Literature DB >> 20538451

Shaping up nucleic acid computation.

Xi Chen1, Andrew D Ellington.   

Abstract

Nucleic acid-based nanotechnology has always been perceived as novel, but has begun to move from theoretical demonstrations to practical applications. In particular, the large address spaces available to nucleic acids can be exploited to encode algorithms and/or act as circuits and thereby process molecular information. In this review we not only revisit several milestones in the field of nucleic acid-based computation, but also highlight how the prospects for nucleic acid computation go beyond just a large address space. Functional nucleic acid elements (aptamers, ribozymes, and deoxyribozymes) can serve as inputs and outputs to the environment, and can act as logical elements. Into the future, the chemical dynamics of nucleic acids may prove as useful as hybridization for computation.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20538451      PMCID: PMC2943001          DOI: 10.1016/j.copbio.2010.05.003

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  31 in total

1.  Solution of a 20-variable 3-SAT problem on a DNA computer.

Authors:  Ravinderjit S Braich; Nickolas Chelyapov; Cliff Johnson; Paul W K Rothemund; Leonard Adleman
Journal:  Science       Date:  2002-03-14       Impact factor: 47.728

Review 2.  The second wave of synthetic biology: from modules to systems.

Authors:  Priscilla E M Purnick; Ron Weiss
Journal:  Nat Rev Mol Cell Biol       Date:  2009-06       Impact factor: 94.444

Review 3.  Functional nucleic acid sensors.

Authors:  Juewen Liu; Zehui Cao; Yi Lu
Journal:  Chem Rev       Date:  2009-05       Impact factor: 60.622

4.  Engineering complex riboswitch regulation by dual genetic selection.

Authors:  Vandana Sharma; Yoko Nomura; Yohei Yokobayashi
Journal:  J Am Chem Soc       Date:  2008-12-03       Impact factor: 15.419

5.  A general purpose RNA-cleaving DNA enzyme.

Authors:  S W Santoro; G F Joyce
Journal:  Proc Natl Acad Sci U S A       Date:  1997-04-29       Impact factor: 11.205

6.  Molecular computation of solutions to combinatorial problems.

Authors:  L M Adleman
Journal:  Science       Date:  1994-11-11       Impact factor: 47.728

7.  Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes.

Authors:  Robert Penchovsky; Ronald R Breaker
Journal:  Nat Biotechnol       Date:  2005-10-23       Impact factor: 54.908

8.  A DNA enzyme with Mg(2+)-dependent RNA phosphoesterase activity.

Authors:  R R Breaker; G F Joyce
Journal:  Chem Biol       Date:  1995-10

9.  Construction of an in vitro bistable circuit from synthetic transcriptional switches.

Authors:  Jongmin Kim; Kristin S White; Erik Winfree
Journal:  Mol Syst Biol       Date:  2006-12-12       Impact factor: 11.429

Review 10.  Modelling amorphous computations with transcription networks.

Authors:  Zack Booth Simpson; Timothy L Tsai; Nam Nguyen; Xi Chen; Andrew D Ellington
Journal:  J R Soc Interface       Date:  2009-05-27       Impact factor: 4.118

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  16 in total

1.  Molecular computing: DNA as a logic operator.

Authors:  Thomas Carell
Journal:  Nature       Date:  2011-01-06       Impact factor: 49.962

Review 2.  Dynamic DNA nanotechnology using strand-displacement reactions.

Authors:  David Yu Zhang; Georg Seelig
Journal:  Nat Chem       Date:  2011-02       Impact factor: 24.427

3.  Stacking nonenzymatic circuits for high signal gain.

Authors:  Xi Chen; Neima Briggs; Jeremy R McLain; Andrew D Ellington
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-18       Impact factor: 11.205

Review 4.  Challenges and opportunities for structural DNA nanotechnology.

Authors:  Andre V Pinheiro; Dongran Han; William M Shih; Hao Yan
Journal:  Nat Nanotechnol       Date:  2011-11-06       Impact factor: 39.213

5.  Using RecA protein to enhance kinetic rates of DNA circuits.

Authors:  J N Milligan; A D Ellington
Journal:  Chem Commun (Camb)       Date:  2015-06-11       Impact factor: 6.222

Review 6.  Synthetic in vitro circuits.

Authors:  Adam J Hockenberry; Michael C Jewett
Journal:  Curr Opin Chem Biol       Date:  2012-06-05       Impact factor: 8.822

7.  Design, synthesis, and application of Spinach molecular beacons triggered by strand displacement.

Authors:  Sanchita Bhadra; Andrew D Ellington
Journal:  Methods Enzymol       Date:  2015-01-05       Impact factor: 1.600

8.  Optochemical control of deoxyoligonucleotide function via a nucleobase-caging approach.

Authors:  Qingyang Liu; Alexander Deiters
Journal:  Acc Chem Res       Date:  2013-08-28       Impact factor: 22.384

Review 9.  Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic acid-functionalized nanomaterials.

Authors:  Peiwen Wu; Yang Yu; Claire E McGhee; Li Huey Tan; Yi Lu
Journal:  Adv Mater       Date:  2014-09-10       Impact factor: 30.849

10.  Nucleic acid based logical systems.

Authors:  Da Han; Huaizhi Kang; Tao Zhang; Cuichen Wu; Cuisong Zhou; Mingxu You; Zhuo Chen; Xiaobing Zhang; Weihong Tan
Journal:  Chemistry       Date:  2014-04-01       Impact factor: 5.236

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