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Title: The rotary zone thermal cycler: A low-power system enabling automated rapid PCR

Abstract

In this study, advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, portable, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology such as aliquoting, centrifuging, mixing, and thermal cycling to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We further demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system using low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, preliminary results are presented for rapid single-plex PCR, multiplex short tandem repeat (STR)more » amplification, and second strand cDNA synthesis.« less

Authors:
 [1];  [2];  [3];  [1];  [4];  [1];  [1];  [5];  [6];  [1];  [1];  [1];  [7]
  1. Sandia National Lab. (SNL-CA), Livermore, CA (United States)
  2. Sandia National Lab. (SNL-CA), Livermore, CA (United States); Gas Transmission Systems, Walnut Creek, CA (United States)
  3. Sandia National Lab. (SNL-CA), Livermore, CA (United States); California State Univ., Los Angeles, CA (United States)
  4. Sandia National Lab. (SNL-CA), Livermore, CA (United States); Utah State Univ., Logan, UT (United States)
  5. Sandia National Lab. (SNL-CA), Livermore, CA (United States); Canon U.S. Life Sciences, Rockville, MD (United States)
  6. SequoiaTek Corp., Bakersfield, CA (United States)
  7. Northeastern Univ., Boston, MA (United States)
Publication Date:
Research Org.:
Sandia National Lab. (SNL-CA), Livermore, CA (United States); Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
Sponsoring Org.:
RRTO/USACIL; USDOE
OSTI Identifier:
1182998
Alternate Identifier(s):
OSTI ID: 1213408
Report Number(s):
SAND-2014-16371J
Journal ID: ISSN 1932-6203; 534052
Grant/Contract Number:  
AC04-94AL85000
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 3; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
47 OTHER INSTRUMENTATION; 59 BASIC BIOLOGICAL SCIENCES; polymerase chain reaction; microfluidics; thermal conductivity; automation; complementary DNA; polycarbonates; polymerases; thermocouples; DNA amplification; PCR wheel; sample prep automation; portable; low-resource; point of care; online cleaning; 60 APPLIED LIFE SCIENCES

Citation Formats

Bartsch, Michael S., Edwards, Harrison S., Lee, Daniel, Moseley, Caroline E., Tew, Karen E., Renzi, Ronald F., Van de Vreugde, James L., Kim, Hanyoup, Knight, Daniel L., Sinha, Anupama, Branda, Steven S., Patel, Kamlesh D., and Wanunu, Meni. The rotary zone thermal cycler: A low-power system enabling automated rapid PCR. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0118182.
Bartsch, Michael S., Edwards, Harrison S., Lee, Daniel, Moseley, Caroline E., Tew, Karen E., Renzi, Ronald F., Van de Vreugde, James L., Kim, Hanyoup, Knight, Daniel L., Sinha, Anupama, Branda, Steven S., Patel, Kamlesh D., & Wanunu, Meni. The rotary zone thermal cycler: A low-power system enabling automated rapid PCR. United States. doi:10.1371/journal.pone.0118182.
Bartsch, Michael S., Edwards, Harrison S., Lee, Daniel, Moseley, Caroline E., Tew, Karen E., Renzi, Ronald F., Van de Vreugde, James L., Kim, Hanyoup, Knight, Daniel L., Sinha, Anupama, Branda, Steven S., Patel, Kamlesh D., and Wanunu, Meni. Tue . "The rotary zone thermal cycler: A low-power system enabling automated rapid PCR". United States. doi:10.1371/journal.pone.0118182. https://www.osti.gov/servlets/purl/1182998.
@article{osti_1182998,
title = {The rotary zone thermal cycler: A low-power system enabling automated rapid PCR},
author = {Bartsch, Michael S. and Edwards, Harrison S. and Lee, Daniel and Moseley, Caroline E. and Tew, Karen E. and Renzi, Ronald F. and Van de Vreugde, James L. and Kim, Hanyoup and Knight, Daniel L. and Sinha, Anupama and Branda, Steven S. and Patel, Kamlesh D. and Wanunu, Meni},
abstractNote = {In this study, advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, portable, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology such as aliquoting, centrifuging, mixing, and thermal cycling to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We further demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system using low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, preliminary results are presented for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.},
doi = {10.1371/journal.pone.0118182},
journal = {PLoS ONE},
number = 3,
volume = 10,
place = {United States},
year = {Tue Mar 31 00:00:00 EDT 2015},
month = {Tue Mar 31 00:00:00 EDT 2015}
}

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