DNA Bending by Asymmetric Phosphate Neutralization

Strauss, Juliane K.; Maher, L. James

doi:10.1126/science.7997878

Cited by 278 publications

(311 citation statements)

References 48 publications

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“…These results define two phosphates as a minimal element required for DNA bending by asymmetric charge neutralization. Neutralization bends DNA toward the neutral surface, as predicted (Mirzabekov & Rich, 1979) and observed in a model GC-rich sequence (Strauss & Maher, 1994;Strauss et al, 1996a,b).…”

Section: Dna Bending Results From Neutralization Of Two Tpcmentioning

confidence: 79%

Electrostatic Mechanism for DNA Bending by bZIP Proteins

et al. 1997

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Biology is replete with examples of protein-induced DNA bending, yet the forces responsible for bending have been neither established nor quantified. Mirzabekov and Rich proposed in 1979 that asymmetric neutralization of the anionic phosphodiester backbone by basic histone proteins could provide a thermodynamic driving force for DNA bending in the nucleosome core particle [Mirzabekov, A. D., & Rich, A. (1979) A. 93, 9515-9520]. Here it is shown that bZIP proteins bend DNA via a mechanism involving direct contacts between one or two basic side chains and a symmetry-related pair of unique, nonbridging phosphate oxygens. The locations of these phosphates provide direct experimental support for a protein-induced bending mechanism based on asymmetric charge neutralization. This straightforward mechanism is compatible with many DNA-recognition motifs and may represent a general strategy for the assembly of protein-DNA complexes of defined stereochemistries.

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Section: Dna Bending Results From Neutralization Of Two Tpcmentioning

confidence: 79%

Electrostatic Mechanism for DNA Bending by bZIP Proteins

et al. 1997

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“…Attempts to characterize and separate the effects of static curvatures from those of the flexibility thus far were made only on peculiar DNA constructs with anomalous flexibility such as single-stranded segments (10), mismatches (20,21), asymmetric charge neutralizations (22), a single nick (23), a double-stranded (ds) linker connecting two triple-helix tracts (24), or with controlled curvature obtained by phased (10) or unphased A-tracts (8). The problem is open still for a ''natural'' dsDNA of any arbitrary sequence, as very recently pointed out also by Crothers and coworkers (25).…”

Section: Biochemistry For the Article ''Functional Transitions In Mymentioning

confidence: 99%

Mapping the intrinsic curvature and flexibility along the DNA chain

Zuccheri

Scipioni

Cavaliere

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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The energy of DNA deformation plays a crucial and active role in its packaging and its function in the cell. Considerable effort has gone into developing methodologies capable of evaluating the local sequence-directed curvature and flexibility of a DNA chain. These studies thus far have focused on DNA constructs expressly tailored either with anomalous flexibility or curvature tracts. Here we demonstrate that these two structural properties can be mapped also along the chain of a “natural” DNA with any sequence on the basis of its scanning force microscope (SFM) images. To know the orientation of the sequence of the investigated DNA molecules in their SFM images, we prepared a palindromic dimer of the long DNA molecule under study. The palindromic symmetry also acted as an internal gauge of the statistical significance of the analysis carried out on the SFM images of the dimer molecules. It was found that although the curvature modulus is not efficient in separating static and dynamic contributions to the curvature of the population of molecules, the curvature taken with its direction (its sign in two dimensions) permits the direct separation of the intrinsic curvature from the flexibility contributions. The sequence-dependent flexibility seems to vary monotonically with the chain's intrinsic curvature; the chain rigidity was found to modulate as its local thermodynamic stability and does not correlate with the dinucleotide chain rigidities evaluation made from x-ray data by other authors.

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“…This process is quite important for storing long DNA molecules in the nucleus. Spontaneous bending of the DNA molecule by neutralization of the ionic repulsion at one helical face was demonstrated by incorporation of a neutral analog of the phosphate group into DNA [8].…”

Section: Introductionmentioning

confidence: 99%

Conformational change in DNA induced by cationic bilayer membranes

et al. 1996

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The effect of synthetic cationic lipids on the structure of DNA was studied. The fluorescence enhancement of ethidium bromide on intercalation into DNA was suppressed by the addition of bilayer-forming lipids, but not by micellar ones. Results on the fluorescence depolarization index suggest that ethidinm bromide is not released from DNA by lipids intercalated into DNA. CD spectra of the DNA-lipid complexes revealed that the structure of DNA was changed only by bilayer-forming lipids at temperatures lower than their Tc values. Thus, the conformation of DNA is forced to change by cationic lipids forming the rigid bilayer membrane so that ethidium bromide fluorescence might be reduced, and the conformation can be controlled by selection of the appropriate lipid and temperature.Key words: Bilayer membrane; Cationic lipid; DNA conformation; Ethidium bromide Bilayer membranes formed with cationic lipids have been successfully used as DNA carriers into cultured eukaryotic cells [9][10][11][12][13]. Since these membranes have fluid two-dimensional surface cationic groups neutralizing the anionic phosphate groups of the DNA, DNA interacting with the membranes would exhibit a different conformational change from that interacting with metal ions and proteins. In this communication, we studied the effects on the conformation of DNA of synthetic cationic lipids with various properties of membrane fluidity and aggregate morphology, and show that cationic lipids forming the rigid bilayer membrane can induce a structural change in DNA and that the structure of DNA can be controlled by selection of the lipids and temperature. Materials and methods

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DNA Bending by Asymmetric Phosphate Neutralization

Cited by 278 publications

References 48 publications

Electrostatic Mechanism for DNA Bending by bZIP Proteins

Electrostatic Mechanism for DNA Bending by bZIP Proteins

Mapping the intrinsic curvature and flexibility along the DNA chain

Conformational change in DNA induced by cationic bilayer membranes

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