Biomaterial Database

Sequence-dependent effects of spermine on the thermodynamics of the B-DNA to Z-DNA transition. 1996

M L Howell, and G P Schroth, and P S Ho

Department of Biochemistry and Biophysics, Oregon State University, Corvallis 97331, USA.

Spermine has been shown to bind to and stabilize a number of altered DNA conformations, including left-handed Z-DNA. Here, we have quantitatively studied the effects of spermine on the negative supercoil-induced transition from B- to Z-DNA. We have determined the intrinsic association constants for and the effective number of ligands that bind to both B- and Z-DNA. The intrinsic affinity of spermine for Z-DNA is approximately 10 times higher for d(CA/TG) (KZP = 1.2 x 10(8) M-1) than for d(CG) dinucleotides (KZP = 1.5 x 10(7) M-1), and both are greater than that for B-DNA (KBP = 1.4 x 10(5) M-1). This accounts for the stabilization of Z-DNA by spermine. The number of spermine accommodated by Z-DNA (nZ) is sequence-dependent [nZ = 0.6 spermine per 18 d(CA/TG) dinucleotides and 2.3 for 12 d(CG) dinucleotides]. The value of nZ of < 1 was interpreted as evidence for negative cooperativity in spermine binding to d(CA/TG) dinucleotides. Thus, although d(CA/TG) sequences saturate at lower spermine concentrations, the ligand has an overall greater effect on the stability of d(CG) dinucleotides as Z-DNA. B-DNA accommodates more spermines per base pair than either sequence as Z-DNA. At higher concentrations (> 10 microM), spermine destabilizes Z-DNA. Using these parameters in a model for competitive spermine binding to B-DNA and Z-DNA, we can make predictions for how potential Z-DNA sequences found in the human genome are affected by cellular levels of superhelical density and spermine.

UI	MeSH Term	Description	Entries
D009690	Nucleic Acid Conformation	The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.	DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247	DNA	A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).	DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D013096	Spermine	A biogenic polyamine formed from spermidine. It is found in a wide variety of organisms and tissues and is an essential growth factor in some bacteria. It is found as a polycation at all pH values. Spermine is associated with nucleic acids, particularly in viruses, and is thought to stabilize the helical structure.
D013816	Thermodynamics	A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)	Thermodynamic
D015180	Electrophoresis, Gel, Two-Dimensional	Electrophoresis in which a second perpendicular electrophoretic transport is performed on the separate components resulting from the first electrophoresis. This technique is usually performed on polyacrylamide gels.	Gel Electrophoresis, Two-Dimensional,Polyacrylamide Gel Electrophoresis, Two-Dimensional,2-D Gel Electrophoresis,2-D Polyacrylamide Gel Electrophoresis,2D Gel Electrophoresis,2D PAGE,2D Polyacrylamide Gel Electrophoresis,Electrophoresis, Gel, 2-D,Electrophoresis, Gel, 2D,Electrophoresis, Gel, Two Dimensional,Polyacrylamide Gel Electrophoresis, 2-D,Polyacrylamide Gel Electrophoresis, 2D,Two Dimensional Gel Electrophoresis,2 D Gel Electrophoresis,2 D Polyacrylamide Gel Electrophoresis,Electrophoresis, 2-D Gel,Electrophoresis, 2D Gel,Electrophoresis, Two-Dimensional Gel,Gel Electrophoresis, 2-D,Gel Electrophoresis, 2D,Gel Electrophoresis, Two Dimensional,PAGE, 2D,Polyacrylamide Gel Electrophoresis, 2 D,Polyacrylamide Gel Electrophoresis, Two Dimensional,Two-Dimensional Gel Electrophoresis