Diaminoalkanes with an odd number of carbon atoms induce compaction of a single double‐stranded DNA chain

Yoshikawa, Yuko; Yoshikawa, Kunio

doi:10.1016/0014-5793(95)00190-k

Cited by 66 publications

(58 citation statements)

References 30 publications

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“…We have experimentally confirmed that the fluorescence dye, Gelgreen, at the adapted concentration exhibits negligible effect on the conformation of DNA molecules, referring to the past studies on the higher-order structure of DNA. [25][26][27][28][29][30][31] All observations were carried out at room temperature (24 • C).…”

Section: B Dna Conformation In Solution As Observed By Fluorescence mentioning

confidence: 99%

“…Nevertheless, divalent cations also cause shrinkage of the DNA chain at relatively high concentrations of several to several tens of mM. 27 In usual biological systems, polyamines with 3 or 4 positive charges and divalent metal cation, such as Mg(2+) or Ca(2+), are typical poly-cationic species. Thus, it may be of interest to clarify the effect of the coexistence of multivalent polyamines and divalent metal cations on the higher-order structure of a giant DNA molecule.…”

Section: Introductionmentioning

confidence: 99%

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Divalent cation shrinks DNA but inhibits its compaction with trivalent cation

Tongu

Kondo

Yoshikawa

et al. 2016

The Journal of Chemical Physics

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Our observation reveals the effects of divalent and trivalent cations on the higher-order structure of giant DNA (T4 DNA 166 kbp) by fluorescence microscopy. It was found that divalent cations, Mg(2+) and Ca(2+), inhibit DNA compaction induced by a trivalent cation, spermidine (SPD(3+)).On the other hand, in the absence of SPD(3+), divalent cations cause the shrinkage of DNA.As the control experiment, we have confirmed the minimum effect of monovalent cation, Na(+) on the DNA higher-order structure. We interpret the competition between 2+ and 3+ cations in terms of the change in the translational entropy of the counterions. For the compaction with SPD(3+), we consider the increase in translational entropy due to the ion-exchange of the intrinsic monovalent cations condensing on a highly charged polyelectrolyte, double-stranded DNA, by the 3+ cations. In contrast, the presence of 2+ cation decreases the gain of entropy contribution by the ion-exchange between monovalent and 3+ ions. C 2016 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution (CC BY) license

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Section: B Dna Conformation In Solution As Observed By Fluorescence mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation

Tongu

Kondo

Yoshikawa

et al. 2016

The Journal of Chemical Physics

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“…48 We found that giant DNA molecules undergo an on/off transition from an expanded coil state to a compact state accompanied by a difference in density on the order of 10 4 -10 5 upon the addition of various condensing agents including polyamines, 40,41 basic proteins, 49 and neutral polymers, 50 while short DNA fragments behave like rigid rods and cannot undergo such a folding transition. 4,38,51 Here, we extended our investigation to a megabase-size genomic DNA (S120-1 DNA) that was successfully extracted from Rhodoligotrophos appendicifer (strain 120-1 T = JCM 16873 T = ATCC BAA 2115 T ).…”

Section: Introductionmentioning

confidence: 97%

“…38 Over the past decade, we have investigated the changes in the higher-order structure of a large DNA molecule through a single-molecule observation using FM. [39][40][41][42][43][44][45][46][47] To visualize individual DNA molecules, we used T4 phage DNA (166 kbp) as a model large DNA, and its size is on the order a) Author to whom correspondence should be addressed. Electronic mail:…”

Section: Introductionmentioning

confidence: 99%

Critical behavior of megabase-size DNA toward the transition into a compact state

Yoshikawa

Suzuki

Yamada

et al. 2011

The Journal of Chemical Physics

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Naturally occurring branched-chain polyamines induce a crosslinked meshwork structure in a giant DNA The Journal of Chemical Physics 145, 235103 (2016) We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.

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“…Diaminoalkanes with three and five methylene groups have been reported to be more effective than diamines with two, four, and six methylene groups [80].…”

Section: Formulation Parametersmentioning

confidence: 99%

Rationally Designed Synthetic Vectors for Gene Delivery

Rao¹,

Yadava²,

Hughes³

2007

TODDJ

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Vector development is one of the most important challenges facing the successful use of genes for treatment of diseases. Although chemically produced vectors offer distinct advantages over biological systems such as viruses, there are still some hurdles that have to be overcome before synthetic gene delivery vectors can be successfully implemented. This brief review discusses the biological barriers that limit current delivery strategies and reviews currently employed strategies for plasmid delivery. Nanoparticle-based gene delivery is reviewed along with methods for their characterization, physiochemical properties and toxicity. Finally a prospectus is provided for future development of an ideal synthetic gene delivery vector.

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Diaminoalkanes with an odd number of carbon atoms induce compaction of a single double‐stranded DNA chain

Cited by 66 publications

References 30 publications

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation

Divalent cation shrinks DNA but inhibits its compaction with trivalent cation

Critical behavior of megabase-size DNA toward the transition into a compact state

Rationally Designed Synthetic Vectors for Gene Delivery

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