Circular Structures in Retroviral and Cellular Genomes (*)
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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.
Footnotes
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↵§ Supported by National Institutes of Health Training Grant 1-T32-CA09634-01A1.
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↵* Early stages of this work were supported in part by Grant R01 GM41208-03 from the National Institutes of Health (to J. N. A.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore by hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
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↵1 The abbreviations used are:
- bp
-
base pair(s)
- kbp
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kilobase pair(s)
- PCR
-
polymerase chain reaction
- ExoIII
-
exonuclease III
- HIV
-
human immunodeficiency virus
- SIV
-
simian immunodeficiency virus
- ori
-
origin of replication
- IHF
-
integration host factor
- HU
-
histone-like protein
- Fis
-
factor for inversion stimulation
- RT
-
reverse transcriptase.
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↵2 These are GenBank accession numbers M29691[GenBank], M34386[GenBank], M59751[GenBank], M62809[GenBank], M29725[GenBank], and M24197[GenBank].
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↵3 These are defined as the ratio of the equilibrium constants for cyclization to that for biomolecular association (Jacobsson and Stockmayer, 1950).
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- Received May 4, 1995.
- Revision received August 7, 1995.
- © 1995 by The American Society for Biochemistry and Molecular Biology, Inc.
