Strained DNA is Kinked by Low Concentrations of Zn2+

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1997 Oct 6

PMID 9380675

Citations 18

Authors

W Han

M Dlakic

Y J Zhu

S M Lindsay

R E Harrington

Affiliations

Soon will be listed here.

Abstract

A novel atomic force microscope with a magnetically oscillated tip has provided unprecedented resolution of small DNA fragments spontaneously adsorbed to mica and imaged in situ in the presence of divalent ions. Kinks (localized bends of average angle 78 degrees) were observed in axially strained minicircles consisting of tandemly repeated d(A)5 and d(GGGCC[C]) sequences. The frequency of kinks in identical minicircles increased 4-fold in the presence of 1 mM Zn2+ compared with 1 mM Mg2+. Kinking persisted in mixed Mg2+/Zn2+ electrolytes until the Zn2+ concentration dropped below 100 microM, indicating that this type of kinking may occur under physiological conditions. Kinking appears to replace intrinsic bending, and statistical analysis shows that kinks are not localized within any single sequence element. A surprisingly small free energy is associated with kink formation.

Citing Articles

Natural tristability of a confined helical filament with anisotropic bending rigidities.

Zhou Z Sci Rep. 2024; 14(1):13927.

PMID: 38886502 PMC: 11637093. DOI: 10.1038/s41598-024-64903-x.

AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet-Dry Cycling: Implications for the Origin of Life.

Hassenkam T, Damer B, Mednick G, Deamer D Life (Basel). 2020; 10(12).

PMID: 33266191 PMC: 7760185. DOI: 10.3390/life10120321.

Multivalent ions and biomolecules: Attempting a comprehensive perspective.

Matsarskaia O, Roosen-Runge F, Schreiber F Chemphyschem. 2020; 21(16):1742-1767.

PMID: 32406605 PMC: 7496725. DOI: 10.1002/cphc.202000162.

Strong deformations of DNA: Effect on the persistence length.

Simonov K Eur Phys J E Soft Matter. 2018; 41(9):114.

PMID: 30259229 DOI: 10.1140/epje/i2018-11722-8.

DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels.

Henning-Knechtel A, Knechtel J, Magzoub M Nucleic Acids Res. 2017; 45(21):12057-12068.

PMID: 29088457 PMC: 5716084. DOI: 10.1093/nar/gkx990.

References

Crothers D, DRAK J, Kahn J, Levene S . DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol. 1992; 212:3-29. DOI: 10.1016/0076-6879(92)12003-9. View

Price M, Tullius T . Using hydroxyl radical to probe DNA structure. Methods Enzymol. 1992; 212:194-219. DOI: 10.1016/0076-6879(92)12013-g. View

Yang J, Shao Z . Effect of probe force on the resolution of atomic force microscopy of DNA. Ultramicroscopy. 1993; 50(2):157-70. DOI: 10.1016/0304-3991(93)90006-j. View

Lee J, Latimer L, Reid R . A cooperative conformational change in duplex DNA induced by Zn2+ and other divalent metal ions. Biochem Cell Biol. 1993; 71(3-4):162-8. DOI: 10.1139/o93-026. View

Harrington R . Studies of DNA bending and flexibility using gel electrophoresis. Electrophoresis. 1993; 14(8):732-46. DOI: 10.1002/elps.11501401116. View

Kim Y, Geiger J, Hahn S, SIGLER P . Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993; 365(6446):512-20. DOI: 10.1038/365512a0. View

Kim J, Nikolov D, Burley S . Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993; 365(6446):520-7. DOI: 10.1038/365520a0. View

Brukner I, Susic S, Dlakic M, Savic A, Pongor S . Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J Mol Biol. 1994; 236(1):26-32. DOI: 10.1006/jmbi.1994.1115. View

Harrington R, Winicov I . New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. Prog Nucleic Acid Res Mol Biol. 1994; 47:195-270. DOI: 10.1016/s0079-6603(08)60253-6. View

10.

Hansma H, Hoh J . Biomolecular imaging with the atomic force microscope. Annu Rev Biophys Biomol Struct. 1994; 23:115-39. DOI: 10.1146/annurev.bb.23.060194.000555. View

11.

Erie D, Yang G, Schultz H, Bustamante C . DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. Science. 1994; 266(5190):1562-6. DOI: 10.1126/science.7985026. View

12.

Hansma H, Laney D, Bezanilla M, SINSHEIMER R, Hansma P . Applications for atomic force microscopy of DNA. Biophys J. 1995; 68(5):1672-7. PMC: 1282069. DOI: 10.1016/S0006-3495(95)80343-7. View

13.

Mou J, Czajkowsky D, Zhang Y, Shao Z . High-resolution atomic-force microscopy of DNA: the pitch of the double helix. FEBS Lett. 1995; 371(3):279-82. DOI: 10.1016/0014-5793(95)00906-p. View

14.

Dlakic M, Harrington R . Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays. J Biol Chem. 1995; 270(50):29945-52. DOI: 10.1074/jbc.270.50.29945. View

15.

Dlakic M, Harrington R . The effects of sequence context on DNA curvature. Proc Natl Acad Sci U S A. 1996; 93(9):3847-52. PMC: 39447. DOI: 10.1073/pnas.93.9.3847. View

16.

Werner M, Gronenborn A, Clore G . Intercalation, DNA kinking, and the control of transcription. Science. 1996; 271(5250):778-84. DOI: 10.1126/science.271.5250.778. View

17.

Smith S, Cui Y, Bustamante C . Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 1996; 271(5250):795-9. DOI: 10.1126/science.271.5250.795. View

18.

Hansma H, Laney D . DNA binding to mica correlates with cationic radius: assay by atomic force microscopy. Biophys J. 1996; 70(4):1933-9. PMC: 1225162. DOI: 10.1016/S0006-3495(96)79757-6. View

19.

Dlakic M, Park K, Griffith J, Harvey S, Harrington R . The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts. J Biol Chem. 1996; 271(30):17911-9. DOI: 10.1074/jbc.271.30.17911. View

20.

Bustamante C, Rivetti C . Visualizing protein-nucleic acid interactions on a large scale with the scanning force microscope. Annu Rev Biophys Biomol Struct. 1996; 25:395-429. DOI: 10.1146/annurev.bb.25.060196.002143. View