DNA Colorimetric Logic Gates Based on Triplex–Helix Molecular Switch

A horseradish peroxidase (HRP)-mimicking DNAzyme sequence is first blocked by the triplex-based molecular beacon (tMB). Upon hybridization with single-stranded DNA inputs, triplex–helix molecular switch occurs, and the released product strand self-assembles into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. On the basis of this principle, a series of logic gates (OR, XOR, INHIBIT, and AND) have been developed. Moreover, a multilevel circuit (MC) that enforces an overall OR Boolean behavior is developed by connecting the AND and XOR logic gates. The logic output signals can be recognized by naked eyes, thus providing a flexible, secure, economic, and simple method for designing a complex DNA-based logic device.

[1]  Sai Bi,et al.  Colorimetric logic gates based on supramolecular DNAzyme structures. , 2010, Angewandte Chemie.

[2]  Jishan Li,et al.  Time-resolved fluorescent detection of Hg2+ in a complex environment by conjugating magnetic nanoparticles with a triple-helix molecular switch. , 2013, Chemical communications.

[3]  Michael Famulok,et al.  Input-Dependent Induction of Oligonucleotide Structural Motifs for Performing Molecular Logic , 2012, Journal of the American Chemical Society.

[4]  Andreas Offenhäusser,et al.  An electrochemically transduced XOR logic gate at the molecular level. , 2010, Angewandte Chemie.

[5]  I. Willner,et al.  Coherent activation of DNA tweezers: a "SET-RESET" logic system. , 2009, Angewandte Chemie.

[6]  Dan Luo,et al.  Adaptive DNA-based materials for switching, sensing, and logic devices , 2011 .

[7]  Itamar Willner,et al.  Optical analysis of Hg2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines. , 2008, Angewandte Chemie.

[8]  Uwe Pischel,et al.  Chemical approaches to molecular logic elements for addition and subtraction. , 2007, Angewandte Chemie.

[9]  Itamar Willner,et al.  pH-programmable DNA logic arrays powered by modular DNAzyme libraries. , 2012, Nano letters.

[10]  A. P. de Silva,et al.  Molecular-scale logic gates. , 2004, Chemistry.

[11]  A. Turberfield,et al.  A free-running DNA motor powered by a nicking enzyme. , 2005, Angewandte Chemie.

[12]  Ka-Ho Leung,et al.  A luminescent G-quadruplex switch-on probe for the highly selective and tunable detection of cysteine and glutathione. , 2013, Chemical communications.

[13]  Ronghua Yang,et al.  Fabricating a reversible and regenerable Raman-active substrate with a biomolecule-controlled DNA nanomachine. , 2012, Journal of the American Chemical Society.

[14]  Wei Xu,et al.  Ultrasensitive and selective colorimetric DNA detection by nicking endonuclease assisted nanoparticle amplification. , 2009, Angewandte Chemie.

[15]  P. Yin,et al.  A DNAzyme that walks processively and autonomously along a one-dimensional track. , 2005, Angewandte Chemie.

[16]  Jingjing Ma,et al.  Fluorescent nanoparticle beacon for logic gate operation regulated by strand displacement. , 2013, ACS applied materials & interfaces.

[17]  X. Qu,et al.  G-quadruplexes form ultrastable parallel structures in deep eutectic solvent. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[18]  Wei Wang,et al.  Label-free luminescence switch-on detection of T4 polynucleotide kinase activity using a G-quadruplex-selective probe. , 2014, Chemical communications.

[19]  Kemin Wang,et al.  Design of aptamer-based sensing platform using triple-helix molecular switch. , 2011, Analytical chemistry.

[20]  Yi Xiao,et al.  Label-free, dual-analyte electrochemical biosensors: a new class of molecular-electronic logic gates. , 2010, Journal of the American Chemical Society.

[21]  E. Wang,et al.  G-quadruplex DNAzyme based molecular catalytic beacon for label-free colorimetric logic gates. , 2011, Biomaterials.

[22]  Itamar Willner,et al.  Spotlighting of cocaine by an autonomous aptamer-based machine. , 2007, Journal of the American Chemical Society.

