MOTIVATION: The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay. RESULTS: We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps. AVAILABILITY: The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.
MOTIVATION: The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay. RESULTS: We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps. AVAILABILITY: The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.
Authors: Steven A Benner; Nilesh B Karalkar; Shuichi Hoshika; Roberto Laos; Ryan W Shaw; Mariko Matsuura; Diego Fajardo; Patricia Moussatche Journal: Cold Spring Harb Perspect Biol Date: 2016-11-01 Impact factor: 10.005
Authors: Siao Ping Tsai; Anne Wong; Elaine Mai; Pamela Chan; Grace Mausisa; Mark Vasser; Parkash Jhurani; Mogens H Jakobsen; Wai Lee T Wong; Jean-Philippe Stephan Journal: Nucleic Acids Res Date: 2003-03-15 Impact factor: 16.971
Authors: Liqin Zhang; Sai Wang; Zunyi Yang; Shuichi Hoshika; Sitao Xie; Jin Li; Xigao Chen; Shuo Wan; Long Li; Steven A Benner; Weihong Tan Journal: Angew Chem Int Ed Engl Date: 2019-11-19 Impact factor: 15.336
Authors: Nicholas R Staten; Eric A Welsh; Kurex Sidik; Sandra A McDonald; Dawn R Dufield; Botoul Maqsodi; Yunqing Ma; Gary K McMaster; Rodney W Mathews; Robert H Arch; Jaime L Masferrer; Bernard E Souberbielle Journal: Fibrogenesis Tissue Repair Date: 2012-12-27