Journal of Polymer and Biopolymer Physics Chemistry
ISSN (Print): 2373-3403 ISSN (Online): 2373-3411 Website: http://www.sciepub.com/journal/jpbpc Editor-in-chief: Martin Alberto Masuelli
Open Access
Journal Browser
Go
Journal of Polymer and Biopolymer Physics Chemistry. 2021, 9(1), 13-19
DOI: 10.12691/jpbpc-9-1-2
Open AccessReview Article

Molecular Origin for Strong Agarose Gels: Multi-Stranded Hydrogen Bonding

Masakuni Tako1, , Takeshi Teruya1, 2, Yukihioro Tamaki1, 3, Keiko Uechi1 and Teruko Konishi1

1Department of Subtropical Bioscience and Biotechnology, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan

2TaKaRa Bio Inc., 7-4-38 Nojihigashi, Kusatsu, Shiga 525-0058, Japan

3Molecular Bioscience Research Center, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan

Pub. Date: May 14, 2021

Cite this paper:
Masakuni Tako, Takeshi Teruya, Yukihioro Tamaki, Keiko Uechi and Teruko Konishi. Molecular Origin for Strong Agarose Gels: Multi-Stranded Hydrogen Bonding. Journal of Polymer and Biopolymer Physics Chemistry. 2021; 9(1):13-19. doi: 10.12691/jpbpc-9-1-2

Abstract

Agarose gels are currently used in separation, purification, and characterization of DNA, RNA, proteins, and polysaccharides in gel electrophoresis, gel filtration, affinity chromatography, and ion chromatography techniques. Specifically, it is used in PCR (Polymerase Chain Reaction) test. Although, double stranded intermolecular hydrogen bonding between OH-2 and 3,6-ring oxygen atoms of 1,4-linked anhydro-α-L-galactopyranose residues on different molecules take place, triple- or multi-stranded secondary association occur with increasing concentration. The multi-stranded gelation mechanism of agarose molecules is the first to report. The associated agarose molecules play a dominant role in the centre of tetrahedral cavities that are occupied by ice-like hydrogen bonded water molecules which are caused thermodynamically by cage and hydrophobic effects. Many investigations the gelling properties of the polysaccharides have been undertaken to elucidate the structure-function relationship, but no other researchers have established the mechanisms at the molecular level including water molecules. There are structural and theoretical consistencies in our investigation. This paper provides important information not only academia, but also to industrial fields, such as bio-physicochemical analysis, food, cosmetics, agriculture, pharmaceuticals, drug delivery, drug storage, tissue engineering, and biotechnology.

Keywords:
agarose multi-stranded hydrogen bonding gelation mechanism principles biotechnology

Creative CommonsThis work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Figures

Figure of 5

References:

[1]  Witzler, M., Ottensmeyer, P. F., Gericke, M., Heinze, T., Tobiasch, E. and Schulze, M. Non-cytotoxic agarose/hydroxyapatite composite scaffolds for drug release. Int. J. Mol. Sci., 2019, 20 (14), 3565-3583.
 
[2]  Stefani, R.M., Lee, A. J., Tan, A.R., Halder, S.S., Hu, Y., Guo, X.E., Stoker, A.M., Ateshian, G. A., Marra, K. G. and Hung, J.C.T. Sustained low-dose dexamethasone delivery via a PLGA microsphere-embedded agarose implant for enhanced osteochondral repair. Acta Biomaterialia, 2020, 102 (1), 326-340.
 
[3]  Zarrintaj, P., Manouchehri, S., Ahmadi, Z., Saeb, M.R., Urabanska, A.M., Kaplan, D. L. and Mozafari, M. Agarose based biomaterials for tissue engineering. Carbohydr. Polym. 2018, 187 (1), 66-84.
 
[4]  Tako, M. and Nakamura, S. Indicative evidence for a conformational transition in κ-carrageenan from studies of viscosity-shear rate dependence. Carbohydr. Res. 1986, 155 (1), 200-205.
 
