Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing.

Donna J. Koslowsky, Larissa Reifur, Laura E. Yu, Weiqin Chen

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.

Original languageEnglish (US)
Pages (from-to)28-34
Number of pages7
JournalRNA biology
Volume1
Issue number1
StatePublished - Jan 1 2004
Externally publishedYes

Fingerprint

Guide RNA
RNA Editing
Messenger RNA
Trypanosomiasis
Thermodynamics
Magnesium
Adenosine Triphosphatases
Mitochondria
Binding Sites

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

Cite this

Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. / Koslowsky, Donna J.; Reifur, Larissa; Yu, Laura E.; Chen, Weiqin.

In: RNA biology, Vol. 1, No. 1, 01.01.2004, p. 28-34.

Research output: Contribution to journalArticle

Koslowsky, Donna J. ; Reifur, Larissa ; Yu, Laura E. ; Chen, Weiqin. / Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing. In: RNA biology. 2004 ; Vol. 1, No. 1. pp. 28-34.
@article{e7e2d629b591442e9e0af1b13d670afe,
title = "Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing.",
abstract = "The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.",
author = "Koslowsky, {Donna J.} and Larissa Reifur and Yu, {Laura E.} and Weiqin Chen",
year = "2004",
month = "1",
day = "1",
language = "English (US)",
volume = "1",
pages = "28--34",
journal = "RNA Biology",
issn = "1547-6286",
publisher = "Landes Bioscience",
number = "1",

}

TY - JOUR

T1 - Evidence for U-tail stabilization of gRNA/mRNA interactions in kinetoplastid RNA editing.

AU - Koslowsky, Donna J.

AU - Reifur, Larissa

AU - Yu, Laura E.

AU - Chen, Weiqin

PY - 2004/1/1

Y1 - 2004/1/1

N2 - The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.

AB - The most dramatic example of RNA editing is found in the mitochondria of trypanosomes. In these organisms, U-insertions/deletions can create mRNAs that are twice as large as the gene that encodes them. Guide RNAs (gRNAs) that are complementary to short stretches of the mature message direct the precise placements of the U residues. The binding of gRNA to mRNA is a fundamental step in RNA editing and understanding the relative importance of the elements that confer affinity and specificity on this interaction is critical to our understanding of the editing process. In this study, we have analyzed the relative binding affinities of two different gRNA/mRNA pairs. The affinity of gA6-14 for its message (ATPase 6) is high, with an apparent K(D) in the 5-10 nM range. In contrast, gCYb-558 has a low affinity for its cognate mRNA. Deletion of the gRNA U-tail caused a significant reduction in the binding affinity for only the gCYb-558 pair, and was observed only under physiological magnesium conditions. These results indicate that the U-tail contribution can differ substantially between the different gRNA/mRNA pairs. In addition, our results suggest that the efficiency of gRNA/mRNA interaction is highly dependent on thermodynamic parameters determined by the local sequences and their adopted structures surrounding the anchor-binding site.

UR - http://www.scopus.com/inward/record.url?scp=33646869691&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33646869691&partnerID=8YFLogxK

M3 - Article

VL - 1

SP - 28

EP - 34

JO - RNA Biology

JF - RNA Biology

SN - 1547-6286

IS - 1

ER -