Direct measurement of DNA molecular length in solution using optical tweezers: Detection of looping due to binding protein interactions

Kumiko Sakata-Sogawa, Masashi Kurachi, Kazuhiro Sogawa, Yoshiaki Fujii-Kuriyama, Hideo Tashiro

    Research output: Contribution to journalArticle

    20 Citations (Scopus)

    Abstract

    DNA looping is caused by the interaction between DNA binding proteins located at separate positions on a DNA molecule and may play an important role in transcription regulation. We have developed a system to stretch single DNA molecules and to measure changes in molecular length. DNA molecules were prepared and 5' end-labeled by PCR amplification. Two beads and the intervening DNA molecule were trapped and manipulated independently with dual trap optical tweezers. The trapped DNA molecule was then stretched and the extension (the distance between the two beads) was measured. The extension at the specific tension force of 30 pN was calculated and used as a molecular length. The molecular length was found to be proportional to the base pair number. The rise per residue was calculated to be 3.31±0.05 Å. The length measurement was applied to DNA fragments containing GC box sequences at two different locations separated by a distance of 2.428 kbp. The addition of GC box binding transcription factor Sp1 shortened the molecular length, suggesting DNA looping forms as a result of interaction between transcription factors.

    Original languageEnglish
    Pages (from-to)55-61
    Number of pages7
    JournalEuropean Biophysics Journal
    Volume27
    Issue number1
    DOIs
    Publication statusPublished - 1998 Mar 21

    Keywords

    • DNA binding protein
    • DNA looping
    • Optical tweezers
    • Rise per residue
    • Transcription factor Sp1

    ASJC Scopus subject areas

    • Biophysics

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