B —> A transition

In our previous works the fact of AR-DNA interactions, resulting in modifications of physicochemical properties of this biopolymer with formation of supramolecular complexes has been described [Davydova et al., 2005]. The AR-DNA interactions also leads to B —> A transition of DNA, increase the thermostability of these complexes and improving the resistance of DNA to some external influences [Davydova et al., 2006, 2007]. 

Most chemical reactions are reversible, at least to some extent. We will use Pt(AB) = 0.05 again, and start with all of the cells in the A state. To add the back reaction B A to the forward reaction A B, we need to add a transition probability Pt(BA) for the B A transition. We will initially take Pt(BA) = 0.08 and observe the results, again after 500 iterations. How many A ingredients remain after 500 iterations How many remained in Study 2.3a ... 

The biological relevance of B-A transitions in DNA is of great importance. Protein-DNA association results in an induction of partial deformation in the B-form helix to A-form helix. The cyclic AMP receptor protein is a specific example found to induce a B-A-like transition in its DNA target. Perhaps the most attractive feature of A-DNA is its conformational similarity to duplex RNA. RNA-DNA hybrids, often formed during transcription, are also A-form. 

Nearly all structurally characterized DNA polymerases are found to induce B-A transition in DNA bases adjacent to nucleotide incorporation. This induced A-conformation facilitates sufficient access for the protein to desirable contact points in the DNA minor groove. Negative base-pair displacement in the A-form... 

Equation (3) consists of two matrix elements. The first one determines in how far the optical b- a transition is allowed or forbidden the second one determines the shape of the b->a transition. For low temperatures (i.e. n =0) and equal force constants (i.e. equal vibrational frequencies in ground and excited states), the result for the square of the second matrix element is... 

FIGURE 6.8 The state correlations in the VBSCDs of oxidative—additions of (a) a carbenoid reagent into a C—H bond, and (b) a transition metal complex into a C—X bond. 

The second term in both equations describes stimulated light emission in a similar way. Keeping in mind that stimulated emission may be considered, from the point of view of conservation of angular momentum, as absorption on b — a transition, the physical meaning of the functions G[(0, p O, p ) and G 0, p) becomes clear. 

Figure 6.4 Schematic presentation of metal-carbon bonding in (a) a transition metal carbene electrophilic complex and (b) a transition metal alkylidene nucleophilic complex...

These are polarized along the z, x and y axes, respectively, since they involve /u, /q and nv. This means that when, for example, a B] — A, transition occurs an oscillating electric dipole is set up along the x axis. 

Most native DNAs and certain synthetic polynucleotides are able to undergo a B A conformational transition. In films and fibers, this transition may be induced by decreasing the relative humidity to which the sample is exposed. This is demonstrated by the Raman spectra of fibers (Erfurth et al., 1975 Martin and Wartell, 1982 Prescott et al., 1984) and by the IR spectra of films (Pilet and Brahms, 1973 Taillandier et al., 1985) made of native DNAs. In the case of polynucleotides, the decrease of relative humidity affords different results, depending on the sequence of the polymer. Thus, poly d(A-T) and poly d(A-C). poly d(G-T) - double stranded DNA with one strand adenine and cytosine and in the other guanine and thymine - show a classical B A transition (IR Brahms et al 1976 Taillandier et al., 1984a Adam et al., 1987. Raman Thomas and Benevides, 1985 Jenkins et al., 1986). 

This technique was employed to monitor the B —> A transition of DNA as a function of the relative humidity (Pilet and Brahms, 1973 Pohle et al., 1984). The investigated bands are those which reflect the vibrations of the phosphate groups. As shown by Fig. 4.7-3, which presents the polarized infrared spectra of a salmon sperm DNA hydrated film with 93% RH (top, B form) and 58% RH (bottom, A form), the dichroism of the two phosphate bands changes. The B form of the antisymmetric PO2 stretching vibration around 1230 cm is non-dichroic, while that of the A form is perpendicular. The B form of the symmetric PO2 stretching vibration around 1090 cm is perpendicular, while that of the A form is parallel. A simple computation, for instance for the latter band, shows that the value of the angle between the transition dipole moment of this vibration and the double helical axis varies between 68 ° (B form) and 49 ° (A form). This parameter is an extremely sensitive indicator of a B A transition and may also be employed to show the inhibition of a B —> A transition by various classes of molecules, such as proteins (Liquier et al., 1977 Taillandier et al., 1979) or drugs (Fritzsche and Rupprecht, 1990). 

The second class of drugs (intercalating drugs) involves interaction of the two anthra-cycline derivatives aclacinomycin A and violamycin B1 with DNA, which has recently been investigated by infrared linear dichroism (Fritzsche and Rupprecht, 1990). The restriction of the B —> A transition as a consequence of drug binding turns out to be only slightly dependent on the DNA base composition. 

Figure 40. Negative hyperconjugation in (a) the og conformer of R—Y—C—X, (b) a transition state during heterolysis of the C—X bond, and (c) planar cation R—Y—C. ...

Figure 5.10. Schematic illustration showing how nucleophilic and electrophilic interactions cause (a) a water molecule to align with a Si-O bond to form (b) a transition state that results in electron rearrangement, which disassociates the Si-O bond and forms (c) two Si-OH moieties.

The Tc curve (fig. 104) shows clear anomalies with a discontinuity in the range 13-15% Ca (hatched area) which coincides with the B A transition at 13-14% and A —> B at 14—15% (cf. fig. 93), the abrupt increase of the in-phase phonon width (fig. 101) and of the apex phonon width due to the appearance of new modes. This is additional support for the phase-separation scenario. Figure 105 shows the dependence of on oxygen content. Both Td and scale with oxygen and the data segregate in the two states A and B, indicating a correlation to superconductivity. 

Fig. 24 Example trajectories showing the two different ways of counting, as indicated by the arrows. Left cycle-counting (only B— A transitions are counted), Right event-counting (all transitions are counted). Reprinted with permission from [108], Copyright 2010 by the American Physical Society...

Scheme 4.17 Active site of Candida antarctica lipase B (a) transition-state stabilization in wild type and (b) substrate-assisted transition-state stabilization in Thr-nVal mutant.

Figure 3.21. Top The Al-rich side of the Al-Cu phase diagram. Bottom schematic of the formation of the equilibrium precipitate o phase (a) a supersaturated a solid solution, (b) a transition, 0", precipitate phase, and (c) the precipitate 0 phase within the a-matrix phase. Reproduced with permission from CaUister, W. D. Materials Science and Engineering An Introduction, 7th ed., Wiley New York, 2007. Copyright 2007 John Wiley Sons, Inc.

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