Formation of intramolecular triplex in homopurine-homopyrimidine mirror repeats with point substitutions.
We have used two-dimensional gel electrophoresis to study the structural transition to the triplex H form of sequences 5'-AAGGGAGAAXGGGGTATAGGGGYAAGAGGGAA-3' where X and Y are any DNA bases. The transition was observed at acid pH under superhelical stress. For X = Y = A or X = Y = G the sequences corresponded to homopurine-homopyrimidine mirror repeats (H-palindrome) which are known to adopt the H form under acid pH and superhelical stress. We have shown that the H form is actually formed for all X and Y, though in cases other than X = Y = A and X = Y = G the transition requires larger negative superhelical stress. Different substitutions require different superhelicity levels for the transition to occur. Theoretical analysis of the data obtained made it possible to estimate the energy cost of triplex formation due to all possible mismatched base triads.
Belotserkovskii
B P
BP
Institute of Molecular Genetics, Academy of Sciences of USSR, Moscow.
Veselkov
A G
AG
Filippov
S A
SA
Dobrynin
V N
VN
Mirkin
S M
SM
Frank-Kamenetskii
M D
MD
D001482:Base Composition; D001483:Base Sequence; D003001:Cloning, Molecular; D004247:DNA / Q000737:chemistry*; D015180:Electrophoresis, Gel, Two-Dimensional; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000138:chemical synthesis; D010957:Plasmids; D011685:Purine Nucleotides / Q000235:genetics*; D011742:Pyrimidine Nucleotides / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D015719:Single-Strand Specific DNA and RNA Endonucleases; D013816:Thermodynamics
D009841:Oligonucleotides; D011685:Purine Nucleotides; D011742:Pyrimidine Nucleotides; D004247:DNA; D015719:Single-Strand Specific DNA and RNA Endonucleases