Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment

Sim, Adelene Y. L.

doi:10.1016/j.cis.2015.09.008

Cited by 10 publications

(10 citation statements)

References 130 publications

(180 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Therefore, below 50 nm dsDNA is considered a rigid rod ( 10 , 11 , 12 , 13 , 17 ). ssDNA, on the other hand, has a persistence length on the same order of its chain width (∼1 nm) and thus is considered a flexible polymer ( 10 , 11 , 12 , 17 ). Upon mixing with PLL at 150 mM NaCl, PLL lysine to DNA phosphate ratio (N/P ∼1), and room temperature, phase-separated droplets containing both PLL and ssDNA are formed ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…ssDNA and dsDNA have an order of magnitude difference between their respective persistence lengths ( 10 , 11 , 12 , 13 , 17 ). However, they also differ significantly in their linear charge densities, which could contribute to the observed differences in the phase behavior ( 20 ).…”

Section: Resultsmentioning

confidence: 99%

“…Two interactions are key to the NA structure: electrostatic repulsions (primarily due to the backbone phosphates) and base stacking interactions ( 10 , 11 , 12 ). These interactions, the former being highly salt-dependent and the latter being sequence-dependent, determine the flexibility of NA ( 12 , 13 ).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

Shakya

King

2018

Biophysical Journal

138

View full text Add to dashboard Cite

Phase separation of intracellular components has been recently realized as a mechanism by which cells achieve membraneless organization. Here, we study the associative liquid-liquid phase separation (LLPS) of DNA upon complexation with cationic polypeptides. Comparing the phase behavior of different single-stranded DNA as well as double-stranded DNA (dsDNA) sequences that differ in persistence lengths, we find that DNA local flexibility, not simply charge density, determines the LLPS. Furthermore, in a nucleotide- and DNA-dependent manner, free nucleotide triphosphates promote LLPS of polypeptide-dsDNA complexes that are otherwise prone to precipitation. Under these conditions, dsDNA undergoes a secondary phase separation forming liquid-crystalline subcompartments inside the droplets. These results point toward a role of local DNA flexibility, encoded in the sequence, in the regulation and selectivity of multicomponent LLPS in membraneless intracellular organization.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

Shakya

King

2018

Biophysical Journal

138

View full text Add to dashboard Cite

show abstract

“…Apart from the regulated folding schemes of pDNA, there is an apparent inconsistency in the structures and the intrinsic rigidity of DNA. DNA is assumed as a semiflexible chain in long-range order; however, it is assumed as a rigid rod in the local range shorter than the persistence length, 50 nm, which corresponds to~150 bp [7][8][9]. Then, the globular structure, which is smaller than the persistence length, and the rod-shaped structure, which accompanies back folding of DNA at the rod ends, cannot be explained.…”

Section: Folding Mechanism Of Dna In Pms and Their Structural Polymormentioning

confidence: 99%

“…The behavior of DNA after the polyion complexation is substantially different depends on DNA form whether it is long, short, double-stranded, or single-stranded. Double-stranded DNA is assumed as a rigid rod when it is shorter than 150 bp, which corresponds to its persistence length of 50 nm, whereas it behaves as a semi-flexible chain when it is sufficiently longer than the persistence length [7][8][9]. For latter case, DNA usually undergoes first-order transition by complexation with polycations changing its conformation from a worm-like expanded coil into a compact state.…”

Section: Introductionmentioning

confidence: 99%

Structural Polymorphism of Single pDNA Condensates Elicited by Cationic Block Polyelectrolytes

Osada

2020

Polymers

View full text Add to dashboard Cite

DNA folding is a core phenomenon in genome packaging within a nucleus. Such a phenomenon is induced by polyelectrolyte complexation between anionic DNA and cationic proteins of histones. In this regard, complexes formed between DNA and cationic polyelectrolytes have been investigated as models to gain insight into genome packaging. Upon complexation, DNA undergoes folding to reduce its occupied volume, which often results in multi-complex associated aggregates. However, when cationic copolymers comprising a polycation block and a neutral hydrophilic polymer block are used instead, DNA undergoes folding as a single molecule within a spontaneously formed polyplex micelle (PM), thereby allowing the observation of the higher-order structures that DNA forms. The DNA complex forms polymorphic structures, including globular, rod-shaped, and ring-shaped (toroidal) structures. This review focuses on the polymorphism of DNA, particularly, to elucidate when, how, and why DNA organizes into these structures with cationic copolymers. The interactions between DNA and the copolymers, and the specific nature of DNA in rigidity; i.e., rigid but foldable, play significant roles in the observed polymorphism. Moreover, PMs serve as potential gene vectors for systemic application. The significance of the controlled DNA folding for such an application is addressed briefly in the last part.

show abstract

Simulations of Biomolecules in Electrolyte Solutions

Friedman

2019

Advcd Theory and Sims

View full text Add to dashboard Cite

Biomolecules including proteins, lipid membranes, and nucleic acids operate at an aqueous milieu that includes solvated ions. The interactions with ions affect biomolecules in different ways depending on the nature of the solute and the type of the ions. The dynamic nature of small soluble ions makes it difficult to follow them by structural methods. Consequently, theories were developed to explain how biomolecules interact in an environment that includes electrolytes. Moreover, simulations studies are often used to study such systems at the molecular or atomistic level. The status of the field, and in particular of simulation studies, is the subject of this progress report.

show abstract

Nucleic acid polymeric properties and electrostatics: Directly comparing theory and simulation with experiment

Cited by 10 publications

References 130 publications

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

DNA Local-Flexibility-Dependent Assembly of Phase-Separated Liquid Droplets

Structural Polymorphism of Single pDNA Condensates Elicited by Cationic Block Polyelectrolytes

Simulations of Biomolecules in Electrolyte Solutions

Contact Info

Product

Resources

About