Intrinsically bent DNA in replication origins and gene promoters

Abstract

Intrinsically bent DNA is an alternative conformation of the DNA molecule caused by the presence of dA/dT tracts, 2 to 6 bp long, in a helical turn phase DNA or with multiple intervals of 10 to 11 bp. Other than flexibility, intrinsic bending sites induce DNA curvature in particular chromosome regions such as replication origins and promoters. Intrinsically bent DNA sites are important in initiating DNA replication, and are sometimes found near to regions associated with the nuclear matrix. Many methods have been developed to localize bent sites, for example, circular permutation, computational analysis, and atomic force microscopy. This review discusses intrinsically bent DNA sites associated with replication origins and gene promoter regions in prokaryote and eukaryote cells. We also describe methods for identifying bent DNA sites for circular permutation and computational analysis.

Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

“…The 5 bp duplication generated upon insertion is shown as a stippled box alternating rigid and flexible regions (Pedersen et al 1998) as well as curved sequences (Brukner et al 1995). The presence of sequence-directed bends has been implicated in functionally relevant cellular processes including transcription (Cress and Nevins 1996), replication (Gimenes et al 2008), and recombination (Kusakabe et al 2001). In this study, we present evidence that composition asymmetry directly affects the bendability and configuration of the target region, which in turn, likely modulates IS2 transposition in a way which we do not yet fully understand.…”

Sequence-Directed DNA Curvature in Replication Origins Segments

“…Many methods can be applied to localize intrinsically bent DNA sites, for example, circular permutation (Gimenes et al, 2008b;Wu & Crothers, 1984), computational analysis (Marilley & Pasero, 1996;Pasero et al, 1993), and atomic force microscopy (Marilley et al, 2007). Here we present methods for analyzing bending DNA regions by computational simulation using algorithms for curvature and gel electrophoresis mobility assays, including the circular permutation strategy.…”

“…The number of hydrogen bonds in a base pair, the stacking energy of a given base step and the occupation of both the major and minor grooves by nitrogenous bases are the major determinants of DNA (Calladine et al, 2004;Travers, 2004). The bending of DNA is one of the most important deformations of the DNA structure, which is universal in biology, for both storage and retrieval of information encoded in the base-pair sequence (Gimenes et al, 2008b). Many base sequences can conform to a systematic curvature in DNA; however, a series of A 5-6 (A-tracts) repeats spaced in phase with the DNA helical repeat (10-11 bp intervals) are the most important causative sequences for the presence of intrinsically bent DNA sites.…”

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

“…R-values between 0.90 and 1.09 signify no alteration in the fragment mobility; R-values greater than 1.10 indicate a reduced mobility, whereas R-values less than 0.90 signify an increase in mobility over what is expected for a given molecular size (25). The circular permutation experiments were performed for bent DNA site b5 as described elsewhere (7,11,12,26). A 320 bp fragment (1,072 to 1,391 bp positions) was amplified with the following primers: forward 5'-TGC CCA GCG TTT CTC AGT GC-3' and reverse 5'-ACT CCT GGA GCA CCA GCC AG-3' and cloned into the pTZ57R/T vector (InsTAclone PCR Cloning kit).…”

“…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).…”