Literature DB >> 19562106

Biocomputers: from test tubes to live cells.

Yaakov Benenson1.   

Abstract

Biocomputers are man-made biological networks whose goal is to probe and control biological hosts--cells and organisms--in which they operate. Their key design features, informed by computer science and engineering, are programmability, modularity and versatility. While still a work in progress, biocomputers will eventually enable disease diagnosis and treatment with single-cell precision, lead to "designer" cell functions for biotechnology, and bring about a new generation of biological measurement tools. This review describes the intellectual foundation of the "biocomputer" concept as well as surveys the state of the art in the field.

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Year:  2009        PMID: 19562106      PMCID: PMC2714485          DOI: 10.1039/b902484k

Source DB:  PubMed          Journal:  Mol Biosyst        ISSN: 1742-2051


  100 in total

1.  A biochemical logic gate using an enzyme and its inhibitor. 1. The inhibitor as switching element.

Authors:  S Sivan; N Lotan
Journal:  Biotechnol Prog       Date:  1999 Nov-Dec

2.  Allosteric nucleic acid catalysts.

Authors:  G A Soukup; R R Breaker
Journal:  Curr Opin Struct Biol       Date:  2000-06       Impact factor: 6.809

3.  Reprogramming control of an allosteric signaling switch through modular recombination.

Authors:  John E Dueber; Brian J Yeh; Kayam Chak; Wendell A Lim
Journal:  Science       Date:  2003-09-26       Impact factor: 47.728

4.  MicroRNA genes are transcribed by RNA polymerase II.

Authors:  Yoontae Lee; Minju Kim; Jinju Han; Kyu-Hyun Yeom; Sanghyuk Lee; Sung Hee Baek; V Narry Kim
Journal:  EMBO J       Date:  2004-09-16       Impact factor: 11.598

Review 5.  Regulation of bacterial gene expression by riboswitches.

Authors:  Wade C Winkler; Ronald R Breaker
Journal:  Annu Rev Microbiol       Date:  2005       Impact factor: 15.500

6.  A lentiviral microRNA-based system for single-copy polymerase II-regulated RNA interference in mammalian cells.

Authors:  Frank Stegmeier; Guang Hu; Richard J Rickles; Gregory J Hannon; Stephen J Elledge
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-01       Impact factor: 11.205

7.  Folding DNA to create nanoscale shapes and patterns.

Authors:  Paul W K Rothemund
Journal:  Nature       Date:  2006-03-16       Impact factor: 49.962

8.  Programming biomolecular self-assembly pathways.

Authors:  Peng Yin; Harry M T Choi; Colby R Calvert; Niles A Pierce
Journal:  Nature       Date:  2008-01-17       Impact factor: 49.962

9.  DNA computers for work and play.

Authors:  Joanne Macdonald; Darko Stefanovic; Milan N Stojanovic
Journal:  Sci Am       Date:  2008-11       Impact factor: 2.142

10.  Functional analysis of chemical systems in vivo using a logical circuit equivalent. II. The idea of a molecular automation.

Authors:  M Sugita
Journal:  J Theor Biol       Date:  1963-03       Impact factor: 2.691

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  18 in total

1.  DNA computing circuits using libraries of DNAzyme subunits.

Authors:  Johann Elbaz; Oleg Lioubashevski; Fuan Wang; Françoise Remacle; Raphael D Levine; Itamar Willner
Journal:  Nat Nanotechnol       Date:  2010-05-30       Impact factor: 39.213

2.  All-DNA finite-state automata with finite memory.

Authors:  Zhen-Gang Wang; Johann Elbaz; F Remacle; R D Levine; Itamar Willner
Journal:  Proc Natl Acad Sci U S A       Date:  2010-12-06       Impact factor: 11.205

3.  Implementation of a genetic logic circuit: bio-register.

Authors:  Chun-Liang Lin; Ting-Yu Kuo; Yang-Yi Chen
Journal:  Syst Synth Biol       Date:  2015-11-23

4.  Scaling down DNA circuits with competitive neural networks.

Authors:  Anthony J Genot; Teruo Fujii; Yannick Rondelez
Journal:  J R Soc Interface       Date:  2013-06-12       Impact factor: 4.118

5.  Synthetic biology: Division of logic labour.

Authors:  Bochong Li; Lingchong You
Journal:  Nature       Date:  2011-01-13       Impact factor: 49.962

6.  Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates.

Authors:  Ron Orbach; Françoise Remacle; R D Levine; Itamar Willner
Journal:  Proc Natl Acad Sci U S A       Date:  2012-12-12       Impact factor: 11.205

7.  The molecular basis of memory.

Authors:  Gerard Marx; Chaim Gilon
Journal:  ACS Chem Neurosci       Date:  2012-08-15       Impact factor: 4.418

8.  Bridging the Two Worlds: A Universal Interface between Enzymatic and DNA Computing Systems.

Authors:  Shay Mailloux; Yulia V Gerasimova; Nataliia Guz; Dmitry M Kolpashchikov; Evgeny Katz
Journal:  Angew Chem Int Ed Engl       Date:  2015-04-09       Impact factor: 15.336

9.  DNA Computing Systems Activated by Electrochemically-triggered DNA Release from a Polymer-brush-modified Electrode Array.

Authors:  Maria Gamella; Andrey Zakharchenko; Nataliia Guz; Madeline Masi; Sergiy Minko; Dmitry M Kolpashchikov; Heiko Iken; Arshak Poghossian; Michael J Schöning; Evgeny Katz
Journal:  Electroanalysis       Date:  2016-08-05       Impact factor: 3.223

10.  A biocatalytic cascade with several output signals--towards biosensors with different levels of confidence.

Authors:  Nataliia Guz; Jan Halámek; James F Rusling; Evgeny Katz
Journal:  Anal Bioanal Chem       Date:  2014-04-20       Impact factor: 4.142

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