Parallel self-associated structures formed by T,C-rich sequences at acidic pH.
Oligonucleotides of nonregular heteropyrimidine sequences incorporating or not incorporating purine residues 5'-d(ACTCCCTTCTCCTCTCTA), 5'-d(ACTCCCTGGTCCTCTCTA), 5'-d(TCTCTCCTGGTCCCTCC), and 5'-d(TCTCTCCTCTTCCCTCC) can form self-associated parallel-stranded (ps) structures at pH 4-5.5. The ps structures were identified by studying at neutral and acidic pH UV melting transitions, FTIR spectra, and fluorescence of pyrene-labeled oligonucleotides as well as by chemical joining of 5'-phosphorylated oligonucleotides. A gel electrophoresis run for oligonucleotides 5'-d(TCTCTCCTCTTCCCTCC) and 5'-d(ACTCCCTTCTCCTCTCTA) has shown the formation of homoduplexes at low DNA strand concentrations. 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.
Geinguenaud
F
F
Laboratoire de Spectroscopie Biomoléculaire, UPRES-A CNRS 7031, UFR de Médecine, Université Paris Nord, F-93017 Bobigny Cedex, France.
Liquier
J
J
Brevnov
M G
MG
Petrauskene
O V
OV
Alexeev
Y I
YI
Gromova
E S
ES
Taillandier
E
E
D000143:Acids; D020029:Base Pairing; D001483:Base Sequence; D003596:Cytosine; D004247:DNA / Q000737:chemistry; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry; D004587:Electrophoresis, Agar Gel; D006358:Hot Temperature; D006863:Hydrogen-Ion Concentration; D015636:Magnesium Chloride; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009841:Oligonucleotides / Q000737:chemistry; D011742:Pyrimidine Nucleotides / Q000737:chemistry*; D012965:Sodium Chloride; D013050:Spectrometry, Fluorescence; D013056:Spectrophotometry, Ultraviolet; D017550:Spectroscopy, Fourier Transform Infrared; D013403:Sugar Phosphates / Q000737:chemistry; D013941:Thymine
D000143:Acids; D009841:Oligonucleotides; D011742:Pyrimidine Nucleotides; D013403:Sugar Phosphates; D015636:Magnesium Chloride; D012965:Sodium Chloride; D003596:Cytosine; D004247:DNA; C046545:CCWGG-specific type II deoxyribonucleases; D015252:Deoxyribonucleases, Type II Site-Specific; D013941:Thymine