Antiparallel DNA duplex formation between alternating α d(GA)nand β d(GA)nsequences
| Autor: | J.H. van de Sande, Markus W. Germann, Bernd W. Kalisch |
|---|---|
| Rok vydání: | 1998 |
| Předmět: |
Circular dichroism
Guanine Hot Temperature Oligodeoxynucleotide Base pair Stereochemistry Beta hairpin Biophysics Nucleic Acid Denaturation Antiparallel (biochemistry) Biochemistry 03 medical and health sciences chemistry.chemical_compound Structural Biology GA repeat Genetics Alpha anomer Dinucleotide Repeats Molecular Biology 030304 developmental biology Gel electrophoresis Base Composition 0303 health sciences Adenine Circular Dichroism 030302 biochemistry & molecular biology DNA structure DNA Cell Biology Oligodeoxyribonucleotides chemistry Duplex (building) Nucleic Acid Conformation Hairpin |
| Zdroj: | FEBS Letters. 427:301-304 |
| ISSN: | 0014-5793 |
| DOI: | 10.1016/s0014-5793(98)00453-0 |
| Popis: | Alternating polypurine d(GA)n, sequences exhibit a considerable polymorphism. Here we report that alpha d(GA) x d(GA) sequences form an antiparallel stranded duplex DNA at neutral pH. The spectroscopic, electrophoretic and thermodynamic properties of the alpha/beta chimeric oligodeoxynucleotide, 5'-d(GA)4(T)4 alpha d(AG)4T-3', support the formation of a hairpin structure with antiparallel strands in the stem. The optical properties of this novel antiparallel structure are different from the parallel stranded homoduplex formed by d(GA)G7. This alpha/beta hairpin has a remarkably high Tm of 44.5 degrees C in 0.4 M NaCl with a van't Hoff enthalpy comparable to that of a parallel d(GA)n duplex. Base pairing was confirmed by T4 polynucleotide ligase catalyzed joining of the alpha/beta hairpin to an antiparallel bimolecular duplex and by non-denaturing gel electrophoresis using duplexes containing sequence constraints. Both support the presence of alphaG-G and alphaA-A base pairing in the antiparallel 5'-d(GA)4(T)4 alpha d(AG)4T-3' intramolecular duplex. This study adds to the polymorphic nature of alternating d(GA)n sequences as well as providing novel homopurine base pairing approaches for probing polypurine polypyrimidine sequences. |
| Databáze: | OpenAIRE |
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