Compaction of double-stranded DNA by negatively charged proteins and colloids

Zinchenko, Anatoly; Yoshikawa, Kenichi

doi:10.1016/j.cocis.2014.12.005

Cited by 11 publications

(8 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Nevertheless, in intriguing early studies, Murphy 56 andÅkerman 57 reported some form of interaction between ds-DNA and citrate coated gold nanoparticles and there have been some subsequent similar reports. 33,58,[73][74][75] The interaction is weak and its nature unclear, with suggestions including direct adsorption to the gold with displacement of the citrate. 56 This does demonstrate that anionic charge on the surface of the nanoparticle does not exclude DNA-binding as long as there are sufficient favourable interactions to counter it; on a macromolecule such as a nanoparticle this may be possible.…”

Section: Interaction Of Gnp-lip-based Nanocarriers With Ct-dnamentioning

confidence: 99%

Assisted delivery of anti-tumour platinum drugs using DNA-coiling gold nanoparticles bearing lumophores and intercalators: towards a new generation of multimodal nanocarriers with enhanced action

et al. 2019

View full text Add to dashboard Cite

show abstract

Section: Interaction Of Gnp-lip-based Nanocarriers With Ct-dnamentioning

confidence: 99%

Assisted delivery of anti-tumour platinum drugs using DNA-coiling gold nanoparticles bearing lumophores and intercalators: towards a new generation of multimodal nanocarriers with enhanced action

et al. 2019

View full text Add to dashboard Cite

show abstract

“…using calf thymus DNA referred to the effect of particle size and concentration in DNA condensation that occurs as a result of electrostatic interactions between positively charged NPs and DNA. As DNA compaction due to charged species in the medium is an actual issue, great efforts need to be done to understand the interactions between them as well as to determine the exact mechanisms that cause it and which are involved in multiple biological functions . Employing NPs functionalized with lysine with an average size of 30 nm, Ganguli et al.…”

Section: Aunp Interaction With Dna Polymersmentioning

confidence: 99%

“…As DNA compaction due to charged species in the medium is an actual issue, great effortsn eed to be done to understandt he interactions between them as well as to determinet he exact mechanisms that causei ta nd which are involved in multiple biological functions. [131,132] Employing NPs functionalized with lysine with an average size of 30 nm, Ganguli et al found by AFM that DNA probably wraps around the NP.T hey also observed that at high concentrations of NP/DNA, the DNA-NP complexes are interconnected, forming structures that differ from the linear [133] associationsp reviously described for smaller NPs (around2nm). [134] In the biomedical field, DNA templates made of gold can be used in order to enhance spe-cificity in the conventional DNA amplification technique known as polymerase chain reaction( PCR).…”

Section: Gold Nanoparticles Templated By Dnamentioning

confidence: 99%

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

et al. 2016

View full text Add to dashboard Cite

The interactions of DNA, whether long, hundred base pair chains or short-chained oligonucleotides, with ligands play a key role in the field of structural biology. Its biological activity not only depends on the thermodynamic properties of DNA-ligand complexes, but can and often is conditioned by the formation kinetics of those complexes. On the other hand, gold nanoparticles have long been known to present excellent biocompatibility with biomolecules and are themselves remarkable for their structural, electronic, magnetic, optical and catalytic properties, radically different from those of their counterpart bulk materials, and which make them an important asset in multiple applications. Therefore, thermodynamic and kinetic studies of the interactions of DNA with nanoparticles acting as small ligands are key for a better understanding of those interactions to allow for their control and modulation and for the opening of new venues of research in nanomedicine, analytic and biologic fields. The interactions of gold nanoparticles with both DNA polymers and their smaller subunits; special focus is placed on those interactions taking place with nonfunctionalized gold nanoparticles are reviewed in the present work.

show abstract

“…In solutions with a high concentration of neutral macromolecules (crowders) such as poly(ethylene glycol) (PEG) and in the presence of monovalent or divalent cations at physiological concentrations, double-stranded DNA undergoes compaction into tight condensates (9). Crowding created by anionic proteins (bovine serum albumin) (13) or by anionic nanoparticles (14) also leads to the DNA compaction (15). DNA compaction under MMC is greatly facilitated by confinement into nanogeometries (16) without the need for a high concentration of salt (17).…”

Section: Introductionmentioning

confidence: 99%

Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding

Zinchenko

Berezhnoy

Chen

et al. 2018

Biophysical Journal

Self Cite

View full text Add to dashboard Cite

The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na and K) and divalent (Mg) cations. Both DNA and chromatin demonstrated compaction under comparable conditions in the presence of poly(ethylene glycol) and Na or Mg salt. However, the mechanism of the compaction changed from a first-order phase transition for DNA to a continuous folding for megabase-sized chromatin fibers. A more efficient and pronounced chromatin compaction was observed in the presence of Na compared to K. A flow-stretching technique to unfold DNA and chromatin coils was used to gain further insight into the morphology of partially folded chromatin fibers. The results revealed a distribution of partially folded chromatin fibers. This variability is likely the result of the heterogeneous distribution of nucleosomes on the DNA chain. The packaging of DNA in the form of chromatin in the crowded nuclear environment appears essential to ensure gradual conformational changes of DNA.

show abstract

Compaction of double-stranded DNA by negatively charged proteins and colloids

Cited by 11 publications

References 43 publications

Assisted delivery of anti-tumour platinum drugs using DNA-coiling gold nanoparticles bearing lumophores and intercalators: towards a new generation of multimodal nanocarriers with enhanced action

Assisted delivery of anti-tumour platinum drugs using DNA-coiling gold nanoparticles bearing lumophores and intercalators: towards a new generation of multimodal nanocarriers with enhanced action

Covalent and Non‐Covalent DNA–Gold‐Nanoparticle Interactions: New Avenues of Research

Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding

Contact Info

Product

Resources

About