Robotic hierarchical mixing for the production of combinatorial libraries of proteins and small molecules

被引:5
作者
Avramova, Larisa V. [1 ]
Desai, Jairav [2 ]
Weaver, Shelley [2 ]
Friedman, Alan M. [1 ,3 ,4 ]
Bailey-Kellogg, Chris [2 ]
机构
[1] Purdue Univ, Bindley Biosci Ctr, W Lafayette, IN 47907 USA
[2] Dartmouth Coll, Dept Comp Sci, Hanover, NH 03755 USA
[3] Purdue Univ, Purdue Canc Ctr, Dept Biol Sci, W Lafayette, IN 47907 USA
[4] Purdue Univ, Markey Ctr Struct Biol, W Lafayette, IN 47907 USA
来源
JOURNAL OF COMBINATORIAL CHEMISTRY | 2008年 / 10卷 / 01期
关键词
D O I
10.1021/cc700106e
中图分类号
O69 [应用化学];
学科分类号
081704 ;
摘要
We present a method to automatically plan a robotic process to mix individual combinations of reactants in individual reaction vessels (vials or wells in a multiwell plate), mixing any number of reactants in any desired stoichiometry, and ordering the mixing steps according to an arbitrarily complex treelike assembly protocol. This process enables the combinatorial generation of complete or partial product libraries in individual reaction vessels from intermediates formed in the presence of different sets of reactants. It can produce either libraries of chimeric genes constructed by ligation of fragments from different parent genes or libraries of chemical compounds constructed by convergent synthesis. Given concentrations of the input reactants and desired amounts or volumes of the products, our algorithm, RoboMix, computes the required reactant volumes and the resulting product concentrations, along with volumes and concentrations for all intermediate combinations. It outputs a sequence of robotic liquid transfer steps that ensures that each combination is correctly mixed even when individualized stoichiometries are employed and with any fractional yield for a product. It can also account for waste in robotic liquid handling and residual volume needed to ensure accurate aspiration. We demonstrate the effectiveness of the method in a test mixing dyes with different UV-vis absorption spectra, verifying the desired combinations spectroscopically.
引用
收藏
页码:63 / 68
页数:6
相关论文
共 14 条
[1]   Chemical library synthesis using convergent approaches [J].
Beeler, AB ;
Schaus, SE ;
Porco, JA .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2005, 9 (03) :277-284
[2]   ENCODED COMBINATORIAL CHEMISTRY [J].
BRENNER, S ;
LERNER, RA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (12) :5381-5383
[3]   Convergent diversity-oriented synthesis of small-molecule hybrids [J].
Chen, C ;
Li, XD ;
Neumann, CS ;
Lo, MMC ;
Schreiber, SL .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2005, 44 (15) :2249-2252
[4]   A NEW GENERAL-APPROACH FOR THE SIMULTANEOUS CHEMICAL SYNTHESIS OF LARGE NUMBERS OF OLIGONUCLEOTIDES - SEGMENTAL SOLID SUPPORTS [J].
FRANK, R ;
HEIKENS, W ;
HEISTERBERGMOUTSIS, G ;
BLOCKER, H .
NUCLEIC ACIDS RESEARCH, 1983, 11 (13) :4365-4377
[5]   DNA-templated organic synthesis and selection of a library of macrocycles [J].
Gartner, ZJ ;
Tse, BN ;
Grubina, R ;
Doyon, JB ;
Snyder, TM ;
Liu, DR .
SCIENCE, 2004, 305 (5690) :1601-1605
[6]   DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution [J].
Halpin, DR ;
Harbury, PB .
PLOS BIOLOGY, 2004, 2 (07) :1022-1030
[7]   General method for sequence-independent site-directed chimeragenesis [J].
Hiraga, K ;
Arnold, FH .
JOURNAL OF MOLECULAR BIOLOGY, 2003, 330 (02) :287-296
[8]   Library analysis of SCHEMA-guided protein recombination [J].
Meyer, MM ;
Silberg, JJ ;
Voigt, CA ;
Endelman, JB ;
Mayo, SL ;
Wang, ZG ;
Arnold, FH .
PROTEIN SCIENCE, 2003, 12 (08) :1686-1693
[9]   Structure-guided recombination creates an artificial family of cytochromes P450 [J].
Otey, Christopher R. ;
Landwehr, Marco ;
Endelman, Jeffrey B. ;
Hiraga, Kaori ;
Bloom, Jesse D. ;
Arnold, Frances H. .
PLOS BIOLOGY, 2006, 4 (05) :789-798
[10]   Automated parallel synthesis of chalcone-based screening libraries [J].
Powers, DG ;
Casebier, DS ;
Fokas, D ;
Ryan, WJ ;
Troth, JR ;
Coffen, DL .
TETRAHEDRON, 1998, 54 (16) :4085-4096