Overview: methods and applications for droplet compartmentalization of biology

Three protocols in this issue highlight applications of emulsification procedures, which deliver high-throughput potential to the molecular biology laboratory, without the need for automation. These procedures have already generated interesting results and spurred the development of exciting new technologies, while requiring only readily available laboratory equipment.

[1]  Dan S. Tawfik,et al.  Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry , 2002, FEBS letters.

[2]  A. Griffiths,et al.  High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions. , 2005, Chemistry & biology.

[3]  S. Wallenstein,et al.  Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes , 2005, Nucleic acids research.

[4]  Y. Murakami,et al.  Development of a microchamber array for picoliter PCR. , 2001, Analytical chemistry.

[5]  R. Westervelt,et al.  Dielectrophoretic manipulation of drops for high-speed microfluidic sorting devices , 2006 .

[6]  Shinji Katsura,et al.  Single-molecule reverse transcription polymerase chain reaction using water-in-oil emulsion. , 2005, Journal of bioscience and bioengineering.

[7]  R. Dalton.  Neanderthal DNA yields to genome foray , 2006, Nature.

[8]  David E. Housman,et al.  Genome complexity reduction for SNP genotyping analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  C. T. Farley,et al.  Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2008 .

[10]  Jan Berka,et al.  A massively parallel PicoTiterPlate™ based platform for discrete picoliter‐scale polymerase chain reactions , 2003, Electrophoresis.

[11]  A. Mizuno,et al.  Indirect micromanipulation of single molecules in water‐in‐oil emulsion , 2001, Electrophoresis.

[12]  D. Bartel,et al.  Synthesizing life : Paths to unforeseeable science & technology , 2001 .

[13]  D. Weitz,et al.  Electric control of droplets in microfluidic devices. , 2006, Angewandte Chemie.

[14]  Christa Lanz,et al.  Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Dan S. Tawfik,et al.  High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. , 2005, Chemistry & biology.

[16]  Andrew D Griffiths,et al.  Directed evolution by in vitro compartmentalization , 2006, Nature Methods.

[17]  Frank Diehl,et al.  BEAMing: single-molecule PCR on microparticles in water-in-oil emulsions , 2006, Nature Methods.

[18]  Andrew D Griffiths,et al.  High-throughput screens and selections of enzyme-encoding genes. , 2005, Current opinion in chemical biology.

[19]  Dan S. Tawfik,et al.  Man-made cell-like compartments for molecular evolution , 1998, Nature Biotechnology.

[20]  N. Doi,et al.  In vitro selection of restriction endonucleases by in vitro compartmentalization. , 2004, Nucleic acids research.

[21]  Takaaki Kojima,et al.  PCR amplification from single DNA molecules on magnetic beads in emulsion: application for high-throughput screening of transcription factor targets , 2005, Nucleic acids research.

[22]  C. Levenson,et al.  Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. , 1990, Nucleic acids research.

[23]  Jennifer L. Ong,et al.  Directed evolution of polymerase function by compartmentalized self-replication , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[24]  S. Giovannoni,et al.  Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR , 1996, Applied and environmental microbiology.

[25]  Hinrich W. H. Göhlmann,et al.  A Diarylquinoline Drug Active on the ATP Synthase of Mycobacterium tuberculosis , 2005, Science.

[26]  A. Griffiths,et al.  Selection of ribozymes that catalyse multiple-turnover Diels-Alder cycloadditions by using in vitro compartmentalization. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[27]  D. Dressman,et al.  Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[28]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[29]  Shinji Katsura,et al.  Single-molecule PCR using water-in-oil emulsion. , 2003, Journal of biotechnology.

[30]  Ian Humphery-Smith,et al.  Regionalized GC content of template DNA as a predictor of PCR success. , 2003, Nucleic acids research.

[31]  Dan S. Tawfik,et al.  Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization , 2003, The EMBO journal.

[32]  Andrew D Griffiths,et al.  Amplification of complex gene libraries by emulsion PCR , 2006, Nature Methods.

[33]  M. Cottrell,et al.  Community Composition of Marine Bacterioplankton Determined by 16S rRNA Gene Clone Libraries and Fluorescence In Situ Hybridization , 2000, Applied and Environmental Microbiology.

[34]  Alexander F. Auch,et al.  Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA , 2006, Science.

[35]  Dan S. Tawfik,et al.  Evolution of new protein topologies through multistep gene rearrangements , 2006, Nature Genetics.

[36]  Y. Murakami,et al.  High-throughput PCR in silicon based microchamber array. , 2001, Biosensors & bioelectronics.

[37]  Klavs Jensen,et al.  Chemical kinetics: Smaller, faster chemistry , 1998, Nature.