Competition between polysaccharide/polynucleotide complexation vs., polynucleotide hybridization; salt concentration dependence of the reaction direction

Ryouji Karinaga, Kazuya Koumoto, Jusaku Minari, Masami Mizu, Takahisa Anada, Kazuo Sakurai, Seiji Shinkai

Research output: Contribution to journalArticle

Abstract

Schizophyllan is a natural β-(1→3)-D-glucan existing as a triple helix in water and as a single chain in dimethylsulfoxide (DMSO), respectively. As we already reported, when a homo-polynucleotide [ex. poly (A) or poly(dA)] was added to the schizophyllan/DMSO solution and subsequently DMSO was exchanged for water, the single chain of schizophyllan formed a complex with the polynucleotide. In this paper, using an adenine-thymine (or uracil) double strand as a model system, we explored whether s-SPG can unzip the polynucleotide duplexes, examining the competition between the schizophyllan/polynucleotide complexation and the polynucleotide hybridization with circular dichroism and fluorescence spectroscopy at various NaCl concentrations. The unzipping reaction happened for the hetero-duplexes (i.e., RNA-DNA duplexes) at low salt concentrations, on the other hand, it was not observed for the homo-duplexes at all the salt concentrations. When we compared dissociation temperatures, the unzipping reaction of the homo-duplexes was expected at low salt concentrations. This discrepancy between the experimental results and the expectation, as well as the different behavior between the hetero- and homo- duplexes, can be ascribed to the difference in the activation energy of intermediate states.

Original languageEnglish
Pages (from-to)38-45
Number of pages8
Journale-Journal of Surface Science and Nanotechnology
Volume3
DOIs
Publication statusPublished - Feb 7 2005

Fingerprint

polynucleotides
Sizofiran
Polynucleotides
polysaccharides
Polysaccharides
Complexation
Salts
salts
Dimethyl Sulfoxide
Circular dichroism spectroscopy
Poly A
uracil
Thymine
Uracil
thymine
Water
Fluorescence Spectrometry
adenines
Fluorescence spectroscopy
Adenine

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Condensed Matter Physics
  • Mechanics of Materials
  • Surfaces and Interfaces
  • Surfaces, Coatings and Films

Cite this

Competition between polysaccharide/polynucleotide complexation vs., polynucleotide hybridization; salt concentration dependence of the reaction direction. / Karinaga, Ryouji; Koumoto, Kazuya; Minari, Jusaku; Mizu, Masami; Anada, Takahisa; Sakurai, Kazuo; Shinkai, Seiji.

In: e-Journal of Surface Science and Nanotechnology, Vol. 3, 07.02.2005, p. 38-45.

Research output: Contribution to journalArticle

@article{e534064cbfab4b89877adc2c5dcbd2d2,
title = "Competition between polysaccharide/polynucleotide complexation vs., polynucleotide hybridization; salt concentration dependence of the reaction direction",
abstract = "Schizophyllan is a natural β-(1→3)-D-glucan existing as a triple helix in water and as a single chain in dimethylsulfoxide (DMSO), respectively. As we already reported, when a homo-polynucleotide [ex. poly (A) or poly(dA)] was added to the schizophyllan/DMSO solution and subsequently DMSO was exchanged for water, the single chain of schizophyllan formed a complex with the polynucleotide. In this paper, using an adenine-thymine (or uracil) double strand as a model system, we explored whether s-SPG can unzip the polynucleotide duplexes, examining the competition between the schizophyllan/polynucleotide complexation and the polynucleotide hybridization with circular dichroism and fluorescence spectroscopy at various NaCl concentrations. The unzipping reaction happened for the hetero-duplexes (i.e., RNA-DNA duplexes) at low salt concentrations, on the other hand, it was not observed for the homo-duplexes at all the salt concentrations. When we compared dissociation temperatures, the unzipping reaction of the homo-duplexes was expected at low salt concentrations. This discrepancy between the experimental results and the expectation, as well as the different behavior between the hetero- and homo- duplexes, can be ascribed to the difference in the activation energy of intermediate states.",
author = "Ryouji Karinaga and Kazuya Koumoto and Jusaku Minari and Masami Mizu and Takahisa Anada and Kazuo Sakurai and Seiji Shinkai",
year = "2005",
month = "2",
day = "7",
doi = "10.1380/ejssnt.2005.38",
language = "English",
volume = "3",
pages = "38--45",
journal = "e-Journal of Surface Science and Nanotechnology",
issn = "1348-0391",
publisher = "Surface Science Society of Japan",

