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Hydrophobic interactions control the self-assembly of DNA and cellulose

Published online by Cambridge University Press:  05 February 2021

Björn Lindman
Affiliation:
Physical Chemistry, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
Bruno Medronho*
Affiliation:
MED–Mediterranean Institute for Agriculture, Environment and Development, Universidade do Algarve, Faculdade de Ciências e Tecnologia, Campus de Gambelas, Ed. 8, 8005-139 Faro, Portugal FSCN, Surface and Colloid Engineering, Mid Sweden University, SE-851 70 Sundsvall, Sweden
Luís Alves
Affiliation:
Department of Chemical Engineering, University of Coimbra, CIEPQPF, Rua Sílvio Lima, Pólo II, PT-3030-790 Coimbra, Portugal
Magnus Norgren
Affiliation:
FSCN, Surface and Colloid Engineering, Mid Sweden University, SE-851 70 Sundsvall, Sweden
Lars Nordenskiöld
Affiliation:
School of Biological Sciences, Nanyang Technology University, 60 Nanyang Drive, Singapore 637551, Singapore
*
Author for correspondence: Bruno Medronho, E-mail: bfmedronho@ualg.pt
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Abstract

Desoxyribosenucleic acid, DNA, and cellulose molecules self-assemble in aqueous systems. This aggregation is the basis of the important functions of these biological macromolecules. Both DNA and cellulose have significant polar and nonpolar parts and there is a delicate balance between hydrophilic and hydrophobic interactions. The hydrophilic interactions related to net charges have been thoroughly studied and are well understood. On the other hand, the detailed roles of hydrogen bonding and hydrophobic interactions have remained controversial. It is found that the contributions of hydrophobic interactions in driving important processes, like the double-helix formation of DNA and the aqueous dissolution of cellulose, are dominating whereas the net contribution from hydrogen bonding is small. In reviewing the roles of different interactions for DNA and cellulose it is useful to compare with the self-assembly features of surfactants, the simplest case of amphiphilic molecules. Pertinent information on the amphiphilic character of cellulose and DNA can be obtained from the association with surfactants, as well as on modifying the hydrophobic interactions by additives.

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Type
Review
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press
Figure 0

Fig. 1. Amphiphilic nature of DNA, cellulose and surfactants.

Figure 1

Fig. 2. Schematic representation of the cavity formation and water structuring. Adapted from Kronberg (2016) with permission of Elsevier.

Figure 2

Fig. 3. Surfactant binding to polymers. For the binding of ionic surfactant to an oppositely charged polymer with some hydrophobic character, there is a two-step binding, involving electrostatic and hydrophobic interactions. Important features are phase separation and redissolution. The redissolution is related to surfactant binding over charge stoichiometry, thus to a charge reversal of the polymer−surfactant complex. The simple (one-step) cooperative binding behaviour shown in the inset is characteristic for surfactant binding to non-ionic polymers and ionic surfactant binding to oppositely charged polymers without hydrophobic character. Adapted from Svensson et al. (2009) with permission of ACS.

Figure 3

Fig. 4. Typical structures formed in mixed systems of a polyelectrolyte and an oppositely charged surfactant. Adapted from Krivtsov et al. (2012) with permission of ACS.

Figure 4

Fig. 5. Intensity weighted distribution functions of 0.5 μM T2DNA solution in the absence (upper curve) and the presence of CTAB. The concentrations of the cationic surfactant are from top to bottom: 0 (only DNA), 1.0, 2.0, 4.0, 6.0, 10.0, and 30.0 μM. Scattering angle (θ) = 90° and T = 27°C. Adapted from Dias et al. (2005) with permission of ACS.

Figure 5

Fig. 6. Visually determined phase map of the DNA−CTAB system presented as a function of (a) CTAB concentration and (b) CTAB:DNA molar ratio, in terms of charges, at four different DNA concentrations (in nucleotides, indicated to the right). Open circles correspond to clear solutions whereas filled circles correspond to turbid or macroscopically phase-separated samples. Adapted from Carlstedt et al. (2012) with permission of ACS.

Figure 6

Fig. 7. Dynamic light scattering (RH app) and electrophoretic mobility (μe) data for aqueous mixtures of DNA and CTAB, with a constant DNA concentration of 120 μM in nucleotides (40 μg ml−1) and varying CTAB concentration. Adapted from Carlstedt et al. (2012) with permission of ACS.

