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  Parallel-stranded DNA with mixed AT/GC composition: role of trans G·C base pairs in sequence dependent helical stability

Shchyolkina, A. K., Borisova, O. F., Livshits, M. A., Pozmogova, G. E., Chernov, B. K., Klement, R., et al. (2000). Parallel-stranded DNA with mixed AT/GC composition: role of trans G·C base pairs in sequence dependent helical stability. Biochemistry, 39: doi:10.1021/bi9913909, pp. 10034-10044.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0012-F971-B Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-E902-5
Genre: Journal Article

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 Creators:
Shchyolkina, A. K., Author
Borisova, O. F., Author
Livshits, M. A., Author
Pozmogova, G. E., Author
Chernov, B. K., Author
Klement, R.1, Author              
Jovin, T. M.2, Author              
Affiliations:
1Emeritus Group Laboratory of Cellular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578629              
2Department of Molecular Biology, MPI for biophysical chemistry, Max Planck Society, ou_578628              

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Free keywords: Base Composition Base Pairing Circular Dichroism Computer Simulation *DNA/ch [Chemistry] Models, Chemical Models, Molecular Nucleic Acid Conformation Nucleic Acid Denaturation Oligodeoxyribonucleotides/ch [Chemistry] Support, Non-U.S. Gov't Temperature Thermodynamics
 Abstract: Parallel-stranded (ps) DNAs with mixed AT/GC content comprising G.C pairs in a varying sequence context have been investigated. Oligonucleotides were devised consisting of two 10-nt strands complementary either in a parallel or in an antiparallel orientation and joined via nonnucleotide linkers so as to form 10-bp ps or aps hairpins. A predominance of intramolecular hairpins over intermolecular duplexes was achieved by choice of experimental conditions and verified by fluorescence determinations yielding estimations of rotational relaxation times and fractional base pairing. A multistate mode of ps hairpin melting was revealed by temperature gradient gel electrophoresis (TGGE). The thermal stability of the ps hairpins with mixed AT/GC content depends strongly on the specific sequence in a manner peculiar to the ps double helix. The thermodynamic effects of incorporating trans G.C base pairs into an AT sequence are context-dependent: an isolated G. C base pair destabilizes the duplex whereas a block of > or =2 consecutive G.C base pairs exerts a stabilizing effect. A multistate heterogeneous zipper model for the thermal denaturation of the hairpins was derived and used in a global minimization procedure to compute the thermodynamic parameters of the ps hairpins from experimental melting data. In 0.1 M LiCl at 3 degrees C, the formation of a trans G.C pair in a GG/CC sequence context is approximately 3 kJ mol(-)(1) more favorable than the formation of a trans A.T pair in an AT/TA sequence context. However, GC/AT contacts contribute a substantial unfavorable free energy difference of approximately 2 kJ mol(-)(1). As a consequence, the base composition and fractional distribution of isolated and clustered G.C base pairs determine the overall stability of ps-DNA with mixed AT/GC sequences. Thus, the stability of ps-DNA comprising successive > or =2 G.C base pairs is greater than that of ps-DNA with an alternating AT sequence, whereas increasing the number of AT/GC contacts by isolating G.C base pairs exerts a destabilizing effect on the ps duplex. Molecular modeling of the various helices by force field techniques provides insight into the structural basis for these distinctions.

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Language(s): eng - English
 Dates: 2005-08-052000
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: Peer
 Identifiers: eDoc: 236884
Other: 23130
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Title: Biochemistry
Source Genre: Journal
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Pages: - Volume / Issue: 39 Sequence Number: doi:10.1021/bi9913909 Start / End Page: 10034 - 10044 Identifier: -