400D

THE INTRINSIC STRUCTURE AND STABILITY OF OUT-OF-ALTERNATION BASE PAIRS IN Z-DNA

Summary for 400D

• Entry DOI: 10.2210/pdb400d/pdb
• Descriptor: DNA (5'-D(*(5CM)P*GP*GP*CP*(5CM)P*G)-3') (2 entities in total)
• Functional Keywords: z-dna double helix, dna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 3676.52

Authors

Eichman, B.F.,Basham, B.,Schroth, G.P.,Ho, P.S. (deposition date: 1998-05-28, release date: 1998-07-09, Last modification date: 2024-02-28)

Primary citation

Eichman, B.F.,Schroth, G.P.,Basham, B.E.,Ho, P.S.
The intrinsic structure and stability of out-of-alternation base pairs in Z-DNA.
Nucleic Acids Res., 27:543-550, 1999

PubMed Abstract: Alternating pyrimidine-purine sequences typically form Z-DNA, with the pyrimidines in the anti and purines in the syn conformations. The observation that dC and dT nucleotides can also adopt the syn conformation (i.e. the nucleotides are out-of-alternation) extends the range of sequences that can convert to this left-handed form of DNA. Here, we study the effects of placing two adjacent d(G*C) base pairs as opposed to a single d(G*C) base pair or two d(A*T) base pairs out-of-alternation by comparing the structure of d(m5CGGCm5CG)2with the previously published structures of d(m5CGGGm5CG)*d(m5CGCCm5CG) and d(m5CGATm5CG)2. A high buckle and loss of stacking interactions are observed as intrinsic properties of the out-of-alternation base pairs regardless of sequence and the context of the dinucleotide. From solution titrations, we find that the destabilizing effect of out-of-alternation d(G*C) base pairs are identical whether these base pairs are adjacent or isolated. We can therefore conclude that it is these intrinsic distortions in the structure of the base pairs and not neighboring effects that account for the inability of out-of-alternation base pairs to adopt the left-handed Z conformation.

PubMed: 9862978
DOI: 10.1093/nar/27.2.543

Experimental method

X-RAY DIFFRACTION (1.65 Å)