Figure 7

Fig. 8. Illustrations of (a) an NCP, (b) the core histones, and (c) the nucleosome array. (a) Two projections of the NCP where DNA is shown as a surface with electrostatic potential (positive in red and negative in blue) and the histone octamer with schematic secondary structure (each of the eight histones is coloured differently). Approximate dimensions of the NCP are indicated. The core histones shown in panel b illustrate the folded domains of each histone shown with the surface coloured according to its electrostatic potential (positive in blue) and hydrophobicity (orange). In panel c, a nucleosome array comprising 12 nucleosomes formed by the wrapping of 147 bp DNA around the histone octamer, is schematically shown. DNA is red and the histone octamer core light grey with histone tails in blue. Reproduced from Berezhnoy et al. (2012) with permission from ACS.

Figure 8

Fig. 9. Structure of melittin-double-stranded DNA (dsDNA) three-dimensional (3D) tetragonal lattice from molecular simulations verified by X-ray diffraction. View of a melittin-dsDNA square lattice. Columnar dsDNA is coloured red, and the melittin protofibril is coloured green (N to C terminus polarity) and teal (C to N terminus polarity). Reproduced from Lee et al. (2019) with permission from Nature.

Figure 9

Fig. 10. Left: Effective charge of cellobiose as a function of the pH of the solution either using KOH (filled circles) or NaOH (empty circles). Right: Cellulose configurations in the last frame of a 1 μs simulation for (a) neutral and (b) deprotonated cellodecaose. Taken from Bialik et al. (2016) with permission of ACS.

Figure 10

Fig. 11. Schematic representation of glucose-based oligomers with different degrees of polymerization.

Figure 11

Fig. 12. The nuclear frame of a cellobiose residue. The centres of gravity of the atoms of the ring are distributed over two parallel planes. The hydrophobic H atoms are above and below these planes and laterally there are the hydrophilic OH groups. Taken from Hermans (1949) with the permission of John Wiley and Sons, Inc.

Figure 12

Fig. 13. Cryo-transmission electronic microscopy (cryo-TEM) images of 0.5 wt % MCC dissolved in (a) 8 wt % NaOH(aq.) solution and (b) in 8 wt % NaOH(aq.)/12 wt % urea system. Scale bars correspond to 100 nm.

Figure 13

Fig. 14. Elastic modulus, G′ (filled symbols), and viscous modulus, G′′ (open symbols) as a function of temperature for 3.5 wt% microcrystalline cellulose samples dissolved in a 10 wt% NaOH/H2O solvent system: (a), without cocamidopropylbetaine and (b) with cocamidopropylbetaine. Constant heating rate of 1°C min−1 at 0.5 Hz. The temperature of gelation (G′ = G′′) is increased by ca. 10°C in the presence of the amphiphilic additive. The vertical dashed grey line indicates the transition region. Taken from Medronho et al. (2015) with the permission of De Gruyter.

Figure 14

Fig. 15. Scanning electron microscopy images of the cellulose solutions after being deposited onto a glass lamella followed by solvent evaporation. Left: cellulose dissolved in 2 M NaOH aqueous solvent; right: cellulose dissolved in the 1.5 M TBAH aqueous solvent. The scale bar represents 5 μm. Adapted from Alves et al. (2015) with the permission of Elsevier.

Figure 15

Fig. 16. Solubility of cellulose in aqueous quaternary ammonium hydroxides as a function of the cation hydrophobicity. Adapted from Wang et al. (2018) with permission of the Royal Society of Chemistry.

Figure 16

Fig. 17. Synchrotron X-ray diffraction profiles of cellulose solution under regeneration by 5 wt% aq. Na2SO4, control: 10 wt% cellulose solution without coagulant; (a) measured at 2 mm away from the boundary with coagulant and 180 min after coagulant introduction; (b) 2.5 mm, 195 min; (c) 1.75 mm, 190 min; (d) 1.5 mm, 185 min; (e) 1.5 mm, 200 min; (f) 1.5 mm, 270 min, and complete regeneration: 1.5 mm, 1 week. q denotes the scattering vector (2π/d). Adapted from Isobe et al. (2012) with permission of Elsevier.

Figure 17

Fig. 18. Structure of 1-ethyl-3-methylimidazolium acetate.

Figure 18

Fig. 19. Representative cryo-SEM images [(a) secondary and (b) backscattered electron images] of the emulsions prepared with 1.0 wt.% cellulose previously dissolved in 8 wt.% NaOH/6 wt.% thiourea. In (b) the darker areas correspond to the oil domains (white arrows), while the water domains are lighter. The brightest areas correspond to cellulose (arrowheads). The black arrowhead in (a) points to the cellulose layer surrounding the oil that had been plucked away by the fracturing of the cryo-specimen. Taken from Costa et al. (2021) with permission of Elsevier.