M-DNA: pH Stability, Nuclease Resistance and Signal Transmission

Abstract In the presence of divalent metal ions (Zn(2)+, Co(2)+, and Ni(2)+) and at pHs above 8, duplex DNA forms a complex called M-DNA. M-DNA can be converted back to B-DNA by addition of EDTA or lowering the pH. The stability of M-DNA depends on the metal ion and/or the sequence of DNA. For calf thymus DNA the order of stability with decreasing pH is: Ni(2+)> Co(2+)>Zn(2++). The interconversion with B-DNA shows hysteresis; once formed Ni-M- DNA remains stable for more than one hour at pH 7, but conversion of B-DNA to M-DNA is slow at pHs below 8. Among synthetic sequences, poly[d(AT)] does not form M-DNA whereas the phosphorothioate analogues form only at pH 9.0. In contrast, the Ni-M-DNA form of poly[d(GC)] is stable even at pH 6.5. Ni-M-DNA is resistant to cleavage by DNase I whereas B-DNA is digested rapidly under identical conditions. The Co(2)+ and Ni(2+) forms of M-DNA were paramagnetic with increased mass susceptibilities (χ) compared to other metal complexes. Signal transmission in M-DNA was tested by constructing duplexes of 54 base pairs with fluorescein (donor) at one end and rhodamine (acceptor) at the other. Quenching of fluorescein fluorescence was observed for the Zn(2+) form of M-DNA only when the DNA was labeled with both donor and acceptor. Therefore, the pathway of quenching maybe via electron transfer. Taken together, these results suggest that M-DNA is a distinct conformation with tightly bound metal ions, and certain forms may be stable under physiological conditions. Furthermore, M-DNA may be used as a molecular wire for signal transmission over long distances.