Discrimination of DNA mismatches by direct force measurement for identification of tuna species

Tsuyoshi Tanaka, Tomohito Sasaki, Yosuke Amemiya, Haruko Takeyama, Seinen Chow, Tadashi Matsunaga

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

The interaction between oligonucleotides and long DNA fragments was analyzed by force curve measurements using atomic force microscopy (AFM). DNA fragments (150-base or 406-base) from the mitochondrial ATPase and cytochrome oxidase subunit III genes that contained a mismatch of one to three bases among Tunnus species were immobilized on glass slides. The statistical distribution of disruption forces between oligonucleotide probes (21-mer or 29-mer) and single stranded DNA fragments (150-base or 406-base) were analyzed by 40 or 180 force curve measurements. Histograms plotting the frequencies of disruption forces showed a wide distribution with a highest peak. The highest mean values in disruption force were obtained when DNA fragments with perfectly match sequences were employed. These results demonstrated that the specific sequence differences between long DNA fragments can be measured using force-based detection. A single base mismatch yielded a statistically significant 10% decrease in disruption force, furthermore, 2-base and 3-base mismatches provided approximately 20 and 25-30% decreases, respectively. Our results indicated that force-based detection potentially can be applied toward many other mismatched DNA detection techniques besides species-specific identification of tuna.

Original languageEnglish
Pages (from-to)150-155
Number of pages6
JournalAnalytica Chimica Acta
Volume561
Issue number1-2
DOIs
Publication statusPublished - 2006 Mar 2
Externally publishedYes

Fingerprint

Tuna
Force measurement
DNA
Statistical Distributions
Oligonucleotide Probes
Atomic Force Microscopy
Single-Stranded DNA
Electron Transport Complex IV
atomic force microscopy
Oligonucleotides
statistical distribution
Glass
Adenosine Triphosphatases
histogram
Atomic force microscopy
Genes
cytochrome
glass
probe
gene

Keywords

  • Atomic force microscopy
  • Disruption force
  • Force curve measurement
  • Long DNA fragment
  • Tuna species identification

ASJC Scopus subject areas

  • Biochemistry
  • Analytical Chemistry
  • Spectroscopy
  • Environmental Chemistry

Cite this

Discrimination of DNA mismatches by direct force measurement for identification of tuna species. / Tanaka, Tsuyoshi; Sasaki, Tomohito; Amemiya, Yosuke; Takeyama, Haruko; Chow, Seinen; Matsunaga, Tadashi.

In: Analytica Chimica Acta, Vol. 561, No. 1-2, 02.03.2006, p. 150-155.

Research output: Contribution to journalArticle

Tanaka, Tsuyoshi ; Sasaki, Tomohito ; Amemiya, Yosuke ; Takeyama, Haruko ; Chow, Seinen ; Matsunaga, Tadashi. / Discrimination of DNA mismatches by direct force measurement for identification of tuna species. In: Analytica Chimica Acta. 2006 ; Vol. 561, No. 1-2. pp. 150-155.
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