Toward a digital gene response

RNA G-quadruplexes with fewer quartets fold with higher cooperativity

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

Changes in RNA conformation can alter gene expression. The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K + ions. Changes in the conformation of this motif could be especially important in regulating gene expression in plants because intracellular K + concentrations often increase during drought stress. Little is known about the folding thermodynamics of RNA GQS. We show here that RNA GQS with tracts containing three G's [e.g., (GGGxx) 4] have a modest dependence on the K + concentration, folding with no or even negative cooperativity (Hill coefficients ≤1), and are associated with populated folding intermediates. In contrast, GQS with tracts containing just two G's [e.g., (GGxx) 4] have a steep dependence on the K + concentration and fold with positive cooperativity (Hill coefficients of 1.7-2.7) without significantly populating intermediate states. We postulate that in plants, the more stable G3 sequences are largely folded even under unstressed conditions, while the less stable G2 sequences fold only at the higher K + concentrations associated with cellular stress, wherein they respond sharply to changing K + concentrations. Given the binary nature of their folding, G2 sequences may find application in computation with DNA and in engineering of genetic circuits.

Original languageEnglish (US)
Pages (from-to)812-815
Number of pages4
JournalJournal of the American Chemical Society
Volume134
Issue number2
DOIs
StatePublished - Jan 18 2012

Fingerprint

G-Quadruplexes
Guanine
RNA
Genes
Gene expression
Conformations
Molecular Computers
RNA Folding
Nucleic Acid Conformation
Gene Expression
Nucleotide Motifs
Genetic Engineering
Drought
Droughts
Thermodynamics
DNA
Ions
Networks (circuits)

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Chemistry(all)
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

@article{e3f804cdb97b4699ad18edd08aba03f5,
title = "Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity",
abstract = "Changes in RNA conformation can alter gene expression. The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K + ions. Changes in the conformation of this motif could be especially important in regulating gene expression in plants because intracellular K + concentrations often increase during drought stress. Little is known about the folding thermodynamics of RNA GQS. We show here that RNA GQS with tracts containing three G's [e.g., (GGGxx) 4] have a modest dependence on the K + concentration, folding with no or even negative cooperativity (Hill coefficients ≤1), and are associated with populated folding intermediates. In contrast, GQS with tracts containing just two G's [e.g., (GGxx) 4] have a steep dependence on the K + concentration and fold with positive cooperativity (Hill coefficients of 1.7-2.7) without significantly populating intermediate states. We postulate that in plants, the more stable G3 sequences are largely folded even under unstressed conditions, while the less stable G2 sequences fold only at the higher K + concentrations associated with cellular stress, wherein they respond sharply to changing K + concentrations. Given the binary nature of their folding, G2 sequences may find application in computation with DNA and in engineering of genetic circuits.",
author = "Mullen, {Melissa A.} and Assmann, {Sarah Mary} and Bevilacqua, {Philip C.}",
year = "2012",
month = "1",
day = "18",
doi = "10.1021/ja2096255",
language = "English (US)",
volume = "134",
pages = "812--815",
journal = "Journal of the American Chemical Society",
issn = "0002-7863",
publisher = "American Chemical Society",
number = "2",

}

TY - JOUR

T1 - Toward a digital gene response

T2 - RNA G-quadruplexes with fewer quartets fold with higher cooperativity

AU - Mullen, Melissa A.

AU - Assmann, Sarah Mary

AU - Bevilacqua, Philip C.

PY - 2012/1/18

Y1 - 2012/1/18

N2 - Changes in RNA conformation can alter gene expression. The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K + ions. Changes in the conformation of this motif could be especially important in regulating gene expression in plants because intracellular K + concentrations often increase during drought stress. Little is known about the folding thermodynamics of RNA GQS. We show here that RNA GQS with tracts containing three G's [e.g., (GGGxx) 4] have a modest dependence on the K + concentration, folding with no or even negative cooperativity (Hill coefficients ≤1), and are associated with populated folding intermediates. In contrast, GQS with tracts containing just two G's [e.g., (GGxx) 4] have a steep dependence on the K + concentration and fold with positive cooperativity (Hill coefficients of 1.7-2.7) without significantly populating intermediate states. We postulate that in plants, the more stable G3 sequences are largely folded even under unstressed conditions, while the less stable G2 sequences fold only at the higher K + concentrations associated with cellular stress, wherein they respond sharply to changing K + concentrations. Given the binary nature of their folding, G2 sequences may find application in computation with DNA and in engineering of genetic circuits.

AB - Changes in RNA conformation can alter gene expression. The guanine quadruplex sequence (GQS) is an RNA motif that folds in the presence of K + ions. Changes in the conformation of this motif could be especially important in regulating gene expression in plants because intracellular K + concentrations often increase during drought stress. Little is known about the folding thermodynamics of RNA GQS. We show here that RNA GQS with tracts containing three G's [e.g., (GGGxx) 4] have a modest dependence on the K + concentration, folding with no or even negative cooperativity (Hill coefficients ≤1), and are associated with populated folding intermediates. In contrast, GQS with tracts containing just two G's [e.g., (GGxx) 4] have a steep dependence on the K + concentration and fold with positive cooperativity (Hill coefficients of 1.7-2.7) without significantly populating intermediate states. We postulate that in plants, the more stable G3 sequences are largely folded even under unstressed conditions, while the less stable G2 sequences fold only at the higher K + concentrations associated with cellular stress, wherein they respond sharply to changing K + concentrations. Given the binary nature of their folding, G2 sequences may find application in computation with DNA and in engineering of genetic circuits.

UR - http://www.scopus.com/inward/record.url?scp=84855959280&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84855959280&partnerID=8YFLogxK

U2 - 10.1021/ja2096255

DO - 10.1021/ja2096255

M3 - Article

VL - 134

SP - 812

EP - 815

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 2

ER -