DNA B-helix

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. 

B-DNA helix axis not in accordance with intercalation of A - A decreases flow of B-DNA orientation, (reverse expected for intercala- 55... 

DNA Structure Explain how the underwinding of a B-DNA helix might facilitate or stabilize the formation of Z-DNA. 

Fig. 4. (left) Transient-absorption spectra of the B-DNA helix. The dotted line is the steady-state absorption spectrum, the arrow indicates the pump frequency at 1670 cm"1, the red edge of the guanine CO-stretch band, (right) Transient-absorption spectra of the B-DNA helix. The dotted line is the steady-state absorption spectrum, the arrow indicates the pump frequency at 1685 cm 1 (the center frequency of the guanine CO-stretch band). 

The situation is more complicated for the B-DNA helix (see Fig. 4). Because of the stronger overlap between the guanine and cytosine CO-stretch absoiption bands, it is more difficult to directly probe a spectral relaxation as observed for the Z-DNA helix. 

Watson and Crick based their model (known as the B-DNA helix) on x-ray diffraction patterns of DNA fibers, which provided information about properties of the double helix that are averaged over its constituent residues. The results of x-ray diffraction studies of dehydrated DNA fibers revealed a different form called A-D/VA, which appears when the relative humidity is reduced to less than about 75%. A-DNA, like B-DNA, is a right-handed double helix made up of antiparallel strands held together by Watson-Crick base-pairing. The A helix is wider and shorter than the B helix, and its base pairs are tilted rather than perpendicular to the helix axis (Figure 27.4). 

There is a large variability possible in the structures of double stranded DNA due to the fact that (compared to polypeptides) many more bonds can be rotated in the backbone of each monomer (Scheme 14). The most common and physiologically most important structure is the B-DNA helix. It consists of two polynucleotide chains running in opposite direction which coil around a common axis to form a right-handed double helix. In the helix, the phosphate and deoxyribose units of each strand are on the outside, and the purine and pyrimidine bases on the inside. The purine and pyrimidine bases are paired by selective hydrogen bonds adenine is paired with thymine, and guanine with cytosine (Scheme 15). The structure is very flexible and can form a supercoil with itself, or around proteins. It can form a left-handed supercoil around histones to form nucleosomes which assemble in yet another helical structure to form chromatin. ... 

In this context, only the N(7) site on a guanine base is considered to be near the periphery of the helix (these sites are often exposed to the surrounding medium in the major grove of a B-DNA helix) the core sites (N(3) of cytosine and N(l) of guanine), are, of course, involved in the G-C triple hydrogen-bond scheme. Clearly, the utilization of either of these core sites by a Pt(II) reagent will disrupt, at least locally, the continuity of the DNA helix. 

The synthetic variation of molecular shape and functionality, coupled to spectroscopic studies, can be useful in probing the parameters that drive binding to B-form DNA. In the transition metal complexes examined, the most important factor driving overall binding of these molecules to DNA appeared to be the match of shape and overlap between metal complex and the B-DNA helix. 

Describe the major and minor grooves of the B-DNA helix. Distinguish between the four possible base pairs (A-T, T-A, C-G, and G-C) in terms of the unique arrays of hydrogen bond acceptors and donors and methyl groups they present in the grooves of the DNA. 

Fig. 20. Protein-nucleic order-disorder patterns resembling primitive thermotropic action (top to bottom) Hypothetical B-DNA-prealbumin complex in skeletal presentation, viewed along and perpendicular to the B-DNA helix axis. Thermotropic n-alkoxybenzoic acid dimer.58... 

A Helix A right-hand helix structure of nucleic acid duplexes that has a smaller pitch and a larger diameter than the B-DNA helix. It is the structure adopted by RNA duplexes and RNA-DNA hybrid molecules... 

The sum of the different contributions to the Gibbs enthalpy AG of the B-DNA helix is listed in Table 9. 

Table 9. Deconvolution of the different contributions to B-DNA helix stability.

The progress of adiabatic biocalorimetry in the last ten years has enabled us to gain insight into a new field of nucleic acid-conformation-transitions. Besides the canonical B-DNA helix to coil transitions of the linear DNA sequences we have evaluated the conformational changes of a series of new secondary structures and gained access to a complete thermodynamic data set for all linear sequences as function of two fundamental system parameters, namely the net GC content of the given sequence and the counter ion concentration. 

A brief account of some of the better known nucleic acid-protein interactions is presented in later chapters e.g., the EcoRI enzyme which recognizes not only specific base sequences but also an unusual structure of the B-DNA helix (Section II,B, Chapter 4) and DNase I whose interaction is predominently structural in the minor groove of B-DNA (Section I, Chapter 3). DNA looping generated by... 

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