DNA conformations

In complexes with Cro, the overall bend and twist of the DNA are similar to those in the repressor complexes, but there is a significant difference in the local structure of two of the nucleotides in each half-site. Binding of 434 Cro or repressor fragment thus imposes a distinct local structure (Figure 8.13), as a result of differences in both the identity and conformations of various amino acid residues that interact with the DNA. The DNA conformational details are significant for the relative affinities of Cro and repressor for various sites, as we describe in a later section. 

These results indicate that the repressor fragment is unable to impose upon the nonconsensus sequence on the right-hand side of OR3 the DNA conformation that is required for tight binding between repressor and DNA. It thus appears that the weaker binding of repressor to OR3 is a consequence of the resulting less perfect "fit" between protein and DNA backbone (see Figure 8.13). 

Protein-DNA backbone interactions determine DNA conformation Conformational changes of DNA are... 

The HMG (high mobility group) box is a DNA-binding domain found in several transcription factors, that can in some cases bend DNA. Some members of this protein family recognize a unique DNA sequence, whereas others bind to a common DNA conformation. 

Shi, X Hammond, RW Morris, MD, DNA Conformational Dynamics in Polymer Solutions Above and Below the Entanglement Limit, Analytical Chemistry 67, 1132, 1995. 

DNA conformation Occurrence Axial rise per base (nm) Base pair turn Base pair repeat unit... 

Identification of proteins that bind to Z-DNA added one further step to the establishment of the presence of Z-DNA in vivo and its possible biological role. Herbert and Rich [22] demonstrated an in vitro assay system where one type of double-stranded RNA adenosine deaminase, called DRAD-binding Z-DNA. There are evidences that topoisomerase II from Drosophila, hiunan and calf thymus recognizes a number of DNA shapes, including Z-DNA [34,35]. Bloomfield and coworkers [36] have found that the condensation of plasmids is enhanced by Z-DNA conformation in d(CG)n repeats. The information related to B-Z transition [31], the effect of ligands on it [28,29] and X-ray crystal structure data [37,38] appear to suggest that the possible biological role of this polymorphic form of DNA will be soon established. 

Arakawa, H., Nakashiro, S., Maeda, M., and Tsuji, A., Analysis of single-strand DNA conformation polymorphism by capillary electrophoresis, /. Chromatogr. A, 722, 359, 1996. 

M6. Maekawa, M., Sudo, K., Kitajima, M., Matsuura, Y Li, S. S.-L., and Kanno, T., Detection and characterization of new genetic mutations in individuals heterozygous for lactate dehydroge-nase-B (H) deficiency using DNA conformation polymorphism analysis and silver staining. Hum. Genet. 91, 163-168 (1993). 

Three fluorescent purine analogs will be described here 2-aminopurine (2AP) [183] and 8-vinyladenine (8VAD), both of which mimic adenine, and N1,N6-ethenoadenine (e-AD). Their structures are shown in Figure 11-15. 2AP is probably the most widely used fluorescent DNA base analog, being utilized as a probe for DNA conformational dynamics [184, 185], due to the environmental specificity of... 

In Z-DNA, guanine residues are syn, whereas cytosine and thymine residues are anti. Eukaryotic DNA contains several alternating purine-pyrimidine sequences consistent with die Z-DNA conformation however, the biologic significance of Z-DNA is still unclear. 

Figure 11. An externally bound BPDE l(+)-N2(G) adduct, (upper) The pyrene is placed in the major groove after an anti - syn rotation about the glycosidic bond of G by 200° in an otherwise B-DNA conformation. (lower) The pyrene moiety is placed in the minor groove in a DNA conformation with a -70° kink, a(BPDE) = 15° and y(DNA = 35°.

Heller DA, Jeng ES, Yeung TK, Martinez BM, Moll AE, Gastala JB, Strano MS (2006) Optical detection of DNA conformational polymorphism on single-walled carbon nanotubes. Science 311 508-511. 

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