Synthesis of circular double-stranded DNA having single-stranded recognition sequence as molecular-physical probe for nucleic acid hybridization detection based on atomic force microscopy imaging.
A new class of DNA probes having a mechanically detectable tag is reported. The DNA probe, which consists of a single-stranded recognition sequence and a double-stranded circular DNA entity, was prepared by polymerase reaction. M13mp18 single strand and a 32mer oligodeoxynucleotide whose 5'-end is decorated with the recognition sequence were used in combination as template and primer, respectively. We have successfully demonstrated that the DNA probe is useful for bioanalytical purposes: by deliberately attaching target DNA molecules onto Au(111) substrates and by mechanically reading out the tag-entity using a high-resolution microscopy including atomic force microscopy, visualization/detection of the individual target/probe DNA conjugate was possible simply yet straightforwardly. The present DNA probe can be characterized as a 100%-nucleic acid product material. It is simply available by one-pod synthesis. A surface topology parameter, image roughness, has witnessed its importance as a quantitative analysis index with particular usability in the present visualization/detection method.
Nakano
Koji
K
Department of Applied Chemistry, Faculty of Engineering, Kyushu University, Nishi, Fukuoka, Japan. kojitcm@mbox.nc.kyushu-u.ac.jp
Matsunaga
Hideshi
H
Murata
Masaharu
M
Soh
Nobuaki
N
Imato
Toshihiko
T
D004247:DNA / Q000138:chemical synthesis / Q000737:chemistry*; D004277:DNA, Single-Stranded / Q000138:chemical synthesis / Q000737:chemistry*; D011905:Genes, ras / Q000502:physiology; D006801:Humans; D018625:Microscopy, Atomic Force / Q000379:methods; D009693:Nucleic Acid Hybridization; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry*
D004277:DNA, Single-Stranded; D009841:Oligonucleotides; D004247:DNA