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Parallel-stranded DNA with mixed AT/GC composition: role of trans G.C base pairs in sequence dependent helical
A K Shchyolkina1, O F Borisova, M A Livshits
1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
Biochemistry
|August 24, 2000
Summary
Parallel-stranded DNA stability depends on G.C base pair clustering. Isolated G.C pairs destabilize, while blocks of two or more stabilize parallel-stranded DNA structures.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- Parallel-stranded (ps) DNA structures present unique biochemical properties compared to antiparallel DNA.
- Understanding the sequence-dependent stability of ps-DNA is crucial for its potential applications.
Purpose of the Study:
- To investigate the thermal stability of parallel-stranded DNA hairpins with mixed AT/GC content.
- To elucidate the thermodynamic effects of G.C base pair context on ps-DNA stability.
Main Methods:
- Oligonucleotide synthesis of parallel and antiparallel hairpins.
- Fluorescence spectroscopy to determine base pairing and rotational relaxation times.
- Temperature gradient gel electrophoresis (TGGE) to analyze hairpin melting.
- Multistate heterogeneous zipper model for thermodynamic parameter calculation.
Main Results:
- Ps-hairpin melting follows a multistate model.
- Thermal stability is highly sequence-dependent in ps-DNA.
- Isolated G.C pairs destabilize ps-DNA, while blocks of ≥2 G.C pairs stabilize it.
- Formation of trans G.C pairs is more favorable than trans A.T pairs in specific contexts, but GC/AT contacts are unfavorable.
Conclusions:
- The stability of ps-DNA is determined by base composition and the distribution of G.C base pairs (isolated vs. clustered).
- Clustered G.C pairs enhance ps-DNA stability, whereas isolated G.C pairs decrease it.
- Molecular modeling provides structural insights into these observed thermodynamic differences.