The structure of intramolecular triplex DNA: Atomic force microscopy study

William J. Tiner; Vladimir N. Potaman; Richard R. Sinden; Yuri L. Lyubchenko

doi:10.1006/jmbi.2001.5174

The structure of intramolecular triplex DNA: Atomic force microscopy study

William J. Tiner, Vladimir N. Potaman, Richard R. Sinden, Yuri L. Lyubchenko

Research output: Contribution to journal › Article › peer-review

68 Scopus citations

Abstract

We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.

Original language	English (US)
Pages (from-to)	353-357
Number of pages	5
Journal	Journal of Molecular Biology
Volume	314
Issue number	3
DOIs	https://doi.org/10.1006/jmbi.2001.5174
State	Published - Nov 30 2001
Externally published	Yes

Keywords

Alternative DNA structures
Atomic force microscopy
DNA supercoiling
H-DNA
Intramolecular triplexes

ASJC Scopus subject areas

Molecular Biology
Biophysics
Structural Biology

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10.1006/jmbi.2001.5174

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title = "The structure of intramolecular triplex DNA: Atomic force microscopy study",

abstract = "We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.",

keywords = "Alternative DNA structures, Atomic force microscopy, DNA supercoiling, H-DNA, Intramolecular triplexes",

author = "Tiner, {William J.} and Potaman, {Vladimir N.} and Sinden, {Richard R.} and Lyubchenko, {Yuri L.}",

note = "Funding Information: The work was supported by the grants GM 62235 (NIH) and DBI-0070356 (NSF). We are grateful to L. Shlyakhtenko for very useful comments and criticism, and V. Zhurkin and V. Vologodskii for valuable comments. The authors also thank J. J. Bissler for kindly providing the plasmid and the Keck Bioimaging Laboratory at ASU for the use of its facilities.",

year = "2001",

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doi = "10.1006/jmbi.2001.5174",

language = "English (US)",

volume = "314",

pages = "353--357",

journal = "Journal of Molecular Biology",

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T1 - The structure of intramolecular triplex DNA

T2 - Atomic force microscopy study

AU - Tiner, William J.

AU - Potaman, Vladimir N.

AU - Sinden, Richard R.

AU - Lyubchenko, Yuri L.

N1 - Funding Information: The work was supported by the grants GM 62235 (NIH) and DBI-0070356 (NSF). We are grateful to L. Shlyakhtenko for very useful comments and criticism, and V. Zhurkin and V. Vologodskii for valuable comments. The authors also thank J. J. Bissler for kindly providing the plasmid and the Keck Bioimaging Laboratory at ASU for the use of its facilities.

PY - 2001/11/30

Y1 - 2001/11/30

N2 - We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.

AB - We applied atomic force microscopy (AFM) for direct imaging of intramolecular triplexes (H-DNA) formed by mirror-repeated purine-pyrimidine repeats and stabilized by negative DNA supercoiling. H-DNA appears in atomic force microscopy images as a clear protrusion with a different thickness than DNA duplex. Consistent with the existing models, H-DNA formation results in a kink in the double helix path. The kink forms an acute angle so that the flanking DNA regions are brought in close proximity. The mobility of flanking DNA arms is limited compared with that for cruciforms and three-way junctions. Structural properties of H-DNA may be important for promoter-enhancer interactions and other DNA transactions.

KW - Alternative DNA structures

KW - Atomic force microscopy

KW - DNA supercoiling

KW - H-DNA

KW - Intramolecular triplexes

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The structure of intramolecular triplex DNA: Atomic force microscopy study

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Keywords

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