TY - JOUR
T1 - Structure and dynamics of supercoil-stabilized DNA cruciforms
AU - Shlyakhtenko, Luda S.
AU - Potaman, Vladimir N.
AU - Sinden, Richard R.
AU - Lyubchenko, Yuri L.
N1 - Funding Information:
This work was supported in part by grants GM 54991 from NIH and Digital Instruments, Inc. We are grateful to G. Manning, W. Olson, N Seeman and V. Zhurkin for reading the manuscript and valuable comments.
PY - 1998/7/3
Y1 - 1998/7/3
N2 - Understanding DNA function requires knowledge of the structure of local, sequence-dependent conformations that can be dramatically different from the B-form helix. One alternative DNA conformation is the cruciform, which has been shown to have a critical role in the initiation of DNA replication and the regulation of transcription in certain systems. In addition, cruciforms provide a model system for structural studies of Holliday junctions, intermediates in homologous DNA recombination. Cruciforms are not thermodynamically stable in linear DNA due to branch point migration, which makes their study using many biophysical techniques problematic. Atomic Force Microscopy (AFM) was applied to visualize cruciforms in negatively supercoiled plasmid DNA. Cruciforms are seen as clear-cut extrusions on the DNA filament with the lengths of the arms consistent with the size of the hairpins expected from a 106 bp inverted repeat. The cruciform exists in two different conformations, an extended one with the angle of ca. 180°between the hairpin arms and a compact, X-type conformation, with acute angles between the hairpin arms and the main DNA strands. The ratio of molecules with the different conformations of cruciforms depends on ionic conditions. In the presence of high salt or Mg cations, a compact, X-type conformation is highly preferable. Remarkably, the X-conformation was highly mobile allowing the cruciform arms to adopt a parallel orientation. The structure observed is consistent with a model of the Holliday junction with a parallel orientation of the exchanging strands.
AB - Understanding DNA function requires knowledge of the structure of local, sequence-dependent conformations that can be dramatically different from the B-form helix. One alternative DNA conformation is the cruciform, which has been shown to have a critical role in the initiation of DNA replication and the regulation of transcription in certain systems. In addition, cruciforms provide a model system for structural studies of Holliday junctions, intermediates in homologous DNA recombination. Cruciforms are not thermodynamically stable in linear DNA due to branch point migration, which makes their study using many biophysical techniques problematic. Atomic Force Microscopy (AFM) was applied to visualize cruciforms in negatively supercoiled plasmid DNA. Cruciforms are seen as clear-cut extrusions on the DNA filament with the lengths of the arms consistent with the size of the hairpins expected from a 106 bp inverted repeat. The cruciform exists in two different conformations, an extended one with the angle of ca. 180°between the hairpin arms and a compact, X-type conformation, with acute angles between the hairpin arms and the main DNA strands. The ratio of molecules with the different conformations of cruciforms depends on ionic conditions. In the presence of high salt or Mg cations, a compact, X-type conformation is highly preferable. Remarkably, the X-conformation was highly mobile allowing the cruciform arms to adopt a parallel orientation. The structure observed is consistent with a model of the Holliday junction with a parallel orientation of the exchanging strands.
KW - Atomic Force Microscopy
KW - Cruciform conformation
KW - DNA supercoiling
KW - Holliday junction
KW - Inverted repeats in DNA
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U2 - 10.1006/jmbi.1998.1855
DO - 10.1006/jmbi.1998.1855
M3 - Article
C2 - 9653031
AN - SCOPUS:0032479310
SN - 0022-2836
VL - 280
SP - 61
EP - 72
JO - Journal of Molecular Biology
JF - Journal of Molecular Biology
IS - 1
ER -