Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

Eda Koculi, D. Thirumalai, Sarah A. Woodson

Research output: Contribution to journalArticle

Abstract

The self-assembly of RNA structure depends on the interactions of counterions with the RNA and with each other. Comparison of various polyamines showed that the tertiary structure of the Tetrahymena ribozyme is more stable when the counterions are small and highly charged. By monitoring the folding kinetics of the ribozyme as a function of polyamine concentration, we now find that the charge density of the counterions determines the positions of the folding transition states. The transition state ensemble (TSE) between U and N moves away from the native state as the counterion valence and charge density increase, as predicted by the Hammond postulate. The TSE is broader and less structured when the RNA is refolded in polyamines rather than Mg2+. That the charge density of the counterions determines the plasticity of the TSE demonstrates the importance of interactions among condensed counterions for the self-assembly of RNA structures. We propose that the major barrier to RNA folding is dominated by entropy changes when counterion charge density is low and enthalpy differences when it is high.

Original languageEnglish (US)
Pages (from-to)446-454
Number of pages9
JournalJournal of Molecular Biology
Volume359
Issue number2
DOIs
StatePublished - Jun 2 2006

Fingerprint

RNA Folding
Polyamines
Catalytic RNA
RNA
Tetrahymena
Entropy

Keywords

  • counterion condensation
  • group I intron
  • Hammond postulate
  • polyamines
  • RNA folding

ASJC Scopus subject areas

  • Virology

Cite this

Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States. / Koculi, Eda; Thirumalai, D.; Woodson, Sarah A.

In: Journal of Molecular Biology, Vol. 359, No. 2, 02.06.2006, p. 446-454.

Research output: Contribution to journalArticle

Koculi, Eda ; Thirumalai, D. ; Woodson, Sarah A. / Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States. In: Journal of Molecular Biology. 2006 ; Vol. 359, No. 2. pp. 446-454.
@article{fe47874e8a734915b1a97cc552652a78,
title = "Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States",
abstract = "The self-assembly of RNA structure depends on the interactions of counterions with the RNA and with each other. Comparison of various polyamines showed that the tertiary structure of the Tetrahymena ribozyme is more stable when the counterions are small and highly charged. By monitoring the folding kinetics of the ribozyme as a function of polyamine concentration, we now find that the charge density of the counterions determines the positions of the folding transition states. The transition state ensemble (TSE) between U and N moves away from the native state as the counterion valence and charge density increase, as predicted by the Hammond postulate. The TSE is broader and less structured when the RNA is refolded in polyamines rather than Mg2+. That the charge density of the counterions determines the plasticity of the TSE demonstrates the importance of interactions among condensed counterions for the self-assembly of RNA structures. We propose that the major barrier to RNA folding is dominated by entropy changes when counterion charge density is low and enthalpy differences when it is high.",
keywords = "counterion condensation, group I intron, Hammond postulate, polyamines, RNA folding",
author = "Eda Koculi and D. Thirumalai and Woodson, {Sarah A.}",
year = "2006",
month = "6",
day = "2",
doi = "10.1016/j.jmb.2006.03.031",
language = "English (US)",
volume = "359",
pages = "446--454",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "2",

}

TY - JOUR

T1 - Counterion Charge Density Determines the Position and Plasticity of RNA Folding Transition States

AU - Koculi, Eda

AU - Thirumalai, D.

AU - Woodson, Sarah A.

PY - 2006/6/2

Y1 - 2006/6/2

N2 - The self-assembly of RNA structure depends on the interactions of counterions with the RNA and with each other. Comparison of various polyamines showed that the tertiary structure of the Tetrahymena ribozyme is more stable when the counterions are small and highly charged. By monitoring the folding kinetics of the ribozyme as a function of polyamine concentration, we now find that the charge density of the counterions determines the positions of the folding transition states. The transition state ensemble (TSE) between U and N moves away from the native state as the counterion valence and charge density increase, as predicted by the Hammond postulate. The TSE is broader and less structured when the RNA is refolded in polyamines rather than Mg2+. That the charge density of the counterions determines the plasticity of the TSE demonstrates the importance of interactions among condensed counterions for the self-assembly of RNA structures. We propose that the major barrier to RNA folding is dominated by entropy changes when counterion charge density is low and enthalpy differences when it is high.

AB - The self-assembly of RNA structure depends on the interactions of counterions with the RNA and with each other. Comparison of various polyamines showed that the tertiary structure of the Tetrahymena ribozyme is more stable when the counterions are small and highly charged. By monitoring the folding kinetics of the ribozyme as a function of polyamine concentration, we now find that the charge density of the counterions determines the positions of the folding transition states. The transition state ensemble (TSE) between U and N moves away from the native state as the counterion valence and charge density increase, as predicted by the Hammond postulate. The TSE is broader and less structured when the RNA is refolded in polyamines rather than Mg2+. That the charge density of the counterions determines the plasticity of the TSE demonstrates the importance of interactions among condensed counterions for the self-assembly of RNA structures. We propose that the major barrier to RNA folding is dominated by entropy changes when counterion charge density is low and enthalpy differences when it is high.

KW - counterion condensation

KW - group I intron

KW - Hammond postulate

KW - polyamines

KW - RNA folding

UR - http://www.scopus.com/inward/record.url?scp=33646187932&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646187932&partnerID=8YFLogxK

U2 - 10.1016/j.jmb.2006.03.031

DO - 10.1016/j.jmb.2006.03.031

M3 - Article

C2 - 16626736

AN - SCOPUS:33646187932

VL - 359

SP - 446

EP - 454

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 2

ER -