Sequence-induced DNA curvature at the bacteriophage λ origin of replication

Abstract

DNA replication in bacteriophage lambda begins at a unique origin between residues 39,000 and 39,200 of the lambda genome. This segment of DNA serves a dual function since it also lies within the coding sequence of the lambda replication initiator protein O which binds origin DNA. The lambda origin sequence contains four 19-base-pair (bp) segments (iterons) which have dyad symmetry, followed by a 40-bp A + T-rich zone of highly asymmetrical base composition. It was noted earlier that lambda origin DNA exhibits an anomalous electrophoretic mobility on gels; that is, the length of DNA as determined by DNA sequencing is approximately 20% less than is predicted from electrophoretic mobility. Recent studies of kinetoplast minicircle DNA (K-DNA) from the protozoan Leishmania tarentolae have led to the proposal that sequence-induced DNA curvature could account for such electrophoretic anomalies by alteration of the shape of the DNA molecule. We now present evidence that the lambda origin contains a static curve.

Computer modelling of DNA structures involved in chromosome maintenance

“…The method most often used to detect DNA-bending relies on the decreased mobility of bent DNA fragments during polyacrylamide gel electrophoresis (5)(6)(7)(8). This technique has been used to identify bending sequences in a variety of prokaryotic and eukaryotic systems (8)(9)(10)(11) and has been applied to the study of synthetic DNA oligonucleotides in order to identify the major sequence determinants of DNA curvature (6,7). These studies have led to the development of two models for DNA bending.…”

DNA curvature in front of the human mitochondrial L-strand replication origin with specific protein binding

“…The locally curved DNA possibly is a sequencedependent feature recognized by some proteins (2,3,4). Proteins that induce or stabilize bends in specific DNA sequences are involved in a variety of cellular processes including site-specific recombination (5), DNA replication (6,7,8), chromatin organization (1) and gene regulation (9). Since the electrophoretic mobility of DNA fragments gels is dependent on their average shape, a curved DNA molecule migrates at a different rate than a linear fragment with the same number of base pairs; bent protein-DNA complexes behave in a analogous manner.…”

The adenine-thymine domain of the simian virus 40 core origin directs DNA bending and coordinately regulates DNA replication.

“…Thus, DNA bending in the correct conformation and location may be a structural signal for replication in polyomavirus origins and perhaps in other origins of replication with consecutive runs of adenines. The first five base pairs (TGCAT) of the 20-base-pair segment and the T between the AAA and AAAAAAAATT domains serve a sequence-independent function that may establish proper spacing within the core origin.Adenine-thymine (AT) tracts are a common feature of a wide variety of replication origins in both procaryotes and eucaryotes (7,12,13,20,23,26). The relatively weak base pairing of these tracts would facilitate strand separation, an early and indispensable step in the initiation of DNA replication.…”

“…Adenine-thymine (AT) tracts are a common feature of a wide variety of replication origins in both procaryotes and eucaryotes (7,12,13,20,23,26). The relatively weak base pairing of these tracts would facilitate strand separation, an early and indispensable step in the initiation of DNA replication.…”