Limits...
End-to-end attraction of duplex DNA.

Maffeo C, Luan B, Aksimentiev A - Nucleic Acids Res. (2012)

Bottom Line: We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte.We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration.The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA.

ABSTRACT
Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

Show MeSH

Related in: MedlinePlus

The effect of end-to-end attraction in different DNA systems. The binding free energy (black) and the fraction of bound DNA ends (red) are plotted against the reference concentration of DNA ends. Background images schematically illustrate four DNA systems in which the end-to-end attraction may or may not play a role. From top left to bottom right: the maximum local concentration of DNA ends [i.e. the J-factor (51)] is about two orders of magnitude too low to induce an observable fraction of blunt-ended DNA circles of any length (orange); translation and rotational confinement of DNA ends at dsDNA breakage [e.g. by the protein Ku (PDB:1JEY)] will promote binding of the DNA ends, which likely aids repair of DNA during non-homologous end joining (49) (purple); the structure factor obtained from small-angle X-ray scattering experiments of short DNA duplexes in a divalent electrolyte reveals end-to-end attraction (12) (blue); at very high DNA concentrations, long DNA aggregates form and align in liquid crystal phases (11) (green).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3351176&req=5

gkr1220-F5: The effect of end-to-end attraction in different DNA systems. The binding free energy (black) and the fraction of bound DNA ends (red) are plotted against the reference concentration of DNA ends. Background images schematically illustrate four DNA systems in which the end-to-end attraction may or may not play a role. From top left to bottom right: the maximum local concentration of DNA ends [i.e. the J-factor (51)] is about two orders of magnitude too low to induce an observable fraction of blunt-ended DNA circles of any length (orange); translation and rotational confinement of DNA ends at dsDNA breakage [e.g. by the protein Ku (PDB:1JEY)] will promote binding of the DNA ends, which likely aids repair of DNA during non-homologous end joining (49) (purple); the structure factor obtained from small-angle X-ray scattering experiments of short DNA duplexes in a divalent electrolyte reveals end-to-end attraction (12) (blue); at very high DNA concentrations, long DNA aggregates form and align in liquid crystal phases (11) (green).

Mentions: Given the relatively large free energy of the end-to-end interaction, we pose the following question: why has end-to-end association only recently been observed? In most biological and nanotechnological settings, the concentration of DNA ends is too low for end-to-end association to be statistically significant, and the lifetime of end-to-end interactions (∼70 μs) is somewhat shorter than the temporal resolution of many experimental techniques. To illustrate this point, we plot in Figure 5 the fraction of bound DNA ends versus the concentration of free DNA ends in chemical equilibrium. The concentration of DNA ends is relatively high in DNA cyclization assays that measure the fraction of DNA molecules bent into a circle. The J-factor, which represents the concentration of one end in the proximity of the other, has a maximum value of ∼10−4 mM (48), which is two orders of magnitude too small to promote cyclization of a significant fraction of blunt-ended DNA. The introduction of sticky ends increases the interaction energy by a few kcal/mol so that the DNA cyclization can be observed.Figure 5.


End-to-end attraction of duplex DNA.

Maffeo C, Luan B, Aksimentiev A - Nucleic Acids Res. (2012)

The effect of end-to-end attraction in different DNA systems. The binding free energy (black) and the fraction of bound DNA ends (red) are plotted against the reference concentration of DNA ends. Background images schematically illustrate four DNA systems in which the end-to-end attraction may or may not play a role. From top left to bottom right: the maximum local concentration of DNA ends [i.e. the J-factor (51)] is about two orders of magnitude too low to induce an observable fraction of blunt-ended DNA circles of any length (orange); translation and rotational confinement of DNA ends at dsDNA breakage [e.g. by the protein Ku (PDB:1JEY)] will promote binding of the DNA ends, which likely aids repair of DNA during non-homologous end joining (49) (purple); the structure factor obtained from small-angle X-ray scattering experiments of short DNA duplexes in a divalent electrolyte reveals end-to-end attraction (12) (blue); at very high DNA concentrations, long DNA aggregates form and align in liquid crystal phases (11) (green).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351176&req=5

gkr1220-F5: The effect of end-to-end attraction in different DNA systems. The binding free energy (black) and the fraction of bound DNA ends (red) are plotted against the reference concentration of DNA ends. Background images schematically illustrate four DNA systems in which the end-to-end attraction may or may not play a role. From top left to bottom right: the maximum local concentration of DNA ends [i.e. the J-factor (51)] is about two orders of magnitude too low to induce an observable fraction of blunt-ended DNA circles of any length (orange); translation and rotational confinement of DNA ends at dsDNA breakage [e.g. by the protein Ku (PDB:1JEY)] will promote binding of the DNA ends, which likely aids repair of DNA during non-homologous end joining (49) (purple); the structure factor obtained from small-angle X-ray scattering experiments of short DNA duplexes in a divalent electrolyte reveals end-to-end attraction (12) (blue); at very high DNA concentrations, long DNA aggregates form and align in liquid crystal phases (11) (green).
Mentions: Given the relatively large free energy of the end-to-end interaction, we pose the following question: why has end-to-end association only recently been observed? In most biological and nanotechnological settings, the concentration of DNA ends is too low for end-to-end association to be statistically significant, and the lifetime of end-to-end interactions (∼70 μs) is somewhat shorter than the temporal resolution of many experimental techniques. To illustrate this point, we plot in Figure 5 the fraction of bound DNA ends versus the concentration of free DNA ends in chemical equilibrium. The concentration of DNA ends is relatively high in DNA cyclization assays that measure the fraction of DNA molecules bent into a circle. The J-factor, which represents the concentration of one end in the proximity of the other, has a maximum value of ∼10−4 mM (48), which is two orders of magnitude too small to promote cyclization of a significant fraction of blunt-ended DNA. The introduction of sticky ends increases the interaction energy by a few kcal/mol so that the DNA cyclization can be observed.Figure 5.

Bottom Line: We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte.We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration.The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

View Article: PubMed Central - PubMed

Affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801, USA.

ABSTRACT
Recent experiments [Nakata, M. et al., End-to-end stacking and liquid crystal condensation of 6 to 20 basepair DNA duplexes. Science 2007; 318:1276-1279] have demonstrated spontaneous end-to-end association of short duplex DNA fragments into long rod-like structures. By means of extensive all-atom molecular dynamic simulations, we characterized end-to-end interactions of duplex DNA, quantitatively describing the forces, free energy and kinetics of the end-to-end association process. We found short DNA duplexes to spontaneously aggregate end-to-end when axially aligned in a small volume of monovalent electrolyte. It was observed that electrostatic repulsion of 5'-phosphoryl groups promoted the formation of aggregates in a conformation similar to the B-form DNA double helix. Application of an external force revealed that rupture of the end-to-end assembly occurs by the shearing of the terminal base pairs. The standard binding free energy and the kinetic rates of end-to-end association and dissociation processes were estimated using two complementary methods: umbrella sampling simulations of two DNA fragments and direct observation of the aggregation process in a system containing 458 DNA fragments. We found the end-to-end force to be short range, attractive, hydrophobic and only weakly dependent on the ion concentration. The relation between the stacking free energy and end-to-end attraction is discussed as well as possible roles of the end-to-end interaction in biological and nanotechnological systems.

Show MeSH
Related in: MedlinePlus