Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA.
Purine residues located within regions of DNA that have the potential to form left-handed Z-helical structures are modified preferentially by diethyl pyrocarbonate; this hyperreactivity is dependent on the degree of negative superhelicity of the circular DNA molecules. As negative superhelical density increases, guanosines in a 32-base-pair alternating G-C sequence and adenosines (but not guanosines) in a 64-base-pair alternating A-C/G-T sequence become 5- to 10-fold more reactive to diethyl pyrocarbonate. The negative superhelical densities at which enhanced reactivity occurs are similar to those reported for the point at which left-handed helices form within plasmids carrying these DNA sequences. Probing of negatively supercoiled pBR322 with diethyl pyrocarbonate reveals a hyperreactive region 31 base pairs in length of which only 9 base pairs are a perfect alternating purine and pyrimidine sequence; the reactivity of purines within this sequence indicates that purines in the anti conformation, or guanosines in the syn conformation with neighboring 3' thymidines, are not hyperreactive in the Z-DNA form.
D000241:Adenosine; D000478:Alkylation; D001483:Base Sequence; D004247:DNA; D004278:DNA, Superhelical; D004047:Diethyl Pyrocarbonate; D005561:Formates; D006151:Guanosine; D009690:Nucleic Acid Conformation; D011687:Purines; D013329:Structure-Activity Relationship
D004278:DNA, Superhelical; D005561:Formates; D011687:Purines; D006151:Guanosine; D004247:DNA; D000241:Adenosine; D004047:Diethyl Pyrocarbonate