Recognition of a guanine-cytosine base pair by 8-oxoadenine

Abstract

Two oligodeoxyribonucleotides, d-CTTCTTTTTTATTTT, I(A), and d-ATTATTTTTTATTTT, II(A), where C is 5-methylcytosine and A is 8-oxoadenine, were prepared and their interactions with the duplex d-GAAGAAAAAAYAAAA/d-TTTTZTTTTTTCTTC, III.IV(Y.Z), were studied. Oligomers I(A) and II(A) each form triplexes with III.IV(G.C) at temperatures below 20 degrees C as shown by continuous variation experiments, melting experiments, and circular dichroism (CD) spectroscopy. The CD spectra of these triplexes are almost identical to those formed by I(C) and II(C), oligomers which contain cytosine in place of 8-oxoadenine. This suggests that the 8-oxoadenine-containing triplexes have conformations which are very similar to those of the cytosine-containing triplexes. The melting temperature (Tm) for dissociation of the third strand of triplex II.III.IV(A.G.C) is 22 degrees C at pH 7.0 and 8.0, whereas the Tm of the corresponding transition in triplex II.III.IV(C.G.C) decreases from 28 degrees C at pH 7.0 to 17 degrees C at pH 8.0. The pH dependence of the Tm in the latter triplex reflects the necessity of protonating the N-3 of cytosine in order for it to form two hydrogen bonds with G of the G.C base pair. It appears that the keto form of 8-oxoadenine can potentially form two hydrogen bonds with the N-7 and O-6 atoms of G of the G.C base pair, when the 8-oxoadenine is in the syn conformation and in contrast to cytosine does not require protonation of the base. Oligomer I(A) does not form triplexes with III.IV(Y.Z) when Y.Z is A.T or T.A.(ABSTRACT TRUNCATED AT 250 WORDS)

Efficient pH-independent sequence-specific DNA binding by pseudoisocytosine-containing bis-PNA

“…1) abolishes the pH sensitivity of the DNA triplex (12,13) without seriously affecting the stability of the triplex. Likewise, 8-oxoadenine has been employed to recognize guanine in the Hoogsteen mode (14)(15)(16)(17). However, synthesis of the PNA pseudoisocytosine monomer seemed more straightforward (Scheme 1).…”

Targeted Mutagenesis in Mammalian Cells Mediated by Intracellular Triple Helix Formation

“…However, the general applicability of this approach will depend on the extension of the third-strand binding code and the development of nucleotide analogs so that triple helix formation is not limited to polypurine sequences. Much work in this regard is under way (13,16,22,27,28,38). Further experiments to develop a better understanding of cellular repair and replication of the triplex-directed lesion are also needed.…”

Sequence specificity of the non-natural pyrido[2,3-d]pyrimidine nucleoside in triple helix formation

“…Pyrimidine-rich oligodeoxyribonucleotides bind parallel to the Watson-Crick purine strand through formation of Hoogsteen hydrogen bonds between thymine (T) and adenine-thymine (AT) base pairs (T AT) and between protonated cytosine (C +) and guanine -cytosine (GC) base pairs (C +GC) (1-4), whereas purine-rich oligodeoxyribonucleotides bind antiparallel to the Watson-Crick purine strand through reverse Hoogsteen hydrogen bond formation between G and GC base pairs and A or T and AT base pairs (5)(6)(7)(8). The discovery of other natural and non-natural base triplets (9)(10)(11)(12)(13)(14)(15)(16)(17)(18) and the use of alternate strand triple-helix formation (19)(20)(21)(22)(23). has increased the number of double-helical sequences that can be recognized beyond simple purine tracts.…”