Major and minor grooves of DNA

FIGURE 28-8 Groups in DNA available for protein binding. Shown the major and minor grooves of DNA. Groups that can be used for... 

Figure 8.2.5 Base pairing in DNA and RNA. (a) B-DNA (b) tRNA (c) mRNA (no pairs) (d) chemical environment in major and minor grooves of DNA as produced by the heteroatoms and substituents of the GC and AT pairs.

As mentioned earlier, it is difficult to obtain a quantitative measure of entropy. By using the 2PT method (the method will be described later in Chapter 19), one can obtain the entropy of water molecules in both major and minor grooves of DNA. One can also get a measure of the translational diffijsivity of those water molecules from the mean-square displacement or velocity autocorrelation function - all these are fortunately easily available with computer simulations. 

Figure lO.A.l. Possibility of HBs with water moleeules and the base pairs in the major and minor grooves of DNA (schematic). Adapted with permission from J. Chem. Phys., 125 (2006), 234903. Copyright (2006) American Institute of Physics. 

Interestingly, water faces hydrophilic surfaces many times in a confined state, such as in the major and minor grooves of DNA and reverse micelles, to give popular examples. In such situations, the ability of water molecules to form many different nearly isoenergetic structures (polymorphs) becomes really useful. 

Drugs that bind to the major and minor grooves of DNA do so by a combination of hydrogen bonding, van der Waals interactions, and electrostatic attractions—the same forces proteins use to bind their substrates. Leinamycin is an example of an anticancer drug that binds to the major groove. Once leinamycin is bound, it alkylates the N-7 position of a purine ring. 

DNA is a polyelectrolyte with a tightly bound spine of water. Both DNA damage and repair mechanisms involve ET (10). Water is an important determinant of DNA structural stability, both in the form of organized water that occupies the major and minor grooves of the DNA double strand and as bulk solvent (10). 

The major and minor grooves of B-form DNA correspond to what features of A-form RNA ... 

Molecular Recognition in the Major and Minor Grooves of Duplex DNA... 

Bashkin and co-workers have prepared a variety of terpyridine and bipyridine conjugates with nucleosides (207a-d) suitable for incorporation into oligonucleotides. The analogues are designed to deliver metals to the major or minor groove of DNA. 

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. 

The dielectric relaxation spectra of various DNA solutions are also quite complex, actually more complex than those observed for protein solutions. One of the reasons for such complex relaxation behavior of DNA solutions is the presence of free and bound counter ions in solution. Water molecules in the major and minor grooves of water behave differently from those in the buUc. The presence of the positively charged counter ions in turn influences the response of many other water molecules. Negatively charged phosphate ions also influence the surrounding water molecules. 

Figure 107 Left panel number of water molecules (At ) in the major and minor grooves of B- and A-DNA as functions of hydration number (F)- Right panels probability (R) of observing a spanning water cluster in the major and minor grooves of B- and A-DNA molecules as functions of hydration number (F). Reprinted, with permission, from [621].

Figure 34 Mixed representation of the p53 DNA complex. The p53 protein and the DNA is shown as capped stick model, the protein backbone is represented as ribbon model. Parts of the molecular surface indicate the p53 protein DNA interface region. The surfaces are color coded with respect to the electrostatic potential calculated by a finite difference algorithm solving the Poisson-Boltzmann equation - (blue, negative gray, neutral red. positive). The electropositive parts of the p53 protein fit perfectly in the major and minor groove of the almost electronegative DNA...

In B-DNA because the helical axis runs through the center of each base pair and the base pairs are stacked nearly perpendicular to the helical axis (see Figures 7.1 and 7.5), the major and minor grooves are of similar depths. 

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.)...

An analysis of the hydration structure of water molecules in the major and minor grooves in B-DNA has shown that there is a filament of water molecules connecting both the inter and the intra phosphate groups of the two strands of B-DNA. However, such a connectivity is absent in the case of Z-DNA confirming earlier MC simulation results. The probability density distributions of the counterions around DNA shows deep penetration of the counterions in Z-DNA compared to B-DNA. Further, these distributions suggest very limited mobility for the counterions and show well defined counter-ion pattern as originally suggested in the MC study. 

Figure 35-2. A diagrammatic representation of the Watson and Crick modei of the doubie-heiicai structure of the B form of DNA.The horizontai arrow indicates the width of the doubie heiix (20 A), and the verticai arrow indicates the distance spanned by one compiete turn of the doubie heiix (34 A). One turn of B-DNA in-ciudes ten base pairs (bp), so the rise is 3.4 A per bp. The centrai axis of the doubie heiix is indicated by the verticai rod. The short arrows designate the poiarity of the antiparaiiei strands. The major and minor grooves are depicted. (A,adenine C, cytosine G, guanine ...

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... 

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