Using azobenzene incorporated DNA aptamers to probe molecular binding interactions.
The rational design of DNA/RNA aptamers for use as molecular probes depends on a clear understanding of their structural elements in relation to target-aptamer binding interactions. We present a simple method to create aptamer probes that can occupy two different structural states. Then, based on the difference in binding affinity between these states, target-aptamer binding interactions can be elucidated. The basis of our two-state system comes from the incorporation of azobenzene within the DNA strand. Azobenzene can be used to photoregulate the melting of DNA-duplex structures. When incorporated into aptamers, the light-regulated conformational change of azobenzene can be used to analyze how aptamer secondary structure is involved in target binding. Azobenzene-modified aptamers showed no change in target selectivity, but showed differences in binding affinity as a function of the number, position, and conformation of azobenzene modifications. Aptamer probes that can change binding affinity on demand may have future uses in targeted drug delivery and photodynamic therapy.
Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States.
Joseph A
JA
Phillips
Haipeng
H
Liu
Meghan B
MB
O'Donoghue
Xiangling
X
Xiong
Ruowen
R
Wang
Mingxu
M
You
Kwame
K
Sefah
Weihong
W
Tan
D052157:Aptamers, Nucleotide / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*; D001391:Azo Compounds / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D005434:Flow Cytometry; D006801:Humans; D008027:Light; D015335:Molecular Probes / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*; D015394:Molecular Structure; D013237:Stereoisomerism; D014407:Tumor Cells, Cultured
D052157:Aptamers, Nucleotide; D001391:Azo Compounds; D015335:Molecular Probes; C009850:azobenzene
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