Electric potential induced dissociation of hybridized DNA with hairpin motif immobilized on silicon surface.
DNA probes were immobilized on silicon surfaces through ester condensation between the -COOH group on the surface and the terminal -OH group in the oligonucleotide, and the surface density of DNA probes against the concentration of immobilization solution was measured by radioactive labeling. The dissociation of DNA duplex on the surface by an electric potential was studied with the scanning potential hairpin denaturation/dissociation (SPHD). The influence of the stem length in the hairpin probe on the SPHD curve was systematically investigated. It was found that the capability of discrimination on single nucleotide polymorphism (SNP) by a hairpin probe was related to the free energy of formation of the secondary structure in the probe (DeltaG(ss)). In our system, when DeltaG(ss) was around -3 kcal/mol, an optimal recognition of SNP was reached and the SPHD curve was sigmoid. In contrast, the equivalent SPHD curve from a linear probe was exponential-decay alike with a poor discrimination of SNP. The concentration dependent experiments showed good linearity between the melting potential and logarithm of target concentration in the range of 1 x 10(-9) to 5 x 10(-7) M.
Wei
Fang
F
Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
Qu
Peng
P
Zhai
Lin
L
Chen
Chunlai
C
Wang
Haifang
H
Zhao
Xin Sheng
XS
D015342:DNA Probes / Q000737:chemistry*; D004563:Electrochemistry; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide; D012825:Silicon; D013499:Surface Properties; D013816:Thermodynamics
D015342:DNA Probes; D012825:Silicon