Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex

Naoko Makita, Yuko Yoshikawa, Yoshiko Takenaka, Takahiro Sakaue, Mari Suzuki, Chika Watanabe, Tamotsu Kanai, Toshio Kanbe, Tadayuki Imanaka, Kenichi Yoshikawa

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Abstract

We observed single DNA molecules by fluorescence microscopy to clarify the effect of protamine on their higher-order structure. With an increase in the protamine concentration, the conformation of DNA molecules changes from an elongated coil state to a compact state through an intermediate state. Furthermore, the long-axis length of DNA gradually decreases while maintaining a distribution profile with a single peak. Such behavior is markedly different from the conformational transition of DNA induced by small polyamines such as spermidine and spermine, where individual DNA molecules exhibit an all-or-none transition from a coil to a globule state and the size distribution is characterized by twin peaks around the transition region. Next, we examined the effect of salt on the conformation of the DNA-protamine complex. Interestingly, at a fixed concentration of protamine, DNA tends to shrink with an increase in the NaCl concentration up to 300 mM, and then swells with a further increase in the NaCl concentration, that is, biphasic behavior is generated depending on the salt concentration. For comparison, we examined the effect of salt on DNA compaction induced by the trivalent polyamine spermidine. We confirmed that salt always has an inhibitory effect on spermine-induced compaction. To clarify this biphasic effect of salt on protamine-induced DNA compaction, we performed a numerical simulation on a negatively charged semiflexible polyelectrolyte in the presence of polycations with relatively large numbers of positive charges by taking into account the effect of salt at different concentrations. The results showed that salt promotes compaction up to a certain concentration and then tends to unfold the polyelectrolyte chain, which reproduced the experimental observation in a semiquantitative manner. This biphasic effect is discussed in relation to the specific shielding effect that depends on the salt concentration.

Original languageEnglish
Pages (from-to)4453-4459
Number of pages7
JournalJournal of Physical Chemistry B
Volume115
Issue number15
DOIs
Publication statusPublished - Apr 21 2011

Fingerprint

Protamines
DNA
deoxyribonucleic acid
Salts
salts
Compaction
Nucleic Acid Conformation
Spermidine
Spermine
Polyamines
Polyelectrolytes
Molecules
Conformations
coils
molecules
globules
Fluorescence microscopy
Fluorescence Microscopy
Shielding
shielding

All Science Journal Classification (ASJC) codes

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Makita, N., Yoshikawa, Y., Takenaka, Y., Sakaue, T., Suzuki, M., Watanabe, C., ... Yoshikawa, K. (2011). Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex. Journal of Physical Chemistry B, 115(15), 4453-4459. https://doi.org/10.1021/jp111331q

Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex. / Makita, Naoko; Yoshikawa, Yuko; Takenaka, Yoshiko; Sakaue, Takahiro; Suzuki, Mari; Watanabe, Chika; Kanai, Tamotsu; Kanbe, Toshio; Imanaka, Tadayuki; Yoshikawa, Kenichi.

In: Journal of Physical Chemistry B, Vol. 115, No. 15, 21.04.2011, p. 4453-4459.

Research output: Contribution to journalArticle

Makita, N, Yoshikawa, Y, Takenaka, Y, Sakaue, T, Suzuki, M, Watanabe, C, Kanai, T, Kanbe, T, Imanaka, T & Yoshikawa, K 2011, 'Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex', Journal of Physical Chemistry B, vol. 115, no. 15, pp. 4453-4459. https://doi.org/10.1021/jp111331q
Makita N, Yoshikawa Y, Takenaka Y, Sakaue T, Suzuki M, Watanabe C et al. Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex. Journal of Physical Chemistry B. 2011 Apr 21;115(15):4453-4459. https://doi.org/10.1021/jp111331q
Makita, Naoko ; Yoshikawa, Yuko ; Takenaka, Yoshiko ; Sakaue, Takahiro ; Suzuki, Mari ; Watanabe, Chika ; Kanai, Tamotsu ; Kanbe, Toshio ; Imanaka, Tadayuki ; Yoshikawa, Kenichi. / Salt has a biphasic effect on the higher-order structure of a DNA-protamine complex. In: Journal of Physical Chemistry B. 2011 ; Vol. 115, No. 15. pp. 4453-4459.
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