Hairpin properties of single-stranded DNA containing a GC-rich triplet repeat: (CTG)₁₅

Abstract

Although triplet repeat DNA sequences are scattered throughout the human genome, their biological function remains obscure. To aid in correlating potential structures of these nucleic acids with their function, we propose their classification based on the presence or absence of a palindromic dinucleotide within the triplet, the G + C content, and the presence or absence of a homopolymer. Five classes of double-stranded (ds) triplet repeats are distinguished. Class I repeats, which are defined by the presence of a GC or CG palindrome, have the lowest base stacking energies, exhibit the lowest rates of slippage synthesis [Schlötterer and Tautz (1992) Nucleic Acids Res., 20, 211] and are uniquely associated with triplet repeat expansion diseases. The six single-stranded (ss) triplet repeats within Class I also have the potential to form hairpin structures, as determined by energy minimization. To explore the possibility of hairpin formation by ss Class I triplet repeats, studies were performed with a ss oligonucleotide containing 15 prototypic CTG repeats [ss (CTG)15]. Electrophoretic, P1 nuclease and KMnO4 oxidation data demonstrate that ss (CTG)15 forms a hairpin containing base paired and/or stacked thymines in the stem. Potential functions of hairpins containing Class I triplet repeats are discussed with respect to protein translation and mRNA splicing. Further, potential roles of hairpin structures in triplet repeat expansion events are discussed.

Hairpin Structure-forming Propensity of the (CCTG·CAGG) Tetranucleotide Repeats Contributes to the Genetic Instability Associated with Myotonic Dystrophy Type 2

“…The labeled oligomers were then probed with conformation-sensitive enzymatic agents (S1 nuclease, P1 nuclease, and mung bean nuclease) (65, 71, 77, 78, 80 -82, 84, 97). All three enzymes have been used widely to evaluate ordered and H-bonded pseudo-duplex DNA regions within DNA tracts that are otherwise disordered, random-coil structures (65,71,78,79,97). S1 nuclease from Aspergillus oryzae, a zinc requiring enzyme with an acidic pH optimum, cleaves single-stranded and partially unpaired DNA and is not base-specific (77,78,98).…”

DNA Secondary Structures and the Evolution of Hypervariable Tandem Arrays

“…These include the 5Ј-CAG-3Ј repeat that is unstable in triplet expansion diseases such as Huntington's disease and myotonic dystrophy (26,28,29,31) and the centromeric satellite sequence (27). Other simple satellites such as the A ϩ T-rich hypervariable sequence in the 3Ј region of the human apolipoprotein B gene (66) also have the potential to form cruciforms and hairpins.…”

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: Implications for triplet expansion diseases

“…It has been suggested that the relevant DNA sequences either have unusual properties in the duplex state or adopt unusually stable alternative secondary structures involving single-stranded domains, which alter the course of the ''normal'' cellular DNA chemistry (14). Initial structural and some thermodynamic studies of model poly͞oligonucleotides have indeed indicated that single strands consisting of repeated copies of (CAG) n , (CTG) n , and (CCG) n are able to adopt extensive secondary structures (14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28); however, conformational heterogeneity and͞or kinetically trapped metastable states have precluded the determination of reliable thermodynamic data for this important class of DNA sequences (15,(29)(30)(31)(32)(33). The absence of reliable thermodynamic data prevents a rational evaluation of the different models and precludes theoretical predictions as to which sequences may be prone to assume structures that may lead to the disease state (34).…”