Scaffold/matrix attachment regions and intrinsic DNA curvature

Abstract

Recent approaches have failed to detect nucleotide sequence motifs in Scaffold/Matrix Attachment Regions (S/MARs). The lack of any known motifs, together with the confirmation that some S/MARs are not associated to any peculiar sequence, indicates that some structural elements, such as DNA curvature, have a role in chromatin organization and on their efficiency in protein binding. Similar to DNA curvature, S/MARs are located close to promoters, replication origins, and multiple nuclear processes like recombination and breakpoint sites. The chromatin structure in these regulatory regions is important to chromosome organization for accurate regulation of nuclear processes. In this article we review the biological importance of the co-localization between bent DNA sites and S/MARs.

Intrinsic bent DNA sites in the chromosomal replication origin of Xylella fastidiosa 9a5c

“…The b2 site is located inside the dnaA gene. There is no explication for this location, since bent DNA sites have only been described in promoters, intronic regions, and replication origins (14). The b3 site is located in the replication origin of X. fastidiosa and may be involved in the replication process of this bacterium's chromosomal DNA.…”

“…The mobility pattern of each fragment was obtained by the calculation of the R-value (ratio of apparent/real fragment size observed in each gel system). R-values between 0.90 and 1.09 indicate no alterations in mobility, those higher than or equal to 1.10 indicate reduced mobility, and those lower than 0.90 indicate fast mobility (14,26).…”

“…It is known that the intrinsic curvature of DNA plays an important role in cellular processes such as nucleosome compaction (8), recombination processes (9), fragile sites (10), tandem repeated sequences (11), replication origins (12,13), Scaffold/Matrix Attachment Regions (S/MARs) (14) and MARs associated with replication origins (13,15).…”

Sequence-Directed DNA Curvature in Replication Origins Segments

“…After running, the gel is stained with 1 µg/ml of ethidium bromide or another DNA intercalating agent and photographed under UV light. After running, the mobility pattern of each fragment can be obtained through the calculation of the R-value (ratio of apparent/real fragment size) (de Souza & Ornstein, 1998;Fiorini et al, 2006b). The R-values indicate the degree of curvature for a given fragment.…”

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).…”