Structure of d(GT)n.d(GA)n sequences: formation of parallel stranded duplex DNA
| Autor: | Bernd W. Kalisch, Markus W. Germann, J.H. van de Sande |
|---|---|
| Rok vydání: | 1998 |
| Předmět: |
Circular dichroism
Base Composition Dna duplex Guanine Base Sequence Chemistry Base pair Adenine Circular Dichroism Nucleic Acid Heteroduplexes DNA Biochemistry Electrophoresis Crystallography Oligodeoxyribonucleotides Duplex (building) Nucleic Acid Conformation Thermodynamics Base sequence Electrophoresis Polyacrylamide Gel Spectrophotometry Ultraviolet Neutral ph Polyacrylamide gel electrophoresis Thymine |
| Zdroj: | Biochemistry. 37(37) |
| ISSN: | 0006-2960 |
| Popis: | Alternating polypurine sequences exhibit remarkable polymorphism. In this study, we report that dGA.dGT sequences form parallel stranded duplex DNA at neutral pH. Using two model hairpins, 3'-d(GT)3-5'5'-T4(AG)3-3' (I) and 3'-d(GT)4-5'5'-T4(AG)4-3' (II), containing 5'5' linkages which direct parallel strand formation, we systematically explored the spectroscopic and thermodynamic properties of parallel stranded d(GA)n.d(GT)n. The parallel stranded hairpins are remarkably stable structures with TM's of 41.5 and 47.5 degreesC (in 0.4 M NaCl) for the shorter and longer hairpins, respectively. The van't Hoff enthalpies of 80.7 and 114 kJ mol-1 are relatively low but are comparable to a parallel stranded d(GA)n duplex. On the basis of the spectroscopic and electrophoretic characteristics, we conclude that parallel strand formation is not restricted to hairpin systems, but also readily occurs in unconstrained dimeric duplexes with the appropriate sequence homologies. Both melting curves and electrophoretic analyses of parallel stranded heteroduplexes in which the sequence enforces specific base pairing demonstrate that G-G and A-T base pairs are formed in d(GA)n.d(GT)n segments. |
| Databáze: | OpenAIRE |
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