[5]  Tako, M.; and Nakamura, S. Synergistic interaction between κ-carrageenan and locust bean gum in aqueous media. Agric. Biol. Chem., 1986, 50 (11), 2817-2822.
 
[6]  Tako, M., Nakamura, S. and Kohda, Y. Indicative evidence for a conformational transition in ι-carrageenan. Carbohydr. Res., 1987, 161 (2), 247-255.
 
[7]  Tako, M. and Nakamura, S. Gelation mechanism of agarose. Carbohydr. Res. 1988, 180 (2), 277-284.
 
[8]  Tako, M., Sakae, A. and Nakamura, S. Rheological properties of gellan gum in aqueous media. Agric. Biol Chem. 1989, 53 (3), 771-776.
 
[9]  Tako, M., Teruya, T., Tamaki, Y. and Konishi, T. Molecular origin for rheological characteristics of native gellan gum. Colloid Polym. Sci. 2009, 287 (9), 1445-1454.
 
[10]  Tako M. and Hizukuri, S. Evidence for conformational transition in amylose, J. Carbohydr. Chem. 1995, 14 (4-5), 613-622.
 
[11]  Tamaki, Y., Konishi, T. and Tako, M. Gelation and retrogradation mechanism of wheat amylose. Materials, 2011, 4 (10), 1763-1775.
 
[12]  Tako, M. and Hanashiro, I. Evidence for a conformational transition in curdlan. Polym. Gels Networks, 1997, 5 (2), 241-250.
 
[13]  Tako, M. and Kohda, Y. Calcium induced association characteristics of alginate. J. Appl. Glycosci., 1997, 44 (2), 153-159.
 
[14]  Teruya, T., Tamaki, Y., Konishi, T. and Tako, M. Rheological characteristics of alginate isolated from commercially cultured Nemacystus decipiens (Itomozuku). J. Appl. Glycosci., 2010, 57 (1), 7-12.
 
[15]  Tako, M., Tohma, S., Taira, T. and Ishihara, M. Gelation mechanism of deacetylated rhamsan gum. Carbohydr. Polym. 2003, 54 (3), 279-285.
 
[16]  Tako, M., Nagahama, T. and Nomura, D. Non-Newtonian flow and dynamic viscoelasticity of xanthan gum., Nippon Nogeikagaku Kaishi., 1977, 51 (8), 513-518.(in Japanese).
 
[17]  Tako, M. and Nakamur, S. Rheological properties of deacetylated xanthan gum in aqueous media, Agric. Biol. Chem., 1984, 48 (12), 2987-2993.
 
[18]  Tako, M. Molecular origin for rheological characteristics of xanthan gum. ACS Symp. Ser,, 1992, 489, 268-281.
 
[19]  Tako, M., Asato, A. and Nakamura, S. Rheological aspect of the intermolecular interaction between xanthan gum and locust bean gum in aqueous media, Agric. Biol. Chem., 1984, 48 (12), 2995-3000.
 
[20]  Tako, M. and Nakamura, S. Synergistic interaction between xanthan and guar gum. Carbohydr. Res. 1985, 138 (1), 207-213.
 
[21]  Tako, M. and Nakamura, S. Synergistic interaction between xanthan and D-galacto-D-mannan. FEBS Lett. 1986, 204 (1), 33-36. (Special issue at 17th FEBS Meeting, August 24-26, 1986, West Berlin, West Germany).
 
[22]  Tako, M. Synergistic interaction between xanthan and tara-bean gum. Carbohydr. Polym., 1991, 15 (3), 227-239.
 
[23]  Tako, M. Binding sites for D-mannose-specific interaction between xanthan and galactomannan, and glucomannan. Colloid Sur. B Biointerface, 1993, 1 (2), 125-131.
 
[24]  Tako, M., Teruya, T., Tamaki, Y. and Ohkawa, K. Co-gelation mechanism of xanthan and galactomannan. Colloid Polym. Sci., 2010, 288 (10-11), 1161-1166.
 
[25]  Tako, M. Synergistic interaction between xanthan and konjac glucomannan in aqueous media. Biosci. Biotechnol. Biochem., 1992, 56 (8), 1188-1192.
 
