DNA persistence length revisited

Lu, Yongjun; Weers, Brock; Stellwagen, Nancy C.

doi:10.1002/bip.10151

Cited by 165 publications

(241 citation statements)

References 59 publications

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“…Above Ϸ1 mM monovalent cation concentration the persistence length of DNA does not vary for higher salt concentrations (35)(36)(37). Thus, the average size of the loops that spontaneously form along a 3kbDNA should be approximately the same for all solution conditions of this study, given that the 0.5ϫ TE buffer alone is Ͼ2 mM in monovalent cations.…”

Section: Resultsmentioning

confidence: 82%

“…Several theories have been put forth as attempts to explain why toroids and other DNA condensate morphologies grow to a particular size (19,21,22,24,37). A common target of these theories has been to determine the origin of a limitation on DNA bundle size, or thickness͞number of windings in the case of toroids.…”

Section: Mgcl2 Causes a Greater Increase In Toroid Diameter Thanmentioning

confidence: 99%

See 1 more Smart Citation

Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength

Conwell

Vilfan

Hud

2003

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

203

190

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The process of DNA condensation into nanometer-scale particles has direct relevance to several fields, including cell biology, virology, and gene delivery for therapeutic purposes. DNA condensation has also attracted the attention of polymer physicists, as the collapse of DNA molecules from solution into well defined particles represents an exquisite example of a polymer phase transition.Here we present a quantitative study of DNA toroids formed by condensation of 3 kb DNA with hexammine cobalt (III). The presence or absence of static loops within this DNA molecule demonstrates the effect of nucleation loop size on toroid dimensions and that nucleation is principally decoupled from toroid growth. A comparison of DNA condensates formed at low ionic strength with those formed in the presence of additional salts (NaCl or MgCl2) shows that toroid thickness is a salt-dependant phenomenon. Together, these results have allowed the development of models for DNA toroid formation in which the size of the nucleation loop directly influences the diameter of the fully formed toroid, whereas solution conditions govern toroid thickness. The data presented illustrate the potential that exists for controlling DNA toroid dimensions. Furthermore, this study provides a set of data that should prove useful as a test for theoretical models of DNA condensation.DNA ͉ gene delivery ͉ packaging ͉ condensation W ithin living cells, DNA is highly condensed as compared with free DNA in solution (1). In sperm cells and viruses, where gene transcription is inactive, DNA condensation approaches the limits of molecular compaction (2, 3). The condensation of free DNA in vitro has long been of interest as a potential model for DNA condensation in vivo, particularly as a model of DNA packaging in viruses (4-6). More recently, DNA condensation has attracted much attention for its direct relevance to the preparation of DNA for delivery as a part of gene therapies (7-10).More than 25 years ago it was discovered that multivalent cations cause DNA to collapse from solution into toroid-shaped condensates (11). These structures have typically been reported to measure Ϸ100 nm in outside diameter with a 30-nm hole; however, the generation of substantially larger toroids has also been reported (12, 13). Toroidal DNA condensates have been reported to be the morphology of DNA packaged within some bacterial phages and vertebrate sperm cells (4,5,(14)(15)(16). Thus, the DNA toroid is a morphology used by nature for the high-density packing of genomes. The condensation of DNA for artificial gene delivery has also used toroids (17, 18). However, researchers have yet to develop a method to package DNA that produces particles as homogeneous, both in terms of size and shape, as is achieved by natural packing systems.A considerable number of theoretical studies have sought to explain why DNA toroids and other condensate morphologies (e.g., rods) favor a particular size. These theories include growth limits based on the build-up of uncompensated electrostatic repulsio...

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Section: Resultsmentioning

confidence: 82%

Section: Mgcl2 Causes a Greater Increase In Toroid Diameter Thanmentioning

confidence: 99%

Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength

Conwell

Vilfan

Hud

2003

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

203

190

View full text Add to dashboard Cite

show abstract

“…40 Notably, methods wherein the rotational relaxation time of the DNA is measured even generate different values depending on the model that is used to calculate the persistence length from the experimental results. 42 The general consensus is that at low salt concentrations, the self-interaction of the negatively charged DNA backbone results in a higher apparent persistence length. At higher salt concentrations this negative charge is screened by the positive ions in the buffer.…”

Section: Discussionmentioning

confidence: 99%

The persistence length of double stranded DNA determined using dark field tethered particle motion

