Destabilization of i-motif by submolar concentrations of a monovalent cation

Sung Eun Kim, Il Buem Lee, Changbong Hyeon, Seok Cheol Hong

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li +-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li +. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs.

Original languageEnglish
Pages (from-to)4753-4760
Number of pages8
JournalJournal of Physical Chemistry B
Volume118
Issue number18
DOIs
Publication statusPublished - 2014 May 8

Fingerprint

Monovalent Cations
Cytosine
destabilization
Protons
Positive ions
Nucleic acids
nucleic acids
Ions
cations
folding
Nucleic Acids
Kinetics
protons
kinetics
ions
Self assembly
self assembly
Electrostatics
Hydrogen bonds
Screening

ASJC Scopus subject areas

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

Cite this

Destabilization of i-motif by submolar concentrations of a monovalent cation. / Kim, Sung Eun; Lee, Il Buem; Hyeon, Changbong; Hong, Seok Cheol.

In: Journal of Physical Chemistry B, Vol. 118, No. 18, 08.05.2014, p. 4753-4760.

Research output: Contribution to journalArticle

Kim, Sung Eun ; Lee, Il Buem ; Hyeon, Changbong ; Hong, Seok Cheol. / Destabilization of i-motif by submolar concentrations of a monovalent cation. In: Journal of Physical Chemistry B. 2014 ; Vol. 118, No. 18. pp. 4753-4760.
@article{cfed5086f32d476887acf54b0bf463b6,
title = "Destabilization of i-motif by submolar concentrations of a monovalent cation",
abstract = "Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li +-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li +. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs.",
author = "Kim, {Sung Eun} and Lee, {Il Buem} and Changbong Hyeon and Hong, {Seok Cheol}",
year = "2014",
month = "5",
day = "8",
doi = "10.1021/jp500120d",
language = "English",
volume = "118",
pages = "4753--4760",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "18",

}

TY - JOUR

T1 - Destabilization of i-motif by submolar concentrations of a monovalent cation

AU - Kim, Sung Eun

AU - Lee, Il Buem

AU - Hyeon, Changbong

AU - Hong, Seok Cheol

PY - 2014/5/8

Y1 - 2014/5/8

N2 - Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li +-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li +. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs.

AB - Counterions are crucial for self-assembly of nucleic acids. Submolar monovalent cations are generally deemed to stabilize various types of base pairs in nucleic acids such as Watson-Crick and Hoogsteen base pairs via screening of electrostatic repulsion. Besides monovalent cations, acidic pH is required for i-motif formation because protons facilitate pairing between cytosines. Here we report that Li+ ions destabilize i-motif, whereas other monovalent cations, Na+ and K+, have the usual stabilizing effect. The thermodynamics data alone, however, cannot reveal which mechanism, enhanced unfolding or suppressed folding or both, is responsible for the Li +-induced destabilization. To gain further insight, we examined the kinetics of i-motif. To deal with slow kinetics of i-motif, we developed a method dubbed HaRP to construct a long FRET time trace to observe a sufficient number of transitions. Our kinetics analysis shows clearly that Li+ ions promote unfolding of i-motif but do not hinder its folding, lending strong support for our hypothesis on the origin of this unusual effect of Li +. Although the subangstrom size of Li+ ions allows them to infiltrate the space between cytosines in competition with protons, they cannot adequately fulfill the role of protons in mediating the hydrogen bonding of cytosine pairs.

UR - http://www.scopus.com/inward/record.url?scp=84900326986&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84900326986&partnerID=8YFLogxK

U2 - 10.1021/jp500120d

DO - 10.1021/jp500120d

M3 - Article

VL - 118

SP - 4753

EP - 4760

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 18

ER -