[23]  Chunhai Fan,et al.  Reconfigurable three-dimensional DNA nanostructures for the construction of intracellular logic sensors. , 2012, Angewandte Chemie.

[24]  D. Chan,et al.  A highly selective G-quadruplex-based luminescent switch-on probe for the detection of gene deletion. , 2012, Chemical communications.

[25]  Jing Yang,et al.  Circular DNA logic gates with strand displacement. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[26]  Gang Bao,et al.  Structure-function relationships of shared-stem and conventional molecular beacons. , 2002, Nucleic acids research.

[27]  J. Feigon,et al.  Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT). , 1998, Biochemistry.

[28]  Chengde Mao,et al.  An autonomous DNA nanomotor powered by a DNA enzyme. , 2004, Angewandte Chemie.

[29]  Cheulhee Jung,et al.  "Illusionary" polymerase activity triggered by metal ions: use for molecular logic-gate operations. , 2010, Angewandte Chemie.

[30]  P. Riccelli,et al.  Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. , 2001, Nucleic acids research.

[31]  Lingwen Zeng,et al.  Computational lateral flow biosensor for proteins and small molecules: a new class of strip logic gates. , 2012, Analytical chemistry.

[32]  Itamar Willner,et al.  Sensing of UO22+ and design of logic gates by the application of supramolecular constructs of ion-dependent DNAzymes. , 2009, Nano letters.

[33]  C. Dohno,et al.  Guanine of the third strand of C.G*G triplex serves as an effective hole trap. , 2002, Journal of the American Chemical Society.

[34]  M. Win,et al.  Higher-Order Cellular Information Processing with Synthetic RNA Devices , 2008, Science.

[35]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[36]  Ka-Ho Leung,et al.  Detection of base excision repair enzyme activity using a luminescent G-quadruplex selective switch-on probe. , 2013, Chemical communications.

[37]  Itamar Willner,et al.  Ion-induced DNAzyme switches. , 2010, Chemical communications.

[38]  P. A. Rachwal,et al.  Intramolecular DNA quadruplexes with different arrangements of short and long loops , 2007, Nucleic acids research.

[39]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[40]  Tao Li,et al.  Potassium-lead-switched G-quadruplexes: a new class of DNA logic gates. , 2009, Journal of the American Chemical Society.

[41]  L. Marky,et al.  DNA complexes containing joined triplex and duplex motifs: melting behavior of intramolecular and bimolecular complexes with similar sequences. , 2010, The journal of physical chemistry. B.

[42]  Thomas Carell,et al.  Molecular computing: DNA as a logic operator , 2011, Nature.

[43]  Itamar Willner,et al.  pH-programmable DNAzyme nanostructures. , 2011, Chemical communications.

[44]  N. Sugimoto,et al.  DNA logic gates based on structural polymorphism of telomere DNA molecules responding to chemical input signals. , 2006, Angewandte Chemie.

[45]  D. Chan,et al.  Oligonucleotide-based luminescent detection of metal ions. , 2011, Chemistry, an Asian journal.

[46]  Robert L. Letsinger,et al.  Control of folding and binding of oligonucleotides by use of a nonnucleotide linker , 1992 .

[47]  Chengde Mao,et al.  Molecular gears: a pair of DNA circles continuously rolls against each other. , 2004, Journal of the American Chemical Society.

[48]  Itamar Willner,et al.  Parallel Analysis of Two Analytes in Solutions or on Surfaces by Using a Bifunctional Aptamer: Applications for Biosensing and Logic Gate Operations , 2008, Chembiochem : a European journal of chemical biology.

[49]  I. Willner,et al.  Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold. , 2009, ACS nano.

[50]  Chengde Mao,et al.  A DNA nanomachine based on a duplex-triplex transition. , 2004, Angewandte Chemie.

[51]  Jianding Qiu,et al.  DNA electronic logic gates based on metal-ion-dependent induction of oligonucleotide structural motifs. , 2013, Chemistry.

[52]  Itamar Willner,et al.  Amplified detection of DNA through the enzyme-free autonomous assembly of hemin/G-quadruplex DNAzyme nanowires. , 2012, Analytical chemistry.