Molecular Genetics

Facts

	Intercalating agents cause partial unwinding of the DNA helix. When these agents are applied to isolated nuclei, the unwinding of the DNA causes the extrusion of DNA strands in a mass surrounding the nucleus. Treatment of such "swollen" nuclei with DNase removes the extruded DNA, leaving 10% or less of the total DNA associated with nuclear particles.
The remaining DNA is thought to be attached to nuclear substructure and is called scaffold attached regions or matrix attached regions, abbreviated SAR or MAR. SAR DNA has these characteristics: A-T rich; binds HMG-1, a non-histone chromosomal protein; binds topoisomerase II. Similar chromosome banding patterns are seen with: Q-banding; G-banding; Fluorescein conjugated anti-topoisomerase II; Daunomycin (a DNA-binding dye whose fluorescence is quenched by G-C base pairs, and is thus an indicator of AT-rich regions). Reverse banding occurs with YOYO-1 [a dye that fluoresces when bound to DNA] in the presence of methyl green [binds to A-T rich regions, quenching YOYO-1 fluorescence].

Interpretations

• Q and G-banding patterns are due to the location of SAR's in the chromatin.
• SAR's divide the chromatin into loops.
• Torsional stress of replication of each loop may be isolated from the stress experienced by adjacent loops.
• The SAR, through topoisomerases, may be the site of relief of torsional stress occurring during replication.

Further information

• Inclusion of SAR's or MAR's in transgene-containing constructs tends to make transgene expression levels less variable among transformant clones.
• SARs' influences on transcription regulation are under investigation.
• The difference between SAR and MAR is an operational one (rev). The nuclear matrix is prepared by high salt extraction of nuclear chromatin. Sequences binding to this preparation are MARs. The nuclear scaffold is prepared by extracting with lithium diiodosalicylate (ref). The scaffold binds SARs.
• The average distance between SAR/MARs is 30 kbp, while DNA chromosome loops range from 25 to 600 kbp. Thus, not all SAR/MARs are actually attached.
• Whether SAR/MARs function as origins of replication is debated.

This is page 1327 of Molecular Genetics by Ulrich Melcher, © 1997, 1998, 1999, 2003