Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.
Molecular dynamics and thermodynamic integration calculations have been carried out on a set of G-rich single-strand, duplex, triplex, and quadruplex DNAs to study the structural and stability changes connected with the guanine --> 6-thioguanine (G --> S) mutation. The presence of 6-thioguanine leads to a shift of the geometry from the B/A intermediate to the pure B-form in duplex DNA. The G --> S mutation does not largely affect the structure of the antiparallel triplex when it is located at the reverse-Hoogsteen position, but leads to a non-negligible local distortion in the structure when it is located at the Watson-Crick position. The G --> S mutation leads to destabilization of all studied structures: the lowest effect has been observed for the G --> S mutation in the reverse-Hoogsteen strand of the triplex, a medium effect has been observed in the Watson-Crick strand of the triplex and duplex, and the highest influence of the G -->S mutation has been found for the quadruplex structures.
Spacková
Nad'a
N
Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic.
Cubero
Elena
E
Sponer
Jirí
J
Orozco
Modesto
M
D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D013816:Thermodynamics; D013866:Thioguanine / Q000737:chemistry*
C051802:triplex DNA; D006147:Guanine; D004247:DNA; D013866:Thioguanine