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Updated: Feb 5, 2026

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

Molecular architecture of G-quadruplex structures generated on duplex Rif1-binding sequences.

Hisao Masai¹, Naoko Kakusho², Rino Fukatsu²

¹From the Department of Genome Medicine, Tokyo Metropolitan Institute of Medical Science, Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan, masai-hs@igakuken.or.jp.

The Journal of Biological Chemistry

|September 16, 2018

Summary

DNA G-quadruplexes (G4s) form complex structures on duplex DNA. This study reveals that both strands of Rif1-binding sequences adopt higher-order structures, with G4 formation on one strand influencing the other.

Keywords:

DNA replication DNase I G-quadruplex Rif1 S1 nuclease chromosomes non-B DNA nuclease footprinting nucleic acid nucleic acid structure

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Interfacial Molecular-level Structures of Polymers and Biomacromolecules Revealed via Sum Frequency Generation Vibrational Spectroscopy

Published on: August 13, 2019

Area of Science:

Genetics
Molecular Biology
Biochemistry

Background:

G-quadruplexes (G4s) are four-stranded DNA structures with significant biological roles.
Rap1-interacting factor 1 (Rif1) binds to Rif1-binding sequences (Rif1BS) and regulates DNA replication timing.
Rif1BS contains multiple G-tracts, suggesting potential for complex DNA structures.

Purpose of the Study:

To elucidate the precise molecular architecture of higher-order DNA structures formed at Rif1BS.
To investigate the structural behavior of both DNA strands within Rif1BS upon heat denaturation.

Main Methods:

Gel-shift DNA binding assays.
DNA footprinting using various nuclease probes.
Analysis of DNA structures under different conditions, including mutations and deazaguanine replacement.

Main Results:

Both G-strand and C-strand of Rif1BS adopt specific higher-order structures upon heat denaturation.
The G-strand forms a G4 structure with extended loops, while the C-strand forms a non-i-motif structure dependent on G4 formation.
Multiple G-tracts allow for alternative structures, demonstrating the robustness of these DNA higher-order structures.

Conclusions:

Higher-order DNA structures at Rif1BS involve both strands, with potential for G4 formation on both.
The formation of structures on the C-strand is contingent upon G4 formation on the G-strand.
These findings offer general insights into DNA structures formed at G4-forming sequences within duplex DNA.