Supercoiling and Left-handed Z-DNA

Nordheim, Alfred; Peck, Lawrence J.; Lafer, Eileen M.; Stollar, B. David; Wang, J.C.; Rich, Ashley

doi:10.1101/sqb.1983.047.01.012

Cited by 15 publications

(3 citation statements)

References 0 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The results of the calculations are shown diagrammatically in Fig.3 and summarized in Table 2. For large DNA circles they are consistent with previous calculations (15)(16)(17)19) and with experiments. Supercoils can drive the B to Z transition readily, but are much less likely to melt a duplex.…”

Section: Ag (Kcol)supporting

confidence: 92%

“…gro It turns out that the two terms of this equation partially compensate. Thus, it is possible to assign the likely length of the most stable alternate structure as 8-18 bp, if the structure is left-handed Z-like DNA, or as [16][17][18][19][20][21][22][23][24][25][26][27][28][29] bp, if the structure is not twisted at all, or as an even larger length if the structure is some kind of partially unwound right-handed helix. The lengths found experimentally for the homopurine-homopyrimidine SHS are 9-17 bp (when the outer limits of hypersensitivity are considered for both strands together, in the cases of bilateral nicking).…”

Section: Possible Structures Of Shsmentioning

confidence: 99%

See 1 more Smart Citation

Possible structures of homopurine-homopyrimidine S1-hypersensitive sites

Cantor¹,

Efstratiadis²

1984

Nucl Acids Res

122

View full text Add to dashboard Cite

S1 nuclease hypersensitive sites in the 5' flanking regions of eukaryotic genes, present in small artificial supercoiled DNA circles, reside in homopurine-homopyrimidine stretches. The hierarchical behavior which these sites exhibit is consistent with the notion that they act as sinks of torsional free energy. By employing DMS as a single-strand-specific reagent, we show that these sites (despite their S1 sensitivity) are regions of duplex DNA. A simple thermodynamic treatment indicates that the high torsional stress in the small DNA circles is almost certain to be relieved by the formation of alternate DNA structures. The same treatment places some constraints on the types and sizes of the regions with alternate conformation. While no definitive structural conclusions can be drawn, left-handed helices seem most consistent with the extent and the pattern of sensitivity to S1 nuclease.

show abstract

Section: Ag (Kcol)supporting

confidence: 92%

Section: Possible Structures Of Shsmentioning

confidence: 99%

Possible structures of homopurine-homopyrimidine S1-hypersensitive sites

Cantor¹,

Efstratiadis²

1984

Nucl Acids Res

122

View full text Add to dashboard Cite

show abstract

“…Alternatively, chromatin remodeling mediated by the Em/ MARs elements might facilitate the adoption of a non-B-DNA conformation within the Cm repeats. Regions of alternating purines and pyrimidines readily form left-handed Z-DNA when contained in negatively supercoiled DNA (48). Interestingly, a potential Z-DNA forming run of 28 repeats of the dinucleotide, GT, is present within the Cm region of homology (49).…”

Section: Discussionmentioning

confidence: 99%

Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells

Raynard

Baker

2004

Nucleic Acids Research

View full text Add to dashboard Cite

In mammalian cells, little is known about the nature of recombination-prone regions of the genome. Previously, we reported that the immunoglobulin heavy chain (IgH) mu locus behaved as a hotspot for mitotic, intrachromosomal gene conversion (GC) between repeated mu constant (Cmu) regions in mouse hybridoma cells. To investigate whether elements within the mu gene regulatory region were required for hotspot activity, gene targeting was used to delete a 9.1 kb segment encompassing the mu gene promoter (Pmu), enhancer (Emu) and switch region (Smu) from the locus. In these cell lines, GC between the Cmu repeats was significantly reduced, indicating that this 'recombination-enhancing sequence' (RES) is necessary for GC hotspot activity at the IgH locus. Importantly, the RES fragment stimulated GC when appended to the same Cmu repeats integrated at ectopic genomic sites. We also show that deletion of Emu and flanking matrix attachment regions (MARs) from the RES abolishes GC hotspot activity at the IgH locus. However, no stimulation of ectopic GC was observed with the Emu/MARs fragment alone. Finally, we provide evidence that no correlation exists between the level of transcription and GC promoted by the RES. We suggest a model whereby Emu/MARS enhances mitotic GC at the endogenous IgH mu locus by effecting chromatin modifications in adjacent DNA.

show abstract

Left-handed Z-DNA regions are present in negatively supercoiled bacteriophage PM2 DNA.

Stockton¹,

Miller²,

Jorgenson³

et al. 1983

The EMBO Journal

View full text Add to dashboard Cite

Bacteriophage PM2 DNA is a 10‐kb covalently closed circular (ccc) molecule with a reported superhelical density of sigma = ‐0.12. Here we describe the binding of anti‐Z‐DNA antibodies to PM2 form I DNA under high and low salt conditions. The binding to PM2 DNA has been demonstrated by competitive radioimmunoassay (RIA), retardation of the DNA:antibody complexes in agarose gels and visualization by electron microscopy. The antibody binding is dependent on the degree of negative supercoiling. Thus, PM2 form II and form III did not bind the antibody. The low salt RIA results indicated the presence of 200‐400 bp of left‐handed DNA per PM2 molecule. This could reduce the effective superhelical density to sigma = ‐0.04 to ‐0.08, a range comparable with those found for other ccc DNAs in vivo. Electron microscopy revealed that a maximum of 22 antibody molecules bind to PM2. Single‐site restriction with HpaII of the fixed DNA:antibody complex showed a cluster of four to five antibody molecules bound near one end of the linear DNA molecule. The evidence presented indicates that PM2 DNA contains regions of left‐handed conformation under physiological conditions (low salt concentration) as well as at high salt concentrations. In addition, electrophoretic analyses of PM2 topoisomers indicate the presence of left‐handed regions at superhelical densities less than that of isolated PM2 DNA.

show abstract

Supercoiling and Left-handed Z-DNA

Cited by 15 publications

References 0 publications

Possible structures of homopurine-homopyrimidine S1-hypersensitive sites

Possible structures of homopurine-homopyrimidine S1-hypersensitive sites

Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells

Left-handed Z-DNA regions are present in negatively supercoiled bacteriophage PM2 DNA.

Contact Info

Product

Resources

About