Oligonucleotide quenchers for ultra‑low background assays: double‑quenched hydrolysis probes, molecular beacons, FRET pairs, and electrochemical formats. RUO → GMP‑like manufacturing with ISO‑aligned QC.
Fluorescence quenching is the intentional suppression of a donor dye’s emission by a nearby quencher. In oligonucleotide probes, this keeps the assay dark until a target‑dependent event (e.g., polymerase cleavage or hairpin opening) separates the pair or disrupts their interaction—yielding high signal‑to‑noise (S/N) precisely when and where it matters.
Quenching can be dominated by contact (static π–π interactions), dynamic (collisional) processes, and/or FRET when a spectral acceptor is used. Modern dark quenchers dissipate energy non‑radiatively and minimize bleed‑through in multiplexed panels.
Bio‑Synthesis, Inc. (Lewisville, Texas) is a U.S. manufacturer of custom fluorescence‑quenched oligonucleotides for research, diagnostics, and therapeutic development. We design and produce double‑quenched qPCR probes, molecular beacons, FRET pairs, and electrochemical probes, with options for internal/3' dark quenchers, spacers, linkers, and alternate backbones.
Representative offering. Additional brands and placements (5', internal, 3') available on request.
Internal placement 8–12 nt from the dye often minimizes baseline while preserving cleavage/readout. C3/C6 spacers or abasic (rSpacer) can tune flexibility and distance.
Internal + 3' quenchers reduce baseline on long probes (>25 nt) and tough amplicons. Internal spacing near the dye (+7 to +10) improves contact quenching; 3' quencher controls exonuclease‑independent leakage.
Include NTCs, passive references as required, and verify purity (HPLC) and mass (ESI‑MS). For regulated studies, request extended QC (bioburden/endotoxin, residual solvents, ds% by UPLC, stability studies).
Reduction of donor fluorescence by a quencher (contact/FRET/collisional), keeping baseline low until target activation.
On longer probes (>25 nt) or high‑GC targets; they reduce baseline and improve S/N.
Yes—request extended QC and documentation for GLP/cGMP‑like needs.
BHQ‑1, QSY 7, Iowa Black FQ, ATTO 540Q, or DYQ‑505 typically perform well with FAM/HEX‑like emissions.
Yes. Match each dye’s emission to a compatible quencher to minimize crosstalk and baseline fluorescence.
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