Molecular Biology Reports

, Volume 45, Issue 4, pp 403–411 | Cite as

Thermal stability and conformation of DNA and proteins under the confined condition in the matrix of hydrogels

  • Shu-ichi Nakano
  • Daisuke Yamaguchi
  • Naoki Sugimoto
Original Article


Spatially confined environments are seen in biological systems and in the fields of biotechnology and nanotechnology. The confinement restricts the conformational space of polymeric molecules and increasing the degree of molecular crowding. Here, we developed preparation methods for agarose and polyacrylamide gels applicable to UV spectroscopy that can evaluate the confinement effects on DNA and protein structures. Measurements of UV absorbance and CD spectra showed no significant effect of the confinement in the porous media of agarose gels on the base-pair stability of DNA polynucleotides [poly(dA)/poly(dT)] and oligonucleotides (hairpin, duplex, and triplex structures). On the other hand, a highly confined environment created by polyacrylamide gels at high concentrations increased the stability of polynucleotides while leaving that of oligonucleotides unaffected. The changes in the base-pair stability of the polynucleotides were accompanied by the perturbation of the helical conformation. The polyacrylamide gels prepared in this study were also used for the studies on proteins (lysozyme, bovine serum albumin, and myoglobin). The effects on the proteins were different from the effects on DNA structures, suggesting different nature of interactions within the gel. The experimental methods and results are useful to understand the physical properties of nucleic acids and proteins under confined conditions.


DNA polynucleotide Oligonucleotide Melting temperature Agarose gel Polyacrylamide gel Molecular crowding 



We thank Junpei Ueno for technical assistance. This work was supported in part by Grants-in-Aid for Scientific Research, Japan Society for the Promotion of Science (JSPS KAKENHI Grant No. 24550200) and the Ministry of Education, Culture, Sports, Science and Technology (MEXT)-Supported Program for the Strategic Research Foundation at Private Universities, 2009–2014, Japan.


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© Springer Science+Business Media B.V., part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)Konan UniversityKobeJapan
  2. 2.Frontier Institute for Biomolecular Engineering Research (FIBER)Konan UniversityKobeJapan

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