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  Input-dependent induction of oligonucleotide structural motifs for performing molecular logic

Li, T., Ackermann, D., Hall, A. M., & Famulok, M. (2012). Input-dependent induction of oligonucleotide structural motifs for performing molecular logic. Journal of the American Chemical Society, 134(7), 3508-16. doi:10.1021/ja2108883.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-640E-3 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0028-640F-1
Genre: Journal Article

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Li, T., Author
Ackermann, D., Author
Hall, A. M., Author
Famulok, M.1, Author
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1External Organizations, ou_persistent22              

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Free keywords: Base Sequence Circular Dichroism *Computers, Molecular DNA/*chemistry G-Quadruplexes Hydrogen/chemistry Nucleic Acid Conformation Nucleic Acid Denaturation Oligonucleotides/*chemistry Potassium/chemistry RNA/*chemistry
 Abstract: The K(+)-H(+)-triggered structural conversion of multiple nucleic acid helices involving duplexes, triplexes, G-quadruplexes, and i-motifs is studied by gel electrophoresis, circular dichroism, and thermal denaturation. We employ the structural interconversions for perfoming molecular logic operations, as verified by fluorimetry and colorimetry. Short G-rich and C-rich cDNA and RNA single strands are hybridized to produce four A-form and B-form duplexes. Addition of K(+) triggers the unwinding of the duplexes by inducing the folding of G-rich strands into DNA- or RNA G-quadruplex mono- and multimers, respectively. We found a decrease in pH to have different consequences on the resulting structural output, depending on whether the C-rich strand is DNA or RNA: while the protonated C-rich DNA strand folds into at least two isomers of a stable i-motif structure, the protonated C-rich RNA strand binds a DNA/RNA hybrid duplex to form a Y.RY parallel triplex. When using K(+) and H(+) as external stimuli, or inputs, and the induced G-quadruplexes as reporters, these structural interconversions of nucleic acid helices can be employed for performing logic-gate operations. The signaling mode for detecting these conversions relies on complex formation between DNA or RNA G-quadruplexes (G4) and the cofactor hemin. The G4/hemin complexes catalyze the H(2)O(2)-mediated oxidation of peroxidase substrates, resulting in a fluorescence or color change. Depending on the nature of the respective peroxidase substrate, distinct output signals can be generated, allowing one to operate multiple logic gates such as NOR, INH, or AND.

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 Dates: 2012
 Publication Status: Published in print
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 Identifiers: Other: 22296341
DOI: 10.1021/ja2108883
ISSN: 1520-5126 (Electronic)
ISSN: 0002-7863 (Linking)
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Title: Journal of the American Chemical Society
  Alternative Title : J. Am. Chem. Soc.
Source Genre: Journal
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Pages: - Volume / Issue: 134 (7) Sequence Number: - Start / End Page: 3508 - 16 Identifier: -