B-DNA decamer

Aral S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fu-jimoto Z, Mizuno H, Niimura N. Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements. Nucl. Acids Res. 2005 33 3017-3024. 

Fig. 18.6. Correlation between the helical parameters rise and twist. The correlation coefficient for the three B-DNA decamers (open symbols) is -0.83 19). The dodecamer and the Okazaki fragment both adopt the A conformation. The Okazaki fragment consists of the DNA sequence d(GGGTATACGC) and the chimeric RNA-DNA sequence r(GCG)d(TATACCC)...

Watson-Criek base pairing B-DNA decamer PBB-ID 1D49... 

Figure 2 (a) A B-DNA decamer (PDB ID 1D49) showing one full helical turn, and... 

Fig. 6. Schematic diagram illustrating the kink induced in DNA by ToT (Park et al., 2002). Regular B-DNA decamer and a ToT containing decamer are depicted in green and blue, respectively. The thymines making up the cyclobutane dimer are drawn in red. The view (A) shows part of the major groove, and the view (B) shows the minor groove of the duplex. The phosphodeoxyribose backbone shows a sharply kinked or pinched structure (courtesy of Dr. ChulHee Kang). (See Color Insert.)...

V, P. Chuprina, U. Heinemann, A. A. Nurislamov, P. Zielenkiewicz, and R. E. Dickerson, Proc. Natl. Acad. Set. USA, 88, 593 (1991). Molecular Dynamics Simulation of the Hydration Shell of a B-DNA Decamer Reveals Two Main Types of Minor-Groove Hydration Depending on Groove Width. 

Yanagi, K., Prive, G. G., 8c Dickerson, R. E. (1991). Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. Journal of Molecular Biology, 217, 201. 

The dioxo form for both molecules is more stable by at least about 10 kcal mol than any of the corresponding 12 other species. Optimized geometries for monohydrates and dehydrates, as well as their relative energies help explore the tau-tomerization pathways if they emerge in aqueous solution. Schneider and Berman [67] determined, for example, ordered hydration sites for the nucleotide bases in B-type conformations using crystal structure data on 14 B-DNA decamers. The number of the water molecules, W, within 3.4 A of the atoms of the nucleotide bases were found as 101W/42G, 84W/43C, 92W/43A, and 95W/45T (G, C, A, T the standard code for nucleobases). The two to three water molecules that were identified per base on average in their first hydration shell confirm the importance of such studies. 

Wu P, Norland TM, Gildea B, McLaughlin LW (1990) Base stacking and unstacking as determined from a DNA decamer containing a fluorescent base. Biochem 29 6508-6514... 

Ramakrishnan, B., and Sundaralingam, M. (1993). High resolution crystal structure of the A-DNA decamer d(CCCGGCCGGG). Novel intermolecular base-paired G (G.C) triplets. J. Mol. Biol. 231, 431—444. 

Fig. 1. Two ribbon representations of the crystal structure of the DNA decamer d(CCTCG -CTCTC/GAGAG CGAGG) containing a unique cisplatin interstrand cross-link at d(GpC)-d(GpC) site (asterisks indicate the chelated bases in the adduct). A front view (A) allows to see the structure with the lesion in the minor groove. A side view (B) shows the chicane of the backbone with the helix-sense reversal. Ptn atom, yellow ammine groups, navy blue sugars, pink guanines, navy blue adenines, red thymines, yellow cytosines, hght blue phosphodiester backbone, green.

Privd, GG, Heinemann U, Chandrasegaran S, Kan LS, Kopka ML, Dickerson RE (1988) A mismatch decamer as a model for general sequence B-DNA. In Sarma MH, Sarma RH (eds) Structure and expression, vol 2. DNA and its drug complexes. Adenine Press, Schenectady, NY USA, pp 27-47... 

NOESY walks. For the assignment of non-labile H NMR resonances in B-DNA it is standard practice to employ two major NOE pathways, specifically the sugar HI <-> base H6/H8 and sugar H2 /H2" <-> base H6/H8 pathways (13). In all of the a-containing decamers we observe that the Hr network remains intact, as in the control. However, in each case the Hl /Hl" pathway is broken between the a-nucleotide and the subsequent residue. This effect is due to a flip in the orientation of deoxyribose ring of the a-nucleotide, which places the H2" proton too far away from the base moiety in the following residue to make an NOE contact (Figure 7 also see Models below). 

Fig. 3 Sticky-ended cohesion, (a) Cohesion between two molecular overhangs. Two duplex molecules are shown (top). Each has a single-stranded molecular overhang that is complementary to the overhang on the other molecule. When mixed, the two molecules can cohere in solution (center). The four strands can be ligated to form two strands from the original four (bottom). (b) Structural features of stick-ended cohesion. A crystal structure [4] is shown that contains DNA decamers whose cohesion in the direction of the helix axis (horizontal) is directed by dinucleotide sticky ends. This interaction is seen readily In the center box, where the continuity of the chains is interrupted by gaps caused by the absence of phosphate linkages. The two outer boxes contain B-form duplex DNA. It is a half-turn away from the DNA in the center box, so it is upside-down from it, but otherwise the structure is the same. Thus, sticky ends cohere to form B-DNA, and one can use this information in a predictive fashion to estimate the local structures of DNA constructs held together by sticky ends...

Douki, T, Voituriez, L., and Cadet, J., Characterization of the (6-4) photoproduct of 2 -deoxycyti-dylyl-(3 — 5 )-thymidine and of its Dewar valence isomer, Photochem. Photobiol, 53, 293,1991. Hwang, G.S., Kim, J.-K., and Choi, B.S., NMR structural studies of DNA decamer duplex containing the Dewar photoproduct of thymidylyl(3 —> 5 )thymidine. Conformational changes of the oHgonucleotide duplex by photoconversion of a (6-4) adduct to its Dewar valence isomer, Eur. J. Biochem., 235, 359,1996. 

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