[26]  Tako, M. and Hizukuri, S. Gelatinization mechanism of rice starch. J. Carbohydr. Chem., 1999, 18 (5), 573-584.
 
[27]  Tako, M. and Hizukuri, S. Retrogradation mechanism of rice starch. Cereal Chem., 2000, 77 (4), 473-477.
 
[28]  Tako, M. and Hizukuri, S. Gelatinization mechanism of potato starch. Carbohydr. Polym., 2002, 48 (4), 397-401.
 
[29]  Tako, M., Tamaki, Y., Konishi, T., Shibanuma, K., Hanashiro, I. and Takeda, Y. Gelatinization and retrogradation characteristics of wheat (Rosella) starch, Food. Res. Int., 2008, 41 (8), 797-802.
 
[30]  Tako, M. Molecular origin for thermal stability of schizopyllan. Polym. Gels Network., 1996, 4 (4), 303-313.
 
[31]  Tako, M. and Hizukuri, S. Molecular origin for thermal stability of rice amylopectin. J. Carbohydr. Chem., 1997, 16 (4-5), 655-666.
 
[32]  Tako M. Molecular origin for thermal stability of waxy-rice (Kogane) starch. Starch. 1996, 48 (11-12), 414-417.
 
[33]  Tako, M. and Hizukuri, S. Molecular origin for thermal stability of Koshihikari rice amylopectin. Food Res. Int., 2000, 33 (1), 35-40.
 
[34]  Rees, D. A. Shapely polysaccharides. Biochem. J. 1972, 126, 257-273.
 
[35]  Tako, M., Qi, Z. Q. and Toyama, S. Synergistic interaction between κ-carrageenan isolated from Hypnea charoides and galactomannan on its gelation, Food Res. Int., 1998, 31 (8), 543-548.
 
[36]  Arnott, S., Scott, W. E., Rees, D. A. and McNab, C. G. A. ι-Carrageenan: Molecular structure and packing of polysaccharide double helices in oriented fibres of divalent cation salts. J. Mol. Biol., 1974, 90 (2), 253-267.
 
[37]  Morris, E. R., Rees, D. A. and Robinson, G. Cation-specific aggregation of carrageenan helices: Domain model of polymer gel structure. J. Mol. Biol., 1980, 138 (2), 349-362.
 
[38]  Arnott, S., Fulmer, A., Scott, W. E., Dea, I. C. M., Moorhouse, R.; and Rees, D.A. The agarose double helix and its function in agarose gel structure. J. Mol. Biol., 1974, 90 (2), 269-272.
 
[39]  Mohammed, Z. H., Hember, M. W. N., Richardson, R. K. and Morris, E. R. Kinetic and equilibrium processes in the formation and melting of agarose gels. Carbohydr. Polym., 1998, 36 (1), 15-26.
 
[40]  Tako, M., Higa, M., Medoruma, K. and Nakasone, Y. A highly methylated agar from red seaweed, Gracilaria arcuate, Botanica Marina, 1999, 42 (5), 513-517.
 
[41]  Tako, M. and Konishi, T. Discovery of κ-carrageenan-like agarose from red seaweed, Gracilaria coronopifolia. Int. Res. J. Pure Appl. Chem., 2018, 17 (2), 1-11.
 
[42]  Gamini, A., Toffanin, R., Murano, E. and Rizzo, R. Hydrogen bonding and conformation of agarose in methyl sulfoxide and aqueous solutions investigated by 1H- and 13C NMR spectroscopy. Carbohydr. Res. 1997, 304 (3-4), 293-302.
 
[43]  Tako, M. Structural principles of polysaccharide gels, J. Appl. Glycosci. 2000, 47 (1), 49-53.
 
[44]  Tako, M., Tamaki, Y., Teruya, T. and Takeda, Y. The principles of starch gelatinization and retrogradation, Food Nutr. Sci. 2014, 5 (3), 280-291.
 
[45]  Tako, M. The principle of polysaccharide gels. Adv. Biosci. Biotechnol. 2015, 6 (1), 22-35.