Mapping Z-DNA in the human genome. Computer-aided mapping reveals a nonrandom distribution of potential Z-DNA-forming sequences in human genes.

Functional analysis of the human annexin A5 gene promoter: a downstream DNA element and an upstream long terminal repeat regulate transcription

“…In the absence of a TATA box, basal transcription is likely to be controlled by the Sp1 sites in the immediate 5h flanking region, although full activity clearly requires additional upstream determinants. These Sp1 sites lie in the middle of a CpG island spanning bp k300 to j300 bp and close to a potential Z-DNA-forming segment (Figure 2), which signify both compositional and conformational changes influencing the genomic landscape, the accessibility of cis-acting elements and the activation of gene transcription [35].…”

“…BLAST and QUERY e-mail servers were utilized for sequence database searches and retrieval respectively, from the National Center for Biotechnology Information (NCBI) ; http :\\ www.ncbi.nlm.nih.gov. Programs from DNASIS (Hitachi Software Engineering, San Francisco, CA, U.S.A.) calculated the sequence GjC content, and Z-Hunt 2.0 [35] was used for Z-DNA detection. SIGNAL SCAN 4.0 [36] identified sequence matches to known DNA cis-regulatory elements in conjunction with the Transcription Factor Database (NCBI) and TRANSFAC database [37].…”

“…Major structural elements comprising the 5h flanking region include various potential regulatory elements identified by SIGNAL SCAN [36], a 437 bp endogenous retroviral (ERV) LTR homologous to LTR47B in REPBASE 5.0 [38], a 60 bp adenine-rich segment and a 25 bp stretch of Z-DNA, drawn to scale. Below the scale is a plot of promoter Z-DNA-forming potential in arbitrary units [35], with a sharp peak around k70 bp corresponding to the inset sequence. A plot of the (GjC)/(AjT) ratio over a 10 bp floating window (bottom panel) identifies a CpG island in the core promoter region, p300 bp surrounding tsp1.…”

“…A CpG island with an average 75 % GjC nucleotide content spanned the region 300 bp in either direction from tsp1 and contained the presumptive core promoter. A prominent, 25 bp Z-DNA segment of alternating purine\pyrimidine nucleotides was detected by the Z-Hunt-II program [35] 75 bp upstream of the tsp in both the human and chick annexin A5 genes.…”

Progress and perspective on chiral plasmonic nanostructures enabled by DNA programming methodology

“…32-35 Apart from the canonical B-form DNA RH helix found by Watson and Crick, there are two other primary conformations of DNA helices: A-DNA, which is also RH but more rigid than B-DNA; 37,38 and Z-DNA, which is surprisingly LH and found in some eukaryotic genomes. 39 In addition to three helical structures, researchers have found various other DNA conformations that enriched the structural diversity of DNA, such as triplex (H-DNA), 40 minidumbbell, 41 intermediate Holliday junction. 42 Some nucleic acid aptamers with G-rich sequences are folded into four-stranded structures with the help of metal ions (Fig.…”