Abstract
A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830-base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I). This unusual structure displayed relatively smooth planar bending throughout its length. The structure is conserved in diverse isolates of HIV-I, HIV-II, and simian immunodeficiency viruses, which implies that it is under selective constraints. A search of all sequences in the GenBank data base was carried out in order to identify similar circular structures in cellular DNA. The results revealed that the structures are associated with a wide range of sequences that undergo recombination, including most known examples of DNA inversion and subtelomeric translocation systems. Circular structures were also associated with replication and transposition systems where DNA looping has been implicated in the generation of large protein-DNA complexes. Experimental evidence for the structures was provided by studies which demonstrated that two sequences detected as circular by computer preferentially formed covalently closed circles during ligation reactions in vitro when compared to nonbent fragments, bent fragments with noncircular shapes, and total genomic DNA. In addition, a single T-->C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization. These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes.
Highlights
Potential to give rise to complex higher order structures, which may be important in regulating genome packaging and function
The results show that large circular structures are associated with a wide range of DNA recombination systems and we suggest that this unusual structure plays a general role in DNA looping
In order to determine if DNA circularity is a characteristic of invertible systems, we examined the inversion regions responsible for the well characterized phase variation of flagellin genes in Salmonella typhimurium and fimbrial protein genes in E. coli.The invertible DNA segments in both systems appear as C-shaped structures as shown in Fig. 4 (E and F)
Summary
A computer program for predicting DNA bending from nucleotide sequence was used to identify circular structures in retroviral and cellular genomes. An 830base pair circular structure was located in a control region near the center of the genome of the human immunodeficiency virus type I (HIV-I) This unusual structure displayed relatively smooth planar bending throughout its length. A single T 3 C substitution in one of these sequences rendered it less planar as seen by computer analysis and significantly reduced its rate of ligase-catalyzed cyclization These results permit us to speculate that intrinsically circular structures facilitate DNA looping during formation of the large protein-DNA complexes that are involved in site- and region-specific recombination and in other genomic processes. The results show that large circular structures are associated with a wide range of DNA recombination systems and we suggest that this unusual structure plays a general role in DNA looping
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