DNA helix

The protein dimer binds so that the recognition a helices at opposite ends of the protein molecule are in the major groove of the DNA as predicted, where they interact with base pairs at the end of the DNA molecule. Since these binding sites are separated by one turn of the DNA helix, it follows that at the center of the DNA molecule the narrow groove faces the protein... 

The DNA helix has major and minor grooves Z-DNA forms a zigzag pattern B-DNA is the preferred conformation in vivo Specific base sequences can be recognized in B-DNA Conclusion Selected readings... 

FIGURE 12.31 A model for chromosome structure, human chromosome 4. The 2-um DNA helix is wound twice around histone octamers to form 10-um uucleosomes, each of which contains 160 bp (80 per turn). These uucleosomes are then wound in solenoid fashion with six uucleosomes per turn to form a 30-nm filament. In this model, the 30-nm filament forms long DNA loops, each containing about 60,000 bp, which are attached at their base to the nuclear matrix. Eighteen of these loops are then wound radially around the circumference of a single turn to form a miniband unit of a chromosome. Approximately 10 of these minibands occur in each chromatid of human chromosome 4 at mitosis. 

Binding of cisplatin to the neighbouring bases in the DNA disrupts the orderly stacking of the purine bases when it forms a 1,2-intrastrand crosslink, it bends the DNA helix by some 34° towards the major groove and unwinds the helix by 13°. These cross-links are believed to block DNA replication. 

Some purely major groove-binding TFs, such as the basic-region leucine zipper (bZIP) protein GCN4, can co-occupy the DNA helix in the presence of polyamides [72]. Modified polyamides with an attached Arg-Pro-Arg tripeptide can interfere with major groove-binding proteins by disrupting key phosphate contacts, distort-... 

TBP binds to the TATA box in the minor groove of DNA (most transcription factors bind in the major groove) and causes an approximately 100-degree bend or kink of the DNA helix. This bending is thought to facilitate the interaction of TBP-associated factors with other components of the transcription initiation complex and possibly with factors bound to upstream elements. Although defined as a component of class II gene promoters, TBP, by virtue of its association with... 

These observations were significant to our choice of reactants for probing CT at DNA-modified surfaces. In particular, an upright orientation of the DNA relative to the surface is required to probe DNA-mediated reactions otherwise a more direct reaction between an intercalating probe and the electrode might be possible. Consequently, reactants were selected such that a negative potential could be apphed, thereby initiating reduction of an intercalated redox probe distantly bound within DNA helix. Importantly, the... 

Intercalators with asymmetric substituents, such as the phenyl and ethyl groups of ethidium bromide (21), frequently cause a smaller increase in DNA length than expected from the simple model described above. In such cases these groups are inserted into the minor groove of the DNA helix with concomitant bending of the double helix towards the major groove. This alternative type of complexation is supported by X-ray studies on model systems, 25). 

A -DNA The Watson-Crick model of DNA is based on the x-ray diffraction patterns of B-DNA. Most DNA is B-DNA however, DNA may take on two other conformations, A-DNA and Z-DNA. These conformations are greatly favored by the base sequence or by bound proteins. When B-DNA is slightly dehydrated in the laboratory, it takes on the A conformation. A-DNA is very similar to B-DNA except that the base pairs are not stacked perpendicular to the helix axis rather, they are tilted because the deoxyribose moiety puckers differently. An A-DNA helix is wider and shorter than the B-DNA helix. 

The dispersive tendency dominates in a high-temperature system containing only a few particles, while the order tendency is important in a system in which the particles are themselves ordered, as in a crystal or the DNA helix. The real states of systems of matter lie somewhere between these two extremes. 

Site II is characterized by a relatively small 2-3 nm red shift in the absorption spectrum and a positive AA spectrum. In this conformation, the planes of the pyrene moeities tend to align parallel rather than perpendicular to the axis of the DNA helix. 

While it is reasonable to assume that kinks are formed at the site of the covalent binding of BaPDE (34), it is also possible that such bends arise elsewhere on the double helix, due to the known formation of nicks and single-strand breaks (35,36). Therefore, the existence of kinks in the DNA helix at site I or site II binding sites should be further investigated, before such a model can be adopted definitively. 

The level of DNA modification in any biological system is low, ranging up to about one adduct per 105 bases in the DNA helix. Any methods used to detect such damage must therefore either be very sensitive or involve some method by which the effect of such damage is amplified to measurable levels. 

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