Influence of Sequence Context and Length on the Structure and Stability of Triplet Repeat DNA Oligomers
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- 作者：Anthony M. Paiva and Richard D. Sheardy
- 刊名：Biochemistry
- 出版年：2004
- 出版时间：November 9, 2004
- 年：2004
- 卷：43
- 期：44
- 页码：14218 - 14227
- 全文大小：145K
- 年卷期：v.43,no.44(November 9, 2004)
- ISSN：1520-4995
文摘
Genetic expansion diseases have been linked to the properties of triplet repeat DNA sequencesduring replication. The most common triplet repeats associated with such diseases are CAG, CCG, CGG,and CTG. It has been suggested that gene expansion occurs as a result of hairpin formation of longstretches of these sequences on the leading daughter strand synthesized during DNA replication [Gellibolian,R., Bacolla, A., and Wells, R. D. (1997) J. Biol. Chem. 272, 16793-7]. To test the biophysical basis forthis model, oligonucleotides of general sequence (CNG)n, where N = A, C, G, or T and n = 4, 5, 10, 15,or 25, were synthesized and characterized by circular dichroism (CD) spectropolarimetry, optical meltingstudies, and differential scanning calorimetry (DSC). The goal of these studies was to evaluate the influenceof sequence context and oligomer length on their secondary structures and stabilities. The results indicatethat all single oligomers, even those as short as 12 nucleotides, form stable hairpin structures at 25 
C.Such hairpins are characterized by the presence of N:N mismatched base pairs sandwiched between G:Cbase pairs in the stems and loops of three to four unpaired bases. Thermodynamic analysis of these structuresreveals that their stabilities are influenced by both the sequence of the particular oligomer and its length.Specifically, the stability order of CGG > CTG > CAG > CCG was observed. In addition, longer oligomerswere found to be more stable than shorter oligomers of the same sequence. However, a stability plateauabove 45 nucleotides suggests that the length dependence reaches a maximum value where the stabilityof the G:C base pairs can no longer compensate the instability of the N:N mismatches in the stems of thehairpins. The results are discussed in terms of the above model proposed for gene expansion.
C.Such hairpins are characterized by the presence of N:N mismatched base pairs sandwiched between G:Cbase pairs in the stems and loops of three to four unpaired bases. Thermodynamic analysis of these structuresreveals that their stabilities are influenced by both the sequence of the particular oligomer and its length.Specifically, the stability order of CGG > CTG > CAG > CCG was observed. In addition, longer oligomerswere found to be more stable than shorter oligomers of the same sequence. However, a stability plateauabove 45 nucleotides suggests that the length dependence reaches a maximum value where the stabilityof the G:C base pairs can no longer compensate the instability of the N:N mismatches in the stems of thehairpins. The results are discussed in terms of the above model proposed for gene expansion.