Unexpected formation of parallel duplex in GAA and TTC trinucleotide repeats of Friedreich's ataxia

J Mol Biol. 2000 Oct 6;302(5):1063-80. doi: 10.1006/jmbi.2000.4073.


The onset and progress of Friedreich's ataxia (FRDA) is associated with the genetic instability of the (GAA).(TTC) trinucleotide repeats located within the frataxin gene. The instability of these repeats may involve the formation of an alternative DNA structure. Poly-purine (R)/poly-pyrimidine (Y) sequences typically form triplex DNA structures which may contribute to genetic instability. Conventional wisdom suggested that triplex structures formed by these poly-purine (R)/poly-pyrimidine (Y) sequences may contribute to their genetic instability. Here, we report the characterization of the single-stranded GAA and TTC sequences and their mixtures using NMR, UV-melting, and gel electrophoresis, as well as chemical and enzymatic probing methods. We show that the FRDA GAA/TTC, repeats are capable of forming various alternative structures. The most intriguing is the observation of a parallel (GAA).(TTC) duplex in equilibrium with the antiparallel Watson-Crick (GAA).(TTC) duplex. We also show that the GAA strands form self-assembled structures, whereas the TTC strands are essentially unstructured. Finally, we demonstrate that the FRDA repeats form only the YRY triplex (but not the RRY triplex) at neutral pH and the complete formation of the YRY triplex requires the ratio of GAA to TTC strand larger than 1:2. The structural features presented here and in other studies distinguish the FRDA (GAA)¿(TTC) repeats from the fragile X (CGG).CCG), myotonic dystrophy (CTG).(CAG) and the Huntington (CAG).(CTG) repeats.

Publication types

  • Letter
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Base Pairing / genetics
  • Base Sequence
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism
  • DNA Methylation
  • DNA, Single-Stranded / chemistry
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Electrophoresis, Polyacrylamide Gel
  • Exodeoxyribonucleases / metabolism
  • Fragile X Syndrome / genetics
  • Frataxin
  • Friedreich Ataxia / genetics*
  • Humans
  • Huntington Disease / genetics
  • Hydrogen-Ion Concentration
  • Intercalating Agents / metabolism
  • Intercalating Agents / pharmacology
  • Iron-Binding Proteins*
  • Magnesium / pharmacology
  • Magnetic Resonance Spectroscopy
  • Myotonic Dystrophy / genetics
  • Nuclease Protection Assays
  • Nucleic Acid Conformation* / drug effects
  • Nucleic Acid Denaturation / drug effects
  • Oligodeoxyribonucleotides / chemistry
  • Oligodeoxyribonucleotides / genetics
  • Oligodeoxyribonucleotides / metabolism
  • Phosphates / metabolism
  • Phosphotransferases (Alcohol Group Acceptor) / genetics*
  • Spectrophotometry, Ultraviolet
  • Temperature
  • Thermodynamics
  • Titrimetry
  • Trinucleotide Repeats / genetics*


  • DNA, Single-Stranded
  • Intercalating Agents
  • Iron-Binding Proteins
  • Oligodeoxyribonucleotides
  • Phosphates
  • triplex DNA
  • DNA
  • Phosphotransferases (Alcohol Group Acceptor)
  • Exodeoxyribonucleases
  • exodeoxyribonuclease III
  • Magnesium