Easy design of logic gates based on aptazymes and noncrosslinking gold nanoparticle aggregation

Chemical Communications

Volumn , Issue 31, 2009, Pages 4666-4668

  Ogawa, Atsushi ^a,b   Maeda, Mizuo ^b  

^a EHIME UNIVERSITY   (Japan)

^b RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

APTAZYME; GOLD NANOPARTICLE; MESSENGER RNA; NUCLEIC ACID; RIBOZYME; TRANSFER RNA; UNCLASSIFIED DRUG;

ARTICLE; COMBINATORIAL CHEMISTRY; CROSS LINKING; DNA PROBE; HYBRIDIZATION; NANOTECHNOLOGY; PARTICLE SIZE; PRECIPITATION; PROTEIN AGGREGATION; RNA CLEAVAGE;

EID: 68149120494     PISSN: 13597345     EISSN: None     Source Type: Journal    
DOI: 10.1039/b910288d     Document Type: Article

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26. K. Sato M. Onoguchi Y. Sato K. Hosokawa M. Maeda Anal. Biochem. 2006 350 162. In the case that oligonucleotides hybridized to the probe-DNA are not DNA but RNA, the color of the AuNP solution after aggregation is more colorless than purple. 11 See the Supplementary Information for absorbance spectra Aggregation can be induced by a small amount of the cleaved RNA that is equivalent to only 7.5% amounts of the probe-DNA on AuNPs 11 Aggregation effects in each pair (the theophylline-dependent aptazyme and the AuNP pair or the cGMP-dependent aptazyme and the AuNP pair) have previously been verified. 11 We also verified that these two pairs are orthogonal (theophylline didn't cleave the cGMP-aptazyme and cGMP didn't cleave the theophylline-aptazyme) The sequences of the stem I in these two aptazymes were altered from the in vitro-selected sequences. However, it should be noted that the sequence of this stem I is less important for the switching efficiency of the aptazyme if it only forms a duplex. Although interactions between stem I and stem II in the hammer-head ribozyme are important to the ribozyme activity (i.e. reaction rate), the increase (decrease) in the ribozyme activity induced by their alteration leads to an increase (decrease) in the activities of the aptazymes both in the ON and OFF state. 21 Therefore, although activities of the aptazyme in the ON state for the AND gate decreased somewhat, we compensated for this decrease by slightly extending the reaction time (see the Supplementary Information) The 3′-terminal end of the theophylline-dependent aptazyme was designed to partially hybridize to its 5′-terminal so as to prevent hybridization to the probe-DNA on AuNPs before the self-cleavage In fact, a FMN-dependent aptazyme having the same cleaved RNA sequence has high activity 11 Of course, the corresponding aptazymes must be obtained through in vitro selection 7,8 A NOT gate, another logic element, can also be constructed using the same probe-DNA-tethered AuNPs (see the Supplementary Information)
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