Parallel self-associated structures formed by T,C-rich sequences at acidicpH

Oligonucleotides of nonregular heteropyrimidine sequences incorporating or not incorporating purine residues 5'-d(ACTCCCTTCTCCTCTCTA), 5'-d(ACTCCCTGGT CCTCTCTA), 5'-d(TCTCTCCTGGTCCCTCC), and 5'-d(TCTCTCCTCTTCCCTCC) can form se lf-associated parallel-stranded tps) structures at pH 4-5.5. The ps structu res were identified by studying at neutral and acidic pH UV melting transit ions, FTIR spectra, and fluorescence of pyrene-labeled oligonucleotides as well as by chemical joining of 5'-phosphorylated oligonucleotides. A gel el ectrophoresis run for oligonucleotides 5'-d(TCTCTCCTCTTCCCTCC and 5'-d(ACTC CCTTCTCCTCTCTA) has shown the formation of homoduplexes at low DNA strand c oncentrations. Ps structures are held by C-C+ base pairs and have N- and S- types of sugar puckering as detected by FTIR spectroscopy in the millimolar concentration range. Guanine inserts as well as thymine and purine inserts into an oligomeric cytosine sequence make the formation of the tetraplex i -motif unfavorable. MvaI restriction endonuclease, which recognizes the CCT /AGG sequence in DNA, does not cleave parallel pseudosubstrates.