B-DNA conformation

Figure 11. An externally bound BPDE l(+)-N2(G) adduct, (upper) The pyrene is placed in the major groove after an anti - syn rotation about the glycosidic bond of G by 200° in an otherwise B-DNA conformation. (lower) The pyrene moiety is placed in the minor groove in a DNA conformation with a -70° kink, a(BPDE) = 15° and y(DNA = 35°.

Wisniewski, J.R., Krohn, N.M., Heyduk, E., Grasser, K.D., and Heyduk, T. (1999) HMGl proteins from evolutionary distant orgatrisms distort B-DNA conformation in similar way. Biochim. Biophys. Acta 1447, 25-34. 

Double-stranded DNA in solutions of low salt content usually assume the B-DNA conformation with 10.4-10.5 base pairs per turn. If the two ends are joined the resulting covalently closed circular DNA will be "relaxed." However, there are topoisomerases that act on this form of DNA by cutting both strands, holding the ends, and twisting the two chains (Chapter 27). 

Regular helical structure Duplex DNA forms regular helical structures with defined dimensions. In the B-DNA conformation, the base-pair distance along the helical axis is 3.4 A, providing the structural basis for electron transport. 

G and A (Fig. 12.7). Especially the 5-position of the pyrimidine DNA bases dU (and C) seems to be highly suitable for the attachment of electron donors since these base modifications can be regarded as unnatural and functionalized derivatives of the natural DNA base T. It is important to note that the design of this type of modification allows principally that the chromophores should point into the major groove of the DNA duplex while maintaining the natural Watson-Crick base pairing of the dU moiety to A as the counterbase in the complementary oligonucleotide strand. Hence this functionalization by the chromophores introduces only a local perturbation of the normal B-DNA conformation. 

In contrast, the spectra of modified purines Py-G and Py-A showed a significant NOE between H-l of the pyrene part and H-l of the 2 -deoxyribose moiety. The NOESY cross peak was comparably as strong as the cross peaks between H-2 and H-l. These NMR results can only be explained with the preferred syn conformation of the nucleosides. Conclusively, it is expected that the chromophore-modified purines induce a more drastic perturbation into the B-DNA conformation than the modified pyrimidines. 

In order to test the hypothesis that efficient promoter sequences will be more likely to acquire an A-DNA like conformation than other sequences, we carried out a collection of molecular dynamics simulations of the DNA double stranded dodecamers listed in Table 3. All these simulations were done with the CHARMM23 potential [93], in the presence of explicit solvent (-3500 TIP3 [99] water molecules) and 22 sodium ions (the simulation protocol is detailed in [89,100,101]). The DNA sequences were chosen to include known functional promoters (MLP, MLP2, AT, E4, 6T, CYCl, EFIA, and R28), nonfunctional promoters which could function with a mutant TBP (2C and 7G) [69,70], an inosine variant which can promote transcription (I) [102], and negative controls (GC, POLYA). This collection of sequences also includes two pairs of TATA boxes located in different contexts (MLP and MLP2, and AT and E4) in order to explore the sensitivity of the results to end effects. All the simulations started from a canonical B-DNA conformation and relaxed into a structure closer to A-DNA after 2 ns of simulation, not all the sequences achieved the same structure, as shown in Table 3, an indication that the simulation protocol is capable of identifying sequence dependent features. 

CD and absorption spectra of four duplexes with different mixtures of complementary DNA and RNA strands, each duplex containing alternating A T and G C base pairs (except that T in the DNA strands is replaced by U in the analogous RNA strands). The RNA duplex r(AG)i2 r(CU),2 had a negative band at 210 nm and a larger positive band above 250 nm than did the DNA duplex d(AG),2-d(CT) 2. These CD features are characteristics that generally distinguish the A-RNA conformation from the B-DNA conformation. ... 

The CG model of the B-DNA conformation of the dsDNA, developed by Savelyev and Papoian, relied on a rather coarse mapping of one bead per nucleotide. To reproduce the fine features of DNA molecule s atomistic conformational preferences, the Hamiltonian introduced bonded and non-bonded interactions within and between the two DNA strands. The effective Hamiltonian is ... 

CG representation on the B-DNA conformation. In this model, the resolution of three beads per nucleotide gives the appropriate resolution of the major groove without requiring the use of anisotropic potentials. The effective Hamiltonian, for the 3SPN.2 CG... 

The initial DNA structures were built in the standard B-DNA conformation within QUANTA (Molecular Simulations, Inc 1992). The sodium ions were placed along the O-P-0 bisector, SA away from the P atom. The systems thus assembled were solvated with the overlay procedure within Insight II (Biosym Technologies 1993), and the final simulation cells were trimmed to hexagonal prisms of 24A side and Ilk length with Simulaid 26). 

Figure 1.4 Schematic drawing of the (dT)2-(dA)2 tetramer, adopting the B-DNA conformation. The PCM cavity used for calculations in solution is also shown.

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