title: Automated Device for Asynchronous Extraction of RNA, DNA, or Protein Biomarkers from Surrogate Patient Samples.
abstract: Many biomarker-based diagnostic methods are inhibited by nontarget molecules in patient samples, necessitating biomarker extraction before detection. We have developed a simple device that purifies RNA, DNA, or protein biomarkers from complex biological samples without robotics or fluid pumping. The device design is based on functionalized magnetic beads, which capture biomarkers and remove background biomolecules by magnetically transferring the beads through processing solutions arrayed within small-diameter tubing. The process was automated by wrapping the tubing around a disc-like cassette and rotating it past a magnet using a programmable motor. This device recovered biomarkers at ~80% of the operator-dependent extraction method published previously. The device was validated by extracting biomarkers from a panel of surrogate patient samples containing clinically relevant concentrations of (1) influenza A RNA in nasal swabs, (2) Escherichia coli DNA in urine, (3) Mycobacterium tuberculosis DNA in sputum, and (4) Plasmodium falciparum protein and DNA in blood. The device successfully extracted each biomarker type from samples representing low levels of clinically relevant infectivity (i.e., 7.3 copies/µL of influenza A RNA, 405 copies/µL of E. coli DNA, 0.22 copies/µL of TB DNA, 167 copies/µL of malaria parasite DNA, and 2.7 pM of malaria parasite protein).
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
authors.forename: Anna L
authors.initials: AL
authors.lastname: Bitting
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Hali
authors.initials: H
authors.lastname: Bordelon
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Mark L
authors.initials: ML
authors.lastname: Baglia
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
authors.forename: Keersten M
authors.initials: KM
authors.lastname: Davis
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Amy E
authors.initials: AE
authors.lastname: Creecy
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Philip A
authors.initials: PA
authors.lastname: Short
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Laura E
authors.initials: LE
authors.lastname: Albert
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Aditya V
authors.initials: AV
authors.lastname: Karhade
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
authors.forename: David W
authors.initials: DW
authors.lastname: Wright
authors.affiliation: Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Frederick R
authors.initials: FR
authors.lastname: Haselton
authors.affiliation: Department of Chemistry, Vanderbilt University, Nashville, TN, USA n.adams@vanderbilt.edu.|Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA.
authors.forename: Nicholas M
authors.initials: NM
authors.lastname: Adams
mesh_terms: D057205:Automation, Laboratory / Q000295:instrumentation* / Q000379:methods; D015415:Biomarkers / Q000032:analysis*; D004247:DNA / Q000302:isolation & purification*; D006801:Humans; D008828:Microbiological Techniques / Q000295:instrumentation* / Q000379:methods; D011506:Proteins / Q000302:isolation & purification*; D012313:RNA / Q000302:isolation & purification*; D013048:Specimen Handling / Q000379:methods*
chemical_list: D015415:Biomarkers; D011506:Proteins; D012313:RNA; D004247:DNA
keywords: DNA extraction; RNA extraction; automated biomarker extraction; low-resource biomarker extraction; protein extraction