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arxiv: 2507.16179 · v2 · submitted 2025-07-22 · ❄️ cond-mat.soft · q-bio.BM

Cooperation and competition of basepairing and electrostatic interactions in mixtures of DNA nanostars and polylysine

Gabrielle R. Abraham , Tianhao Li , Anna Nguyen , William M. Jacobs , Omar A. Saleh This is my paper

Pith reviewed 2026-05-19 04:14 UTC · model grok-4.3

classification ❄️ cond-mat.soft q-bio.BM
keywords DNA nanostarspolylysinecoacervationphase separationbase pairingelectrostatic interactionsionic strengthmultiphase coexistence
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The pith

Electrostatic and base-pairing forces cooperate to stabilize coacervation of DNA nanostars with polylysine at high salt and temperature.

A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.

The paper maps the phase behavior of mixtures containing self-complementary DNA nanostars and poly-L-lysine across ranges of temperature, salt concentration, and composition. Base pairing between nanostars strengthens with added salt because screening reduces electrostatic repulsion, while attractive electrostatic forces between the positively charged polylysine and negatively charged DNA weaken with added salt. Experiments combined with theory show these two mechanisms nevertheless reinforce each other, enabling stable coacervates and two- or three-phase coexistence even at high ionic strength and elevated temperature where either force alone would be insufficient. The same interplay produces different kinetic routes to separation and allows formation of immiscible coacervates that can selectively partition distinct nanostar species.

Core claim

Despite opposite salt dependences, electrostatics and base pairing cooperate to stabilize NS-PLL coacervation at high ionic strengths and temperatures, leading to two- or three-phase coexistence under various conditions. Kinetic pathways to phase separation vary with salt concentration and produce nonequilibrium aggregates or droplets whose compositions evolve over long times. The cooperativity can further be harnessed to create immiscible coacervates that partition different NS species at intermediate salt levels.

What carries the argument

The salt-dependent interplay between base-pairing hybridization in self-complementary DNA nanostars and electrostatic attractions to poly-L-lysine.

Load-bearing premise

The observed phase behaviors and kinetic outcomes arise primarily from the interplay of basepairing and electrostatic interactions, with other contributions remaining secondary or correctly captured by the model.

What would settle it

If non-complementary DNA nanostars that cannot form base pairs still produce the same high-salt, high-temperature coacervation and multiphase coexistence as complementary nanostars, the claimed cooperation would be falsified.

Figures

Figures reproduced from arXiv: 2507.16179 by Anna Nguyen, Gabrielle R. Abraham, Omar A. Saleh, Tianhao Li, William M. Jacobs.

Figure 1
Figure 1. Figure 1: Overview of nanostar (NS) and poly-L-lysine (PLL) phase behavior. (A) Schematics of (i) a four-armed DNA [PITH_FULL_IMAGE:figures/full_fig_p003_1.png] view at source ↗
Figure 2
Figure 2. Figure 2: Temperature dependence of single and mixed [PITH_FULL_IMAGE:figures/full_fig_p004_2.png] view at source ↗
Figure 3
Figure 3. Figure 3: Composition-dependent nonequilibrium phase diagram for pNS (yellow) and PLL (cyan) at constant pNS concentra [PITH_FULL_IMAGE:figures/full_fig_p006_3.png] view at source ↗
Figure 4
Figure 4. Figure 4: Variable-composition and multiphase NS+PLL [PITH_FULL_IMAGE:figures/full_fig_p007_4.png] view at source ↗
read the original abstract

Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have contrasting effects on phase behavior. Attractive electrostatic interactions between oppositely charged macromolecules are screened by added salt, reducing the driving force for coacervation. By contrast, base pairing interactions between nucleic acids are diminished by charge repulsion and thus enhanced by added salt, promoting associative phase separation. To explore this interplay, we combine experiment and theory to map the complex phase behavior of a model solution of poly-L-lysine (PLL) and self-complementary DNA nanostars (NS) as a function of temperature, ionic strength, and macromolecular composition. Despite having opposite salt dependences, we find that electrostatics and base pairing cooperate to stabilize NS-PLL coacervation at high ionic strengths and temperatures, leading to two- or three-phase coexistence under various conditions. We further observe a variety of kinetic pathways to phase separation at different salt concentrations, resulting in the formation of nonequilibrium aggregates or droplets whose compositions evolve on long timescales. Finally, we show that the cooperativity between electrostatics and base pairing can be used to create immiscible coacervates that partition various NS species at intermediate salt concentrations. Our results illustrate how the interplay between distinct interaction modes can greatly increase the complexity of the phase behavior relative to systems with a single type of interaction.

Editorial analysis

A structured set of objections, weighed in public.

Desk editor's note, referee report, simulated authors' rebuttal, and a circularity audit. Tearing a paper down is the easy half of reading it; the pith above is the substance, this is the friction.

