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Literature DB >> 21135212

All-DNA finite-state automata with finite memory.

Zhen-Gang Wang¹, Johann Elbaz, F Remacle, R D Levine, Itamar Willner.

Abstract

Biomolecular logic devices can be applied for sensing and nano-medicine. We built three DNA tweezers that are activated by the inputs H(+)/OH(-); ; nucleic acid linker/complementary antilinker to yield a 16-states finite-state automaton. The outputs of the automata are the configuration of the respective tweezers (opened or closed) determined by observing fluorescence from a fluorophore/quencher pair at the end of the arms of the tweezers. The system exhibits a memory because each current state and output depend not only on the source configuration but also on past states and inputs.

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Year: 2010 PMID： 21135212 PMCID： PMC3009826 DOI： 10.1073/pnas.1015858107

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

33 in total

1. Molecular gears: a pair of DNA circles continuously rolls against each other.

Authors: Ye Tian; Chengde Mao
Journal: J Am Chem Soc Date: 2004-09-22 Impact factor: 15.419

2. A synthetic DNA walker for molecular transport.

Authors: Jong-Shik Shin; Niles A Pierce
Journal: J Am Chem Soc Date: 2004-09-08 Impact factor: 15.419

Review 3. From genes to machines: DNA nanomechanical devices.

Authors: Nadrian C Seeman
Journal: Trends Biochem Sci Date: 2005-03 Impact factor: 13.807

4. Enzyme-free nucleic acid logic circuits.

Authors: Georg Seelig; David Soloveichik; David Yu Zhang; Erik Winfree
Journal: Science Date: 2006-12-08 Impact factor: 47.728

5. Addressable molecular tweezers for DNA-templated coupling reactions.

Authors: Rahul Chhabra; Jaswinder Sharma; Yan Liu; Hao Yan
Journal: Nano Lett Date: 2006-05 Impact factor: 11.189

6. DNA-based machines.

Authors: Moritz K Beissenhirtz; Itamar Willner
Journal: Org Biomol Chem Date: 2006-08-04 Impact factor: 3.876

7. MercuryII-mediated formation of thymine-HgII-thymine base pairs in DNA duplexes.

Authors: Yoko Miyake; Humika Togashi; Mitsuru Tashiro; Hiroshi Yamaguchi; Shuji Oda; Megumi Kudo; Yoshiyuki Tanaka; Yoshinori Kondo; Ryuichi Sawa; Takashi Fujimoto; Tomoya Machinami; Akira Ono
Journal: J Am Chem Soc Date: 2006-02-22 Impact factor: 15.419

8. 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

9. Concatenated logic gates using four coupled biocatalysts operating in series.

Authors: Tamara Niazov; Ronan Baron; Eugenii Katz; Oleg Lioubashevski; Itamar Willner
Journal: Proc Natl Acad Sci U S A Date: 2006-11-06 Impact factor: 11.205

10. Proteins modified with DNAzymes or aptamers act as biosensors or biosensor labels.

Authors: Bella Shlyahovsky; Di Li; Eugenii Katz; Itamar Willner
Journal: Biosens Bioelectron Date: 2006-11-13 Impact factor: 10.618

7 in total

Review 1. Artificial Molecular Machines.

Authors: Sundus Erbas-Cakmak; David A Leigh; Charlie T McTernan; Alina L Nussbaumer
Journal: Chem Rev Date: 2015-09-08 Impact factor: 60.622

Review 2. Biomolecular computing systems: principles, progress and potential.

Authors: Yaakov Benenson
Journal: Nat Rev Genet Date: 2012-06-12 Impact factor: 53.242

Review 3. The biological microprocessor, or how to build a computer with biological parts.

Authors: Gerd Hg Moe-Behrens
Journal: Comput Struct Biotechnol J Date: 2013-06-26 Impact factor: 7.271

4. Synthesis and Enzymatic Incorporation of a Responsive Ribonucleoside Probe That Enables Quantitative Detection of Metallo-Base Pairs.

Authors: Sudeshna Manna; Seergazhi G Srivatsan
Journal: Org Lett Date: 2019-06-07 Impact factor: 6.005