Brinkers

Dietrich

Groote

et al. 2009

The Journal of Chemical Physics

107

114

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The wormlike chain model describes the micromechanics of semiflexible polymers by introducing the persistence length. We propose a method of measuring the persistence length of DNA in a controllable near-native environment. Using a dark field microscope, the projected positions of a gold nanoparticle undergoing constrained Brownian motion are captured. The nanoparticle is tethered to a substrate using a single double stranded DNA ͑dsDNA͒ molecule and immersed in buffer. No force is exerted on the DNA. We carried out Monte Carlo simulations of the experiment, which give insight into the micromechanics of the DNA and can be used to interpret the motion of the nanoparticle. Our simulations and experiments demonstrate that, unlike other similar experiments, the use of nanometer instead of micrometer sized particles causes particle-substrate and particle-DNA interactions to be of negligible effect on the position distribution of the particle. We also show that the persistence length of the tethering DNA can be estimated with a statistical error of 2 nm, by comparing the statistics of the projected position distribution of the nanoparticle to the Monte Carlo simulations. The persistence lengths of 45 single molecules of four different lengths of dsDNA were measured under the same environmental conditions at high salt concentration. The persistence lengths we found had a mean value of 35 nm ͑standard error of 2.8 nm͒, which compares well to previously found values using similar salt concentrations. Our method can be used to directly study the effect of the environmental conditions ͑e.g., buffer and temperature͒ on the persistence length.

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“…The association of complementary strands into duplexes drastically alters their statistical physical properties, transforming the highly flexible SSs, whose persistence length is of the order of a few bases, to rigid segments of double helix, whose persistence length is much longer than their length (10). As this association proceeds, the concentration of duplexes increases and the system is brought into a metastable state, a condition that leads to the formation and growth of nuclei of a stable equilibrium phase.…”

mentioning

confidence: 99%

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

Zanchetta

Nakata

Buscaglia

et al. 2008

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

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Using optical microscopy, we have studied the phase behavior of mixtures of 12-to 22-bp-long nanoDNA oligomers. The mixtures are chosen such that only a fraction of the sample is composed of mutually complementary sequences, and hence the solutions are effectively mixtures of single-stranded and double-stranded (duplex) oligomers. When the concentrations are large enough, such mixtures phase-separate via the nucleation of duplex-rich liquid crystalline domains from an isotropic background rich in single strands. We find that the phase separation is approximately complete, thus corresponding to a spontaneous purification of duplexes from the single-strand oligos. We interpret this behavior as the combined result of the energy gain from the end-to-end stacking of duplexes and of depletion-type attractive interactions favoring the segregation of the more rigid duplexes from the flexible single strands. This form of spontaneous partitioning of complementary nDNA offers a route to purification of short duplex oligomers and, if in the presence of ligation, could provide a mode of positive feedback for the preferential synthesis of longer complementary oligomers, a mechanism of possible relevance in prebiotic environments.condensation ͉ nucleation ͉ depletion ͉ prebiotic ͉ PEG M olecular crowding of cellular interior is known to play a role in the spontaneous organization of biological macromolecules (1). Several biochemical and physiological processes are found to be influenced by strong packing constraints (2, 3), and complex ordered arrangements, such as liquid-crystalline mesophases, have been shown to arise from highly packed biomolecules (4). Of particular interest is the ordering of highly concentrated DNA in cell nuclei, which can lead to a variety of mesophases in vivo (5). However, whether such ordering caused by packing constraints had represented an evolutionary advantage remains an open question.Concentrated solutions of fully hybridized nanoDNA (nDNA) exhibit various liquid crystalline forms of supramolecular ordering, promoted by end-to-end adhesion of the paired bases at the terminals of the duplexes. This behavior has been reported recently for a wide set of self-complementary (SC) 6-to 20-bp nDNA sequences and for mutually complementary sequences in the same length range (6). Here we explore the phase behavior of mixtures of nDNA in which only some of the sequences are complementary, thus able to pair in double strands (DSs), and part of the sequences are not, and thus always remain in the solution as single strands (SSs). We have found that in concentrated mixtures of duplex and SS nDNA, the system phaseseparates into duplex-rich liquid crystal (LC) domains coexisting with a duplex-poor isotropic phase, leading to the physical segregation of 4-to 6-nm-long complementary chains from noncomplementary ones. This phase separation is a collective effect of the duplex and SS nDNA because the duplexes alone would not form LCs in such solutions, their concentration being well below that required for LC forma...

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DNA persistence length revisited

Cited by 165 publications

References 59 publications

Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength

Controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength

The persistence length of double stranded DNA determined using dark field tethered particle motion

Phase separation and liquid crystallization of complementary sequences in mixtures of nanoDNA oligomers

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