Marked differences in volume phase transitions between gel and single molecule in DNA

Mayama, Hiroyuki; Nakai, T.; Takushi, Eisei; Tsujii, Kaoru; Yoshikawa, Kenichi

doi:10.1063/1.2748767

Cited by 11 publications

(21 citation statements)

References 21 publications

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“…The transition was produced by adding acetone to the solution: at about 60 vol.% acetone the DNA hydrogel suddenly collapses to a volume about 1/15 of that in the swollen state. Similar, but less marked transition is found upon increasing the concentration of divalent calcium cations [112,113], of spermidine, a trivalent cation [114], and of cationic surfactant [115,116]. This multivalent cation induced collapse is interpreted as a result of the association of DNA double strands that follows their charge neutralization [112].…”

Section: Hydrogelsmentioning

confidence: 74%

DNA-Based Soft Phases

Bellini¹,

Cerbino²,

Zanchetta³

2011

Topics in Current Chemistry

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This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.

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Section: Hydrogelsmentioning

confidence: 74%

DNA-Based Soft Phases

Bellini¹,

Cerbino²,

Zanchetta³

2011

Topics in Current Chemistry

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“…25 The observed differences may be related to the different contour lengths of 9 while, as mentioned in the first section, it is 166 nm for ss-DNA gels subjected to the swelling tests. Thus, the number of Kuhn segments N equal to 560 and 83 for the single DNA molecule and for the DNA network chain, respectively.…”

Section: Resultsmentioning

confidence: 95%

“…23 Further, Mayama et al observed first-order volume phase transitions in gels and solutions of DNA induced by spermidine, a trivalent cation. 25 Although DNA hydrogels attracted interest in recent years, [26][27][28][29][30] formation conditions of a cross-linked DNA network starting from single DNA strands as well as the hydrogel properties such as viscoelasticity, swelling and thermal behavior have not been investigated in detail. Recently, we investigated the rheological behavior of DNA gels formed by solution cross-linking of ds-DNA at a concentration of 9.3 w/v %.…”

Section: Introductionmentioning

confidence: 99%

Formation of Hydrogels by Simultaneous Denaturation and Cross-Linking of DNA

Topuz

Okay

2009

Biomacromolecules

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DNA hydrogels with a wide range of tunable properties are desirable for applications to make use the characteristics of DNA. This study describes formation conditions of DNA hydrogels using ethylene glycol diglycidyl ether (EGDE) cross-linker and N,N,N',N'-tetramethylethylenediamine (TEMED) catalyst under various reaction conditions. Rheological measurements indicate that the cross-linking of DNA in semidilute solutions proceeds by alternate gel-sol and sol-gel transitions due to two antagonistic effects of EGDE-TEMED pair; the one destroying the physical bonds (denaturation), the other creating chemical bonds (cross-linking). The viscoelastic properties of the hydrogels and the conformation of DNA network chains could be tuned by adjusting the synthesis parameters. Increasing concentration of DNA at the gel preparation stabilizes its structure so that double stranded (ds-) DNA hydrogels form. The average distance between the effective cross-links in single stranded DNA gel is much larger than that in ds-DNA gel making the former gel stable in aqueous solutions. Creep-recovery tests show that heating a semidilute solution of DNA above the DNA melting temperature (87.5 degrees C) and subsequently cooling down to 25 degrees C increases the elastic response of the solution and produces an elastic DNA mesh. DNA hydrogel undergoes a volume phase transition in aqueous solutions of polyethylene glycol's at which the gel changes about 5 times its volume.

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“…3. By introducing angular dependence on the binary interaction between the segments, the free energy is reformulated as follows (37,38):…”

Section: Theoreticalmentioning

confidence: 99%

“…1 D. Concerning the physicochemical action of SPD(3þ) on the conformational transition of DNA, we have presented rather detailed theoretical discussions in previous papers (37,38), and therefore skip the theoretical details and present here only a short explanation. In contrast to the case of shrinking by Fis, DNA is tightly compacted by SPD, that is, there is a 30-to 60-fold difference in the DNA segment density between the shrunken and compact states (see, e.g., Fig.…”

Section: Theoreticalmentioning

confidence: 99%

Structural Change of DNA Induced by Nucleoid Proteins: Growth Phase-Specific Fis and Stationary Phase-Specific Dps

Sato

Watanabe

Kondo

et al. 2013

Biophysical Journal

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The effects of nucleoid proteins Fis and Dps of Escherichia coli on the higher order structure of a giant DNA were studied, in which Fis and Dps are known to be expressed mainly in the exponential growth phase and stationary phase, respectively. Fis causes loose shrinking of the higher order structure of a genome-sized DNA, T4 DNA (166 kbp), in a cooperative manner, that is, the DNA conformational transition proceeds through the appearance of a bimodal size distribution or the coexistence of elongated coil and shrunken globular states. The effective volume of the loosely shrunken state induced by Fis is 30-60 times larger than that of the compact state induced by spermidine, suggesting that cellular enzymes can access for DNA with the shrunken state but cannot for the compact state. Interestingly, Dps tends to inhibit the Fis-induced shrinkage of DNA, but promotes DNA compaction in the presence of spermidine. These characteristic effects of nucleotide proteins on a giant DNA are discussed by adopting a simple theoretical model with a mean-field approximation.

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Marked differences in volume phase transitions between gel and single molecule in DNA

Cited by 11 publications

References 21 publications

DNA-Based Soft Phases

DNA-Based Soft Phases

Formation of Hydrogels by Simultaneous Denaturation and Cross-Linking of DNA

Structural Change of DNA Induced by Nucleoid Proteins: Growth Phase-Specific Fis and Stationary Phase-Specific Dps

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