Deoxyribozyme-Based Molecular Computation - DNA Nanotechnology: From Structure to Function - page 350

34. Wang ZG, Elbaz J, Remacle F, Levine RD, Willner I (2010) All-DNA finite-state automata
with finite memory. Proc Natl Acad Sci U S A 107:21996-22001
35. Stojanovic MN, de Prada P, Landry DW (2001) Catalytic molecular beacons. Chembiochem
2:411-415
36. Stojanovic MN, Mitchell TE, Stefanovic D (2002) Deoxyribozyme-based logic gates. J Am
Chem Soc 124:3555-3561
37. Stojanovic MN, de Prada P, Landry DW (2000) Homogeneous assays based on deoxyribozyme
catalysis. Nucleic Acids Res 28:2915-2918
38. Stojanovic MN, Semova S, Kolpashchikov DM, Macdonald J, Morgan C, Stefanovic D
(2005) Deoxyribozyme-based ligase logic gates and their initial circuits. J Am Chem Soc
127:6914-6915
39. Kolpashchikov DM, Stojanovic MN (2005) Boolean control of aptamer binding states. J Am
Chem Soc 127:11348-11351
40. Ruslan Y, Sergei R, Stojanovic MN (2007) Networking particles over distance using

oligonucleotide-based devices. J Am Chem Soc 129:15581-15584
41. Stojanovic MN, Stefanovic D (2003) Deoxyribozyme-based half-adder. J Am Chem Soc
125:6673-6676
42. Lederman H, Macdonald J, Stefanovic D, Stojanovic MN (2006) Deoxyribozyme-based three-
input logic gates and construction of a molecular full adder. Biochemistry 45:1194-1199
43. Stojanovic MN, Stefanovic D (2003) Deoxyribozyme-based automaton. Nat Biotechnol

21:1069-1074
44. Macdonald J et al (2006) Medium scale integration of molecular logic gates in an automaton.
Nano Lett 6:2598-2603
45. Pei R, Matamoros E, Liu M, Stefanovic D, Stojanovic MN (2010) Training a molecular
automaton to play a game. Nat Nanotechnol 5:773-777
46. Alves S, Pina F, Albelda MT, Garcia-Espana E, Soriano C, Luis SV (2001) Open-chain
polyamine ligands bearing an anthracene unit-chemosensors for logic operations at the

molecular level. Eur J Inorg Chem 2001:405-412
47. Saghatelian A, Volcker NH, Guchian KM, Lin VSY, Ghadiri MR (2003) DNA-based photonic
logic gates: AND, NAND and INHIBIT. J Am Chem Soc 125:346-347
48. de Silva AP, Dobbin CM, Vance TP, Wannalerse B (2009) Multiply reconfigurable 'plug and
play' molecular logic via self-assembly. Chem Commun :1386-1388
49. Breaker RR, Joyce GF (1995) A DNA enzyme with MG 2C -dependent RNA phosphodiesterase
activity. Chem Biol 2:655-660
50. Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad
Sci U S A 94:4262-4266
51. Tyagi S, Krammer FR (1996) Molecular beacons: probes that fluoresce upon hybridization.
Nat Biotechnol 14:303-309
52. Macdonald J, Stefanovic D, Stojanovic MN (2006) Solution-phase molecular-scale compu-
tation with deoxyribozyme-based logic gates and fluorescent readouts. In: Didenko VV (ed)
Fluorescent energy transfer nucleic acid probes: design and protocols, methods in molecular
biology. Humana, Totowa, pp 343-363
53. Stojanovic MN (2008) Molecular computing with deoxyribozymes. Prog Nucleic Acid Res
Mol Biol 82:199-217
54. Macdonald J, Stojanovic MN (2009) Nucleic acids for computation. In: Li Y, Lu Y (eds)
Functional nucleic acids for analytical applications. Springer, New York, pp 355-375
55. Pei R, Macdonald J, Stojanovic MN (2012) Development of trainable deoxyribozyme-based
game playing automaton. In: Hartig JS (ed) Ribozymes: methods and protocols, methods in
molecular biology. Springer, New York, pp 419-437
56. Breaker RR (2002) Engineered allosteric ribozymes as biosensor components. Curr Opin
Biotechnol 13:31-39
57. Gu H, Furukawa K, Breaker RR (2012) Engineered allosteric ribozymes that sense the bacterial
second messenger cyclic diguanosyl 5 0 -monophosphate. Anal Chem 84:4935-4941