1TNE

NMR STUDY OF Z-DNA AT PHYSIOLOGICAL SALT CONDITIONS, MINIMIZED AVERAGE STRUCTURE

Summary for 1TNE

• Entry DOI: 10.2210/pdb1tne/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*(8MG)P*CP*G)-3') (1 entity in total)
• Functional Keywords: z-dna, dna
• Total number of polymer chains: 2
• Total formula weight: 3648.46

Authors

Robinson, H.,Wang, A.H.-J.,Sugiyama, H.,Kawai, K.,Matsunaga, A.,Fujimoto, K.,Saito, I. (deposition date: 1996-02-13, release date: 1996-07-11, Last modification date: 2024-05-22)

Primary citation

Sugiyama, H.,Kawai, K.,Matsunaga, A.,Fujimoto, K.,Saito, I.,Robinson, H.,Wang, A.H.
Synthesis, structure and thermodynamic properties of 8-methylguanine-containing oligonucleotides: Z-DNA under physiological salt conditions.
Nucleic Acids Res., 24:1272-1278, 1996

PubMed Abstract: Various oligonucleotides containing 8-methylguanine (m8G) have been synthesized and their structures and thermodynamic properties investigated. Introduction Of M8G into DNA sequences markedly stabilizes the Z conformation under low salt conditions. The hexamer d(CGC[M8G]CG)2 exhibits a CD spectrum characteristic of the Z conformation under physiological salt conditions. The NOE-restrained refinement unequivocally demonstrated that d(CGC[m8G]CG)2 adopts a Z structure with all guanines in the syn conformation. The refined NMR structure is very similar to the Z form crystal structure of d(CGCGCG)2, with a root mean square deviation of 0.6 between the two structures. The contribution of m8G to the stabilization of Z-DNA has been estimated from the mid-point NaCl concentrations for the B-Z transition of various m8G-containing oligomers. The presence of m8G in d(CGC[m8G]CG)2 stabilizes the Z conformation by at least deltaG = -0.8 kcal/mol relative to the unmodified hexamer. The Z conformation was further stabilized by increasing the number of m8Gs incorporated and destabilized by incorporating syn-A or syn-T, found respectively in the (A,T)-containing alternating and non-alternating pyrimidine-purine sequences. The results suggest that the chemically less reactive m8G base is a useful agent for studying molecular interactions of Z-DNA or other DNA structures that incorporate syn-G conformation.

PubMed: 8614630
DOI: 10.1093/nar/24.7.1272

Experimental method

SOLUTION NMR