Enhanced recognition of single-base mismatch using locked nucleic acid-integrated hairpin DNA probes revealed by atomic force microscopy nanolithography.
Probe design is a critical parameter in successful DNA and RNA target detection. In this proof-of-concept study, we evaluated the single-base mismatch recognition power of surface immobilized and self-assembled stem-loop hairpin DNA oligonucleotide probes modified to contain locked nucleic acid residues (LNA-HP). The stiffness change in conjunction with the stem opening of the interfacial molecules before and after hybridization led to clear variations of the overall film thickness or miniaturized nanospot height, which could be directly measured using an atomic force microscopy (AFM) nanolithography technique. Particularly, LNA-HP achieved highly differentiable readouts between perfectly complementary and singly mismatched targets (discrimination ratio as high as 2 to 3), outperforming the selectivity of its linear and hairpin counterparts with no LNA modification.
Han
Wen-Hsin
WH
Department of Chemistry, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung, Taiwan 80424.
Liao
Jun-Min
JM
Chen
Kuan-Liang
KL
Wu
Shin-Mou
SM
Chiang
Yi-Wen
YW
Lo
Shu-Ting
ST
Chen
Cheng-Lung
CL
Chiang
Chao-Ming
CM
D020137:Base Pair Mismatch; D001483:Base Sequence; D015342:DNA Probes / Q000737:chemistry*; D018625:Microscopy, Atomic Force / Q000379:methods*; D009693:Nucleic Acid Hybridization; D012680:Sensitivity and Specificity; D013499:Surface Properties
D015342:DNA Probes