Direct Demonstration of DNA Compaction Mediated by Divalent Counterions

Wang, Yanwei; Gao, Tianyong; Li, Shuhang; Xia, Wenyan; Zhang, Wei; Yang, Guangcan

doi:10.1021/acs.jpcb.8b09398

Cited by 10 publications

(8 citation statements)

References 29 publications

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“…The requirement of relatively low level of cation binding for DNA condensation indicates that cation binding to the major groove can be a rather sensitive modulator. One example is that Mg 2 + has been reported to compact λ phage DNA when pH is lowered to ∼4 ( 26 ), which can be explained by H + association in the DNA major groove (e.g. the N7 atom of Adenine has a pKa of ∼3.5) giving the extra bit of positive charge.…”

Section: Discussionmentioning

confidence: 99%

Structure-guided DNA–DNA attraction mediated by divalent cations

Srivastava

Timsina

Heo

et al. 2020

Nucleic Acids Research

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Probing the role of surface structure in electrostatic interactions, we report the first observation of sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and a poly(AT)-poly(TA) duplex (AT-TA). While AT-TA exhibits non-distinguishable behaviors from random-sequence genomic DNA, AA-TT condenses in all alkaline earth metal ions. We characterized these interactions experimentally and investigated the underlying principles using computer simulations. Both experiments and simulations demonstrate that AA-TT condensation is driven by non-specific ion–DNA interactions. Detailed analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as the major difference between AA-TT and AT-TA, which originates from the continuous and close stacking of nucleobase partial charges. These SEGB cations elicit attraction via spatial juxtaposition with the phosphate backbone of neighboring helices, resulting in an azimuthal angular shift between apposing helices. Our study thus presents a distinct mechanism in which, sequence-directed surface motifs act with cations non-specifically to enact sequence-dependent behaviors. This physical insight allows a renewed understanding of the role of repeating sequences in genome organization and regulation and offers a facile approach for DNA technology to control the assembly process of nanostructures.

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Section: Discussionmentioning

confidence: 99%

Structure-guided DNA–DNA attraction mediated by divalent cations

Srivastava

Timsina

Heo

et al. 2020

Nucleic Acids Research

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“…Recently, we unambiguously demonstrated DNA attraction and its regulation mediated by divalent cations Mg 2+ and Ca 2+ , by tethering a DNA single chain by lowering the pH of a solution. It has been found that DNA is compacted when the pH of solution containing these divalent counterions is lowered below 5.0 [25]. In the present study, we try to find the critical charge neutralization needed for DNA attraction or compaction.…”

Section: Introductionmentioning

confidence: 96%

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

et al. 2019

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DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around −1.0 × 10−4 cm2 V−1 s−1 to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.

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“…The interactions between polyelectrolytes and divalent ions are important for diverse biological phenomena. − Multivalent ions can mediate attractive interactions between like-charged objects. − This is useful to biological organisms, for example, in DNA packing, where divalent and higher-valent cations can induce attractions between monomers, leading to the compaction of DNA molecules. − These attractive forces may also generate adverse effects: divalent ions cause polyelectrolyte brushes, which play an important role as lubricants in cartilage tissue, to shrink and aggregate laterally, thereby decreasing their lubricating power. ,, Besides their biological importance, polyelectrolyte solutions and gels are also employed in a wide array of industrial products, − ranging from detergents to toothpastes or drilling muds. These are exposed to divalent ions (primarily Mg 2+ and Ca 2+ ) when dissolved in tap water.…”

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confidence: 99%

Solution Properties of Polyelectrolytes with Divalent Counterions

et al. 2021

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Divalent ions are known to strongly influence the phase behavior, conformation, and flow properties of polyelectrolytes in solution. Here, we report small-angle neutron scattering and viscosity data for the magnesium salt of polystyrene sulfonate (MgPSS) in salt-free water and compare these results with analogous measurements for NaPSS. In a dilute solution, both salts are found to exhibit a rod-like conformation for high degrees of polymerization, but the chain dimensions of MgPSS are significantly smaller than for NaPSS, which is consistent with the lower charge density of MgPSS found from conductivity data. In the semidilute regime, the correlation length scales as ξ ≃ 3.7c −1/2 nm for NaPSS and ξ ≃ 5.4c −1/2 nm for MgPSS. At high concentrations, deviations to weaker power laws are observed for both salts. The variation of the viscosity with the degree of polymerization (η sp ∼ N) is consistent with unentangled, Rouse-like dynamics. Fuoss-law-type behavior (η sp ∼ c 1/2 ) is observed at low polymer concentrations, which turns into a stretched exponential dependence at high c, perhaps due to an increase in the local friction experienced by polymer segments.

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Direct Demonstration of DNA Compaction Mediated by Divalent Counterions

Cited by 10 publications

References 29 publications

Structure-guided DNA–DNA attraction mediated by divalent cations

Structure-guided DNA–DNA attraction mediated by divalent cations

DNA Compaction and Charge Neutralization Regulated by Divalent Ions in very Low pH Solution

Solution Properties of Polyelectrolytes with Divalent Counterions

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