Restoration of native folding of single-stranded DNA sequences through reverse mutations

an indication of a new epigenetic mechanism.

Dionne N. Shepherd, Darren P. Martin, Arvind Varsani, Jennifer A. Thomson, Edward P. Rybicki, Horst H. Klump

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.

Original languageEnglish (US)
Pages (from-to)108-122
Number of pages15
JournalArchives of Biochemistry and Biophysics
Volume453
Issue number1
DOIs
StatePublished - Sep 1 2006
Externally publishedYes

Fingerprint

Single-Stranded DNA
DNA sequences
Epigenomics
Restoration
Nucleotides
Nucleic Acids
Mutation
Viruses
Computer Simulation
Maize streak virus
Plant Viruses
Nucleotide Motifs
Proteins
Virus Replication
Zea mays
Sequence Analysis
Conservation
Population
In Vitro Techniques

ASJC Scopus subject areas

  • Biochemistry
  • Biophysics
  • Molecular Biology

Cite this

Restoration of native folding of single-stranded DNA sequences through reverse mutations : an indication of a new epigenetic mechanism. / Shepherd, Dionne N.; Martin, Darren P.; Varsani, Arvind; Thomson, Jennifer A.; Rybicki, Edward P.; Klump, Horst H.

In: Archives of Biochemistry and Biophysics, Vol. 453, No. 1, 01.09.2006, p. 108-122.

Research output: Contribution to journalArticle

Shepherd, Dionne N. ; Martin, Darren P. ; Varsani, Arvind ; Thomson, Jennifer A. ; Rybicki, Edward P. ; Klump, Horst H. / Restoration of native folding of single-stranded DNA sequences through reverse mutations : an indication of a new epigenetic mechanism. In: Archives of Biochemistry and Biophysics. 2006 ; Vol. 453, No. 1. pp. 108-122.
@article{1f3ab2b3ed5843fa9f44b5f8abf5a9cd,
title = "Restoration of native folding of single-stranded DNA sequences through reverse mutations: an indication of a new epigenetic mechanism.",
abstract = "We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.",
author = "Shepherd, {Dionne N.} and Martin, {Darren P.} and Arvind Varsani and Thomson, {Jennifer A.} and Rybicki, {Edward P.} and Klump, {Horst H.}",
year = "2006",
month = "9",
day = "1",
doi = "10.1016/j.abb.2005.12.009",
language = "English (US)",
volume = "453",
pages = "108--122",
journal = "Archives of Biochemistry and Biophysics",
issn = "0003-9861",
publisher = "Academic Press Inc.",
number = "1",

}

TY - JOUR

T1 - Restoration of native folding of single-stranded DNA sequences through reverse mutations

T2 - an indication of a new epigenetic mechanism.

AU - Shepherd, Dionne N.

AU - Martin, Darren P.

AU - Varsani, Arvind

AU - Thomson, Jennifer A.

AU - Rybicki, Edward P.

AU - Klump, Horst H.

PY - 2006/9/1

Y1 - 2006/9/1

N2 - We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.

AB - We used in vivo (biological), in silico (computational structure prediction), and in vitro (model sequence folding) analyses of single-stranded DNA sequences to show that nucleic acid folding conservation is the selective principle behind a high-frequency single-nucleotide reversion observed in a three-nucleotide mutated motif of the Maize streak virus replication associated protein (Rep) gene. In silico and in vitro studies showed that the three-nucleotide mutation adversely affected Rep nucleic acid folding, and that the single-nucleotide reversion [C(601)A] restored wild-type-like folding. In vivo support came from infecting maize with mutant viruses: those with Rep genes containing nucleotide changes predicted to restore a wild-type-like fold [A(601)/G(601)] preferentially accumulated over those predicted to fold differently [C(601)/T(601)], which frequently reverted to A(601) and displaced the original population. We propose that the selection of native nucleic acid folding is an epigenetic effect, which might have broad implications in the evolution of plants and their viruses.

UR - http://www.scopus.com/inward/record.url?scp=33750587742&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=33750587742&partnerID=8YFLogxK

U2 - 10.1016/j.abb.2005.12.009

DO - 10.1016/j.abb.2005.12.009

M3 - Article

VL - 453

SP - 108

EP - 122

JO - Archives of Biochemistry and Biophysics

JF - Archives of Biochemistry and Biophysics

SN - 0003-9861

IS - 1

ER -