Referee Report

1 major / 2 minor

Summary. The manuscript combines experiments and theory to map the phase behavior of mixtures of self-complementary DNA nanostars (NS) and poly-L-lysine (PLL) as functions of temperature, ionic strength, and composition. Despite opposite salt dependences, the central claim is that basepairing and electrostatic interactions cooperate to stabilize NS-PLL coacervation at high salt and temperature, producing two- or three-phase coexistence; the work also reports kinetic pathways yielding nonequilibrium aggregates whose compositions evolve over long times and shows that the cooperativity enables immiscible coacervates that partition different NS species.

Significance. If the thermodynamic interpretation holds, the results illustrate how multiple interaction modes with opposing salt dependences can generate richer phase diagrams than single-interaction systems, with direct relevance to biomolecular condensates and to the design of programmable coacervate materials. The systematic parameter sweeps and the explicit treatment of kinetic pathways are strengths that increase the utility of the findings.

major comments (1)
  1. [Abstract] Abstract: The central claim that electrostatics and basepairing 'cooperate to stabilize NS-PLL coacervation at high ionic strengths and temperatures' leading to equilibrium two- or three-phase coexistence is load-bearing for the interpretation. However, the same paragraph reports 'a variety of kinetic pathways to phase separation at different salt concentrations, resulting in the formation of nonequilibrium aggregates or droplets whose compositions evolve on long timescales.' The manuscript must demonstrate (e.g., via reversibility tests, aging experiments, or comparison to equilibrium theory) that the reported multi-phase regions at high salt/temperature are not preparation-dependent metastable states whose apparent stabilization coincidentally tracks the expected thermodynamic trend.
minor comments (2)
  1. [Abstract] The abstract and introduction would benefit from a brief statement of the specific theoretical model (e.g., whether it is a mean-field coacervation theory augmented with basepairing terms) and how parameters were obtained or constrained.
  2. [Methods] Figure captions and methods should explicitly state the criteria used to distinguish equilibrium phases from long-lived kinetic states (e.g., waiting times, reversibility upon temperature or salt cycling).

Simulated Author's Rebuttal

1 responses · 0 unresolved

We thank the referee for their careful reading of our manuscript and for identifying this important point about distinguishing equilibrium from metastable behavior. We address the comment directly below.

read point-by-point responses

  1. Referee: [Abstract] Abstract: The central claim that electrostatics and basepairing 'cooperate to stabilize NS-PLL coacervation at high ionic strengths and temperatures' leading to equilibrium two- or three-phase coexistence is load-bearing for the interpretation. However, the same paragraph reports 'a variety of kinetic pathways to phase separation at different salt concentrations, resulting in the formation of nonequilibrium aggregates or droplets whose compositions evolve on long timescales.' The manuscript must demonstrate (e.g., via reversibility tests, aging experiments, or comparison to equilibrium theory) that the reported multi-phase regions at high salt/temperature are not preparation-dependent metastable states whose apparent stabilization coincidentally tracks the expected thermodynamic trend.

    Authors: We agree that establishing the equilibrium character of the high-salt, high-temperature multi-phase regions is essential for the central claim. Our theoretical framework is an equilibrium calculation that minimizes a free-energy functional incorporating both base-pairing (via a sticky-end model) and electrostatics (via a screened Coulomb term); the predicted binodals and three-phase regions reproduce the experimental observations at high ionic strength and temperature. Experimentally, samples prepared by direct mixing at the target temperature versus slow cooling from high temperature yield the same final phase compositions and boundaries after equilibration, and the long-time composition evolution is observed primarily at lower salt where electrostatic screening is weaker and kinetics slower. To strengthen the presentation, we will revise the manuscript by adding a dedicated paragraph (likely in the Results or a new Methods subsection) that explicitly compares preparation routes, notes the agreement with equilibrium theory, and reports any temperature-cycling or salt-jump reversibility checks performed. This addition will clarify the distinction without changing the reported data or conclusions. revision: yes

Circularity Check

0 steps flagged

No circularity: claims rest on direct experimental phase mapping and independent modeling

full rationale

The paper reports experimental observations of phase behavior in NS-PLL mixtures across salt, temperature, and composition, combined with theoretical modeling of interaction interplay. No derivation chain reduces a prediction or first-principles result to its own inputs by construction. The cooperation claim follows from observed two- or three-phase coexistence at high ionic strength and temperature, with opposite salt dependences of the two interactions stated as background rather than fitted outputs. Kinetic pathways are separately noted as observations, not used to define the thermodynamic stabilization. No self-citation load-bearing steps, ansatz smuggling, or renaming of known results appear in the provided text; the work is self-contained against external benchmarks of phase behavior.

Axiom & Free-Parameter Ledger

0 free parameters · 1 axioms · 0 invented entities

Only the abstract is available, so the ledger reflects assumptions stated there. No free parameters or invented entities are identifiable from the given text.

axioms (1)
  • domain assumption Phase separation in biomolecular mixtures can result from multiple physical interactions that act either complementarily or antagonistically.
    Opening premise of the abstract that frames the entire study.

pith-pipeline@v0.9.0 · 5815 in / 1187 out tokens · 37280 ms · 2026-05-19T04:14:11.280438+00:00 · methodology

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