title: Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries.
abstract: Synthetic oligonucleotides are the main cost factor for studies in DNA nanotechnology, genetics and synthetic biology, which all require thousands of these at high quality. Inexpensive chip-synthesized oligonucleotide libraries can contain hundreds of thousands of distinct sequences, however only at sub-femtomole quantities per strand. Here we present a selective oligonucleotide amplification method, based on three rounds of rolling-circle amplification, that produces nanomole amounts of single-stranded oligonucleotides per millilitre reaction. In a multistep one-pot procedure, subsets of hundreds or thousands of single-stranded DNAs with different lengths can selectively be amplified and purified together. These oligonucleotides are used to fold several DNA nanostructures and as primary fluorescence in situ hybridization probes. The amplification cost is lower than other reported methods (typically around US$ 20 per nanomole total oligonucleotides produced) and is dominated by the use of commercial enzymes.
authors.affiliation: Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.|Wyss Institute for Biologically Inspired Engineering at Harvard, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.|Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany.
authors.forename: Thorsten L
authors.initials: TL
authors.lastname: Schmidt
authors.affiliation: Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Beliveau
authors.affiliation: Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062, Dresden, Germany.
authors.forename: Yavuz O
authors.initials: YO
authors.lastname: Uca
authors.affiliation: Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Theilmann
authors.affiliation: Wyss Institute for Biologically Inspired Engineering at Harvard, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.
authors.forename: Felipe
authors.initials: F
authors.lastname: Da Cruz
authors.affiliation: Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA.
authors.forename: Chao-Ting
authors.initials: CT
authors.lastname: Wu
authors.affiliation: Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.|Wyss Institute for Biologically Inspired Engineering at Harvard, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.
authors.forename: William M
authors.initials: WM
authors.lastname: Shih
mesh_terms: D002851:Chromatography, High Pressure Liquid; D004277:DNA, Single-Stranded; D015723:Gene Library; D017404:In Situ Hybridization, Fluorescence; D049329:Nanostructures; D036103:Nanotechnology; D021141:Nucleic Acid Amplification Techniques / Q000191:economics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000191:economics / Q000379:methods*; D009841:Oligonucleotides; D058615:Synthetic Biology
chemical_list: D004277:DNA, Single-Stranded; D009841:Oligonucleotides