. ( a ) EMSA analysis of monoclonal anti-hmC antibodies (1:10 dilution) binding to dsDNA oligos (0.75 pM) bearing a single hmC/mC dyad (for data with hmC-modified ssDNA, see ). HM: MECP2 HM positive control, EG, DG, CS: antibody supplier (see the “Materials and methods” section). ( b ) EMSA analysis of polyclonal anti-hmC antibody binding to dsDNA oligo (0.75 pM) containing the indicated CpG dyad modifications. Antibody dilutions on top. ( c ) Bar diagram of quantification of EMSA data from Fig. , error bars show standard deviation ( n = 2). ( d ) Venn diagram for peaks from MeDIP and MECP2 wt enrichments. ( e ) Enrichment/depletion of CpG islands for selected peak sets. ( f ) Venn diagram for peaks from hMeDIP and MECP2 HM enrichments. ( g, h ) Enrichment/depletion of CpG islands and TTS for selected peak sets.

Article Snippet: Enriched DNA fragments were PCR amplified using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, version 6.1_5/20) using NEBNext Multiplex Oligos (NEB, E73359).

Techniques: Comparison, Methylated DNA Immunoprecipitation, Binding Assay, Modification, Positive Control, Standard Deviation