26.03.2009, 16:15

Superhelically Induced Duplex Destabilization (SIDD) in DNA, and its Roles in Regulation

    Superhelically Induced Duplex Destabilization (SIDD) in DNA, and its Roles in Regulation


    Craig J. Benham

    Professor, Depts of Mathematics and of Biomedical Engineering

    UC Davis



    Separation of the two strands of the DNA duplex is a necessary step in the initiation of both replication and transcription. So the occurrences and locations of duplex strand openings must be stringently controlled in vivo. Although these initiation events commonly are regulated by enzymatic processes, anything that alters the stability of the duplex can affect the ease of opening, and hence serve a regulatory function. In particular, negative superhelicity can destabilize the DNA duplex at specific positions where its thermodynamic stability is low. Substantial amounts of unconstrained superhelicity, sufficient to drive strand opening, have been documented to occur in vivo in both prokaryotes and eukaryotes.


    We have developed computational methods to predict the destabilization properties of superhelical DNA molecules having any specified base sequence, including complete chromosomes. This phenomenon is context-dependent, hence complex to analyze, because superhelical stresses couple together the transition behaviors of all sites that experience them. The energy and conformational parameters used in this analysis are all taken from experimental measurements, so there are no free parameters. Yet when it is used to analyze specific DNA sequences, the results of this method are in quantitatively precise agreement with experimental measurements of the locations and extents of local strand separations. This justifies its use to predict the duplex destabilization properties of other DNA base sequences, on which experiments have not been performed.


    We have analyzed the stress-induced duplex destabilization (SIDD) properties of many complete prokaryotic genomes, and of a wide variety of eukaryotic and viral sequences. Our results have illuminated the role of SIDD in a variety of regulatory processes, including those governing transcription from specific promoters, initiation of replication in viruses and yeast, and scaffold-matrix attachment in eukaryotes. Specific examples will be described as time allows. The use of SIDD properties in designing episomal transfection vectors will also be examined.


    26.03.2009, 16:15


    Forum, X1.013a


    Prof. Dr. Craig J. Benham, Depts of Mathematics and of Biomedical Engineering, UC Davis


    Dr. Siegfried Weiss

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