}

TY - JOUR

T1 - Competition between polysaccharide/polynucleotide complexation vs., polynucleotide hybridization; salt concentration dependence of the reaction direction

AU - Karinaga, Ryouji

AU - Koumoto, Kazuya

AU - Minari, Jusaku

AU - Mizu, Masami

AU - Anada, Takahisa

AU - Sakurai, Kazuo

AU - Shinkai, Seiji

PY - 2005/2/7

Y1 - 2005/2/7

N2 - Schizophyllan is a natural β-(1→3)-D-glucan existing as a triple helix in water and as a single chain in dimethylsulfoxide (DMSO), respectively. As we already reported, when a homo-polynucleotide [ex. poly (A) or poly(dA)] was added to the schizophyllan/DMSO solution and subsequently DMSO was exchanged for water, the single chain of schizophyllan formed a complex with the polynucleotide. In this paper, using an adenine-thymine (or uracil) double strand as a model system, we explored whether s-SPG can unzip the polynucleotide duplexes, examining the competition between the schizophyllan/polynucleotide complexation and the polynucleotide hybridization with circular dichroism and fluorescence spectroscopy at various NaCl concentrations. The unzipping reaction happened for the hetero-duplexes (i.e., RNA-DNA duplexes) at low salt concentrations, on the other hand, it was not observed for the homo-duplexes at all the salt concentrations. When we compared dissociation temperatures, the unzipping reaction of the homo-duplexes was expected at low salt concentrations. This discrepancy between the experimental results and the expectation, as well as the different behavior between the hetero- and homo- duplexes, can be ascribed to the difference in the activation energy of intermediate states.

AB - Schizophyllan is a natural β-(1→3)-D-glucan existing as a triple helix in water and as a single chain in dimethylsulfoxide (DMSO), respectively. As we already reported, when a homo-polynucleotide [ex. poly (A) or poly(dA)] was added to the schizophyllan/DMSO solution and subsequently DMSO was exchanged for water, the single chain of schizophyllan formed a complex with the polynucleotide. In this paper, using an adenine-thymine (or uracil) double strand as a model system, we explored whether s-SPG can unzip the polynucleotide duplexes, examining the competition between the schizophyllan/polynucleotide complexation and the polynucleotide hybridization with circular dichroism and fluorescence spectroscopy at various NaCl concentrations. The unzipping reaction happened for the hetero-duplexes (i.e., RNA-DNA duplexes) at low salt concentrations, on the other hand, it was not observed for the homo-duplexes at all the salt concentrations. When we compared dissociation temperatures, the unzipping reaction of the homo-duplexes was expected at low salt concentrations. This discrepancy between the experimental results and the expectation, as well as the different behavior between the hetero- and homo- duplexes, can be ascribed to the difference in the activation energy of intermediate states.

UR - http://www.scopus.com/inward/record.url?scp=18444418025&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=18444418025&partnerID=8YFLogxK

U2 - 10.1380/ejssnt.2005.38

DO - 10.1380/ejssnt.2005.38

M3 - Article

AN - SCOPUS:18444418025

VL - 3

SP - 38

EP - 45

JO - e-Journal of Surface Science and Nanotechnology

JF - e-Journal of Surface Science and Nanotechnology

SN - 1348-0391

ER -