B-DNA structures

Figure 8.23 The helix-turn-helix motifs of the subunits of both the PurR and the lac repressor subunits bind to the major groove of DNA with the N-terminus of the second helix, the recognition helix, pointing into the groove. The two hinge helices of each arm of the V-shaped tetramer bind adjacent to each other in the minor groove of DNA, which is wide and shallow due to distortion of the B-DNA structure. (Adapted from M.A. Schumacher et al.. Science 266 763-770, 1994.)...

The central 10 base pairs of the palindromic DNA molecule have a regular B-DNA structure. Between base pairs 5 and 6 in each half of the fragment (base pairs are counted from the center) there is a 40° kink which causes these base pairs to be unstacked (Figure 8.24a). After this localized kink the two end regions have an essentially B-DNA structure. The kink occurs at a TG step in the sequence GTG. These TG steps at positions 5 and 6 are highly conserved in both halves of different CAP-binding sites, presumably in part because they facilitate kinking. 

In the two complexes studied by x-ray crystallography, the interactions between TBP and the DNA, as well as the deformation of the B-DNA structure, are very similar, and we will illustrate some of these details for the yeast structure. Minor details of the two complexes vary due to differences in some of the side chains and nucleotides that are present in the interaction areas. 

In conclusion, one important factor that contributes to the strong affinity of TBP proteins to TATA boxes is the large hydrophobic interaction area between them. Major distortions of the B-DNA structure cause the DNA to present a wide and shallow minor groove surface that is sterically complementary to the underside of the saddle structure of the TBP protein. The complementarity of these surfaces, and in addition the six specific hydrogen bonds between four side chains from TBP and four hydrogen bond acceptors from bases in the minor groove, are the main factors responsible for causing TBP to bind to TATA boxes 100,000-fold more readily than to a random DNA sequence. 

The sharp bend of DNA at the TATA box induced by TBP binding is favorable for the formation of the complete DNA control module in particular, for the interaction of specific transcription factors with TFIID. Since these factors may bind to DNA several hundred base pairs away from the TATA box, and at the same time may interact with TBP through one or several TAFs, there must be several protein-DNA interactions within this module that distort the regular B-DNA structure (see Figure 9.2). The DNA bend caused by the binding of TBP to the TATA box is one important step to bring activators near to the site of action of RNA polymerase. 

Interactions that are not sequence specific are also an Important part of the binding and occur between the sugar and phosphate residues of the DNA and the side-chain and main-chain atoms of the protein. In the crystals the DNA fragment retains the B-DNA structure with only minor distortions. 

Trifonov, E.N. (1983) Sequence-dependent variations of B-DNA structure and protein-DNA recognition. Cold Spring Harb. Symp. Quant. Biol. 47, 271-278. 

The average DNA helix diameter used in modeling applications such as the ones described here includes the diameter of the atomic-scale B-DNA structure and— approximately—the thickness of the hydration shell and ion layer closest to the double helix [18]. Both for the calculation of the electrostatic potential and the hydrodynamic properties of DNA (i.e., the friction coefficient of the helix for viscous drag) a helix diameter of 2.4 nm describes the chain best [19-22]. The choice of this parameter was supported by the results of chain knotting [23] or catenation [24], as well as light scattering [25] and neutron scattering [26] experiments. 

Firstly, studies concerned with the forces associated with conformational change [91,92] demonstrated that when large forces (5-15 pN) are applied to the DNA molecule, the natural B-DNA structure is converted into a new overstretched conformation, i.e., S-DNA. Theoretical models and molecular dynamics simulations have been developed to imderstand the overstretching transition, the role of twist stored within the double hehx, and stiffness of DNA [63,92-99]. For example, it has been found [63] that the ohgonu-... 

The detailed analysis of DNA structure in the region of contact with the binding protein often displays distinct divergence from the parameters of classical B-DNA structure. The specific sequence-determined conformation of the DNA is often a prerequisite for a specific recognition. This recognition mechanism is, for example, realized with the Trp-repressor, where the sequence determines a certain spatial arrangement of the... 

A. Fiethen, G. Jansen, A. Hesselmann, M. Schiitz, Stacking energies for average B-DNA structures from the combined density functional theory and symmetry-adapted perturbation theory approach. J. Am. Chem. Soc. 130, 1802-1803 (2008)... 

Proteins that bind the major groove but do not perturb the normal B-DNA structure can enhance CT efficiency in DNA. This was demonstrated by using the restriction endonuclease PvuII and the transcription factor ANTP [17]. As a result of the binding of proteins, the DNA conformation is stiffened, the conformational movements are reduced, and, as a result, CT is facilitated. In contrast with R.PvuII and ANTP, the TATA-box binding protein induces two 90° bends in the DNA... 

At the level of primary structure, several recent experiments have shown the effect of base sequence on the local structure of DNA. A dramatic example is the crystal structure of d(CpG) as determined by Rich and coworkers ( ). This molecule crystallizes in a left-handed double helical form called Z-DNA, which is radically different in its structural properties from the familiar right-handed B-DNA structure. Dickerson and Drew (10) showed in the crystal structure of the dodecanucleotide d(CGCGAATTCGCG) that the local twist angle of a DNA double helix varies with sequence. Deoxyribonuclease I cuts the phosphodiester backbone of the dodecanucleotide preferentially at sites of high twist angle (l 1). From these and other (12,13) experiments we see that the structure of DNA varies with base sequence, and that enzymes are sensitive to these details of structure. 

B-form DNA molecular model. A space-filling model of B-DNA is shown with the helix axis vertical. The phosphate atoms are picked out in dark purple, nitrogens in pale purple, oxygens in purple-grey, carbons in black and hydrogens in light gray. The B-DNA structure may be visualized interactively on the World Wide Web at... 

It is of interest to investigate whether a TC intercalation between base pairs could accelerate the reaction(s) leading to covalently bonded PAHDE -DNA adducts. Surprisingly, DNA-TC complexes have become the object of molecular modelling only very recently [112]. The aim of the studies has been to find an explanation for the enantiomeric stereoselectivity and shape dependence of PAH carcinogenicity in terms of steric and energetic compatibility of the bay-region TC s with the B-DNA structure. 

The B-DNA structure given by Amott and Hukins [171] is taken as initial conformation for the DNA fragment as this structure is close to the native DNA at physiological conditions. According to electric linear dichroism measurements [154], there are several possibilities for the mutual geometrical arrangement of the components of the physical complex. Hence, different initial orientations and conformations of PAH metabolites were considered with the aim to find the most stable structure of the intercalated complex. 

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