Journal: Biophysical Journal

Article Title: Multiplex Single-Molecule DNA Barcoding Using an Oligonucleotide Ligation Assay

doi: 10.1016/j.bpj.2018.08.013

Figure Lengend Snippet: DNA barcoding experimental scheme. Target DNA strands are immobilized on a microscope slide, and dye-labeled barcodes are introduced together with T4 DNA ligase in the microfluidic chamber (1). Complementary barcodes bind transiently to the target site (2), whereas mismatched barcodes bind on an even shorter timescale (2′). Successful ligation is observed for the complementary barcodes (3) but not for the mismatched barcodes (3′). Ligation product shows stable binding to the target DNA (4), whereas mismatched barcodes dissociate and are washed away before imaging. To see this figure in color, go online.

Article Snippet: Barcoding procedure Immobilized target DNA was incubated with 50 nM of each upstream and 50 nM of each downstream barcode (independent of the number of different barcode sequences used) and 14 Weiss units/mL of T4 DNA ligase (Thermo Fisher Scientific, Waltham, MA) in freshly prepared ligation buffer (40 mM Tris-HCl (pH 7.6), 10 mM MgCl 2 , 10 mM dithiothreitol, 0.5 mM ATP) for 1 h at 25°C.

Techniques: Microscopy, Labeling, Ligation, Binding Assay, Imaging

Journal: Biophysical Journal

Article Title: Multiplex Single-Molecule DNA Barcoding Using an Oligonucleotide Ligation Assay

doi: 10.1016/j.bpj.2018.08.013

Figure Lengend Snippet: Enzymatic restriction confirms specificity of DNA barcoding. The number of barcode pairs detected in four-color single-target and four-target experiments is shown, indicated with the sequence at the ligation site (“GA,” “GC,” “GG,” and “GT”) and with “All,” respectively. Hatched bars show barcode pair counts after the addition of a restriction enzyme specific to the bound Cy3-Cy3 barcode pair. To see this figure in color, go online.

Article Snippet: Barcoding procedure Immobilized target DNA was incubated with 50 nM of each upstream and 50 nM of each downstream barcode (independent of the number of different barcode sequences used) and 14 Weiss units/mL of T4 DNA ligase (Thermo Fisher Scientific, Waltham, MA) in freshly prepared ligation buffer (40 mM Tris-HCl (pH 7.6), 10 mM MgCl 2 , 10 mM dithiothreitol, 0.5 mM ATP) for 1 h at 25°C.

Techniques: Sequencing, Ligation

Journal: Foods

Article Title: DNA Barcoding for Identification of Consumer-Relevant Fungi Sold in New York: A Powerful Tool for Citizen Scientists?

doi: 10.3390/foods7060087

Figure Lengend Snippet: Species identification based on internal transcribed spacer (ITS) DNA barcoding from all of the samples analyzed ( n = 10). Each consensus sequence of samples S1–S10 was subjected to three search tools to verify identity (ID), namely: 1) DNA Subway; 2) direct submission to Basic Local Alignment Search Tool (BLAST) search in GenBank; and 3) a serial BLAST search in the curated fungal taxonomic reference database User-friendly Nordic ITS Ectomycorrhiza Database (UNITE). * indicates low-quality sequences, in both instances of the Oyster mushroom samples. N/A: not available.

Article Snippet: The DNA was extracted from approximately 0.1 g of the specimen, using a standard silica- based DNA extraction method (as recommended by the DNA Barcoding 101 webpage [ ]) with one minor modification, which was that for each sample, a small piece was removed, placed in a sterile 1.5 mL microcentrifuge tube, and pre-soaked in dH 2 O, before being ground in a 300 μL lysis buffer (6 M guanidine hydrochloride solution (Sigma-Aldrich, St. Louis, MO, USA)) with a sterile pestle.

Techniques: Sequencing

Journal: Applied and Environmental Microbiology

Article Title: Sources of Bacteria in Outdoor Air across Cities in the Midwestern United States

doi: 10.1128/aem.05498-11

Figure Lengend Snippet: FIG. 1. Most abundant bacterial groups identified using barcoded pyrosequencing at the phylum level (A) and at the order level (B). Proteobacterial groups are designated by the letters , , , and for the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, respectively.

Article Snippet: Bacterial community composition was determined using a barcoded pyrosequencing procedure, which facilitates multiplexed sequencing of partial 16S rRNA genes.

Techniques: