Computer modelling of DNA structures involved in chromosome maintenance

Abstract

Sequence-dependent DNA bending of synthetic and natural molecules was studied by computer analysis.Modelling of synthetic oligonucleotides and of 107 kb of natural sequences gave results which closely resembled published electrophoretic data, demonstrating the powerful predictive capacity of the procedure.The analysis was extended to the study of DNA structures involved in chromosome maintenance.Centromeric DNAs from yeast were found to have sequences in their functional elements which cause them to be unusually straight. Autonomous replicating sequences were found to have two structural domains, one consisting of unusually straight sequences surrounding the consensus and the other of bending elements in flanking DNA. In addition to a structural homology, centromeric and autonomous replicating sequences share common sequence elements.These observations show that computer modelling of natural sequences is a viable approach to the study of the biological implications of alternative DNA structures.

Intrinsic Bent DNA Sites in the Developmentally AmplifiedC3-22Gene Promoter ofRhynchosciara americana(Diptera: Sciaridae)

“…19,23) In silico DNA curvature analysis. The DNA sequence of the region containing the C3-22 gene (U69899) and the flanking regions of the DNA puff C3 of R. americana (pHN3.5, pRR5.5, and pRa400 clones) were analyzed using the algorithm for secondary structures designed by Eckdahl and Anderson,30) implemented in the Map15a and 3D15m1 software.…”

Quaternion modeling of the helical path for analysis of the shape of the DNA molecule

“…Lastly, the curvature of the DNA molecule can be simply characterized by the ratio of the curvilinear distance (contour length) to the linear distance between the ends of the segment (SD value) (Eckdahl, Anderson, 1987;Tan, Harvey, 1987) and vice versa (Qc, (Dlakic, Harrington, 1998;Kanhere, Bansal, 2003;Matyašek et al, 2013)). Large values of C, d-max and SD indicate a more curved DNA fragment.…”

Replication origins oriGNAI3 and oriB of the mammalian AMPD2 locus nested in a region of straight DNA flanked by intrinsically bent DNA sites

“…The 2D projection of the 3D trajectories was obtained with 3D15m1 software using the algorithm of Eckdahl and Anderson (28). The helical parameters were calculated using Map15a software as described elsewhere (11).…”