Abstract：
:We used a combination of optical and calorimetric techniques to investigate the incorporation of deoxythymidine --> deoxyuridine (dT --> dU) substitutions in the duplex and third strand of the parallel intramolecular triplex d(A(7)C(5)T(7)C(5)T(7)) (ATT). UV and differential scanning calorimetry melting experiments show that the incorporation of two substitutions yielded triplexes with lower thermal stability and lower unfolding enthalpies. The enthalpies decrease with an increase in salt concentration, indirectly yielding a heat capacity effect, and the magnitude of this effect was lower for the substituted triplexes. The combined results indicate that the destabilizing effect is due to a decrease in the level of stacking interactions. Furthermore, the minor groove ligand netropsin binds to the minor groove and to the hydrophobic groove, created by the double chain of thymine methyl groups in the major groove of these triplexes. Binding of netropsin to the minor groove yielded thermodynamic profiles similar to that of a DNA duplex with a similar sequence. However, and relative to ATT, binding of netropsin to the hydrophobic groove has a decreased binding affinity and lower binding enthalpy. This shows that the presence of uridine bases disrupts the hydrophobic groove and lowers its cooperativity toward ligand binding. The overall results suggest that the stabilizing effect of methyl groups may arise from the combination of both hydrophobic and electronic effects.
journal_name
Biochemistryjournal_title
Biochemistryauthors
Soto AM,Rentzeperis D,Shikiya R,Alonso M,Marky LAdoi
10.1021/bi052203bsubject
Has Abstractpub_date
2006-03-07 00:00:00pages
3051-9issue
9eissn
0006-2960issn
1520-4995journal_volume
45pub_type
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