B-DNA duplex

Duplex B-DNA is a stable molecule at physiological temperature and helicases are required to unwind the two strands of the helix so that each can serve as a template for DNA polymerases. Because DNA is so stable, energy is required in the form of ATP hydrolysis to drive helicase action. 

Purine-Purine Base Pairs. A G and G G pairs have both been characterised in duplex B-DNA. The A A pairing has only been observed in RNA structures (34, 7... 

In our last example we return to the issue of the possible damaging effects of the standard geometry constraints. Two long trajectories have been computed for a partially hydrated dodecamer DNA duplex of the previous example, first by using ICMD and second with Cartesian coordinate molecular dynamics without constraints [54]. Both trajectories started from the same initial conformation with RMSD of 2.6 A from the canonical B-DNA form. Figure 5 shows the time evolution of RMSD from the canonical A and B conformations. Each point in the figure corresponds to a 15 ps interval and shows an average RMSD value. We see that both trajectories approach the canonical B-DNA, while the RMSD... 

Figure 5 Time dependence of RMSD of atomic coordinates from canonical A- and B-DNA forms m two trajectories of a partially hydrated dodecamer duplex. The A and B (A and B coiTespond to A and B forms) trajectories started from the same state and were computed with internal and Cartesian coordinates as independent variables, respectively. (From Ref. 54.)...

DNA duplex of 400 bp, L is 40 (assuming 10 bp per turn in B-DNA). The linking number for relaxed DNA is usually taken as the reference parameter and is written as Lq. L can be equated to the twist (T) and writhe (W) of the duplex, where twist is the number of helical turns and writhe is the number of supercoils ... 

Performance. The total time for 500 steps of dynamics and 25 nonbond updates for the standard CHARMM benchmark (Brunger, A. T., Harvard University, personal communication, 1985.), a B-DNA eleven-mer duplex with 706 atoms and a 11.5 angstrom nonbond cutoff (77000 nonbond pairs) is found in Table II. 

Berberine increased the contour length of sonicated rod-Uke duplex of all B-DNA depending on base composition (Fig. 6d) and induced the unwinding-rewinding process of covalently closed superheUcal DNA with an unwinding angle of 13°. 

In many investigations of CT, pendant redox probes interact with both bases of abase pair. However, studies of base-base charge transfer can differentiate between discrete intra- and interstrand reactions (Fig. 7). These investigations further attest to the critical role of base stacking in DNA-mediated CT. In B-DNA duplexes, stacking interactions are largely restricted to... 

Studies of base-base CT in B-form DNA duplexes versus A-form DNA R-NA hybrids also confirmed our fundamental tenet that the pathway of efficient charge transfer will be the well-stacked pathway. In A-form duplexes considerable intra- and interstrand stacking exists. Not surprisingly then, in DNA RNA hybrids we observed a similar distance dependence for the yields of intra- and interstrand CT [105]. So, the distinction between intra- and interstrand CT observed in B-DNA duplexes truly correlates with differences in base stacking. 

Modulation of DNA structure and dynamics is also possible using base-pair mismatches. Mismatches exert little influence on the global structure of B-DNA duplexes. Locally, the extent of base stacking perturbation depends sensitively on the nature of the mismatch [139-141]. Therefore, while a CA mismatch introduces a significant distortion in local stacking, the well-stacked GA mismatch is, by many criteria, barely perceptible. The dynamics of mismatched base-pairs may also be significantly distinct from matched Watson-Crick base pairs [9]. We exploit these features of DNA mismatches to probe the sensitivity of DNA-mediated CT to base structure and dynamics. 

Figure 3.7 The crystal structure of DtxR, a 226-residue three-domain dimeric protein, is shown. The protein, activated by cobalt (designated 1 and 2), is bound to a 21-bp DNA duplex based on the consensus operator sequence. Two DtxR dimers surround the DNA duplex, which is distorted compared to canonical B-DNA. Only domain 1, involved in DNA-binding, and domain 2, involved in dimer formation, are shown. The helices of the DNA-binding domain are indicated by HI, H2, and H3. H3 binds to the major groove of the DNA. From Pohl et al., 1999, by permission of Academic Press. 

Energy, AEDjq in kcal/Duplex, Required to Alter B-DNA to Receptor Sites3... 

Figure 7.11 Pictures obtained with high-resolution X-ray diffraction data of G-wire of d(TG4T) (left) and the B-DNA duplex of d(CGCGAATTCGCG). (Reprinted with permission of Wiley— VCH from Chemistry—A European Journal, Vol. 6, p. 3249 ad ff., copyright 2000.)...

The electronic couplings in DNA r-stacks are very sensitive to conformational changes [31]. CT matrix elements were found to be very responsive to variations in the mutual positions of base pairs. As an example, let us compare the electronic couplings calculated for different conformations of the duplex [(GC),(GC)] (Table 4) [41]. In addition to the reference structure with a base-pair arrangement as in ideal B-DNA, we studied 12 distorted configurations each of them differed from the reference by a single step pa-... 

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