A database of 32 DNA triplets to study triple helices by molecular mechanics and dynamics

Piriou, Jean-Marc; Ketterlé, Christophe; Gabarro-Arpa, Jacques; Cognet, Jean A. H.; Bret, Marc Le

doi:10.1016/0301-4622(93)e0103-c

Cited by 25 publications

(16 citation statements)

References 64 publications

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“…Small differences are observed for the rotational parameters (buckle, propeller twist, opening) but not for the translational parameters (shear, stretch, stagger). The triplets observed in the crystal are remarkably similar to the analogous triplet from the database of Morcad, which is based on fibre diffraction data (Piriou et al, 1994) and to both triplets in the CAP-DNA complex (Schultz et al, 1991). Differences are largest for rotational parameters suggesting more rotational than translational freedom in the Hoogsteen pairing.…”

Section: Propellersupporting

confidence: 74%

“…Experimental studies using nuclear magnetic resonance, infrared and Raman spectroscopy, as well as theoretical methods such as molecular modelling and dynamics have indicated different conformations of triple helices depending on the composition of the three strands (Radhakrishnan, de los Santos & Patel, 1991;Cheng & Pettitt, 1992;Laughton & Neidle, 1992a;Raghunathan, Miles & Sasisekharan, 1993;Piriou, Ketterl6, Gabarro-Arpa, Cognet & Le Bret, 1994;Radhakrishnan & Patel, 1994; for review see, Sun & H616ne, 1993).…”

Section: D(t)]poly[d(a)]poly[d(t)]mentioning

confidence: 99%

“…Interbase parameters are calculated according to the conventions adopted by Piriou et al (1994): orthonormal reference frames are calculated for both bases with the x axis in the direction of the line passing through 06 and N7 for Gwc, and for G H through 06 and N l, with the origin in the middle of the line joining both atoms. The z axis is perpendicular to the mean plane through the six-membered ring atoms, the y axis is defined so that the final orthonormal reference frame is right-handed.…”

Section: Values For the Nonamer Are Represented By A Full Line Dottementioning

confidence: 99%

“…The z axis is perpendicular to the mean plane through the six-membered ring atoms, the y axis is defined so that the final orthonormal reference frame is right-handed. (Piriou et al, 1994). In the namecode GCoG/Jpt the o refers to an unoccupied position (see Fig.…”

Section: Values For the Nonamer Are Represented By A Full Line Dottementioning

confidence: 99%

“…In the namecode GCoG/Jpt the o refers to an unoccupied position (see Fig. 3 of Piriou et al, 1994), fl-stands for the /~-anomer of the sugar of the third strand, p for the parallel orientation of the G H in respect to Gwc and t for the anti orientation of the third strand base. ~ Schultz et al (1991). helical parameters adjustments optimize the triplet formation.…”

Section: Values For the Nonamer Are Represented By A Full Line Dottementioning

confidence: 99%

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Formation of (C.G)*G Triplets in a B-DNA Duplex with Overhanging Bases

Vlieghe¹,

Meervelt²,

Dautant³

et al. 1996

Acta Cryst D

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Crystallization of a DNA double helix with overhanging bases at the 5'-ends of both strands, results in the formation of two crystallographically independent (C.G)*G triplets. In a previous report [Van Meervelt, Vlieghe, Dautant, Gallois, Pr6cigoux & Kennard (1995). Nature (London), 374, 742-744] the unique molecular packing of the duplex and the Hoogsteen hydrogen-bond pattern and parallel backbone orientation of the guanine-containing strands in the triplets was described. The fine structural details and hydration of the d(GCGAATTCG) crystal structure refined to 2.05,~ (R --0.168, 86 water molecules, two Mg 2+ cations) are now presented. Helical parameters, stacking effects, the geometry at the duplex-triplex junction, and the hydration of the minor groove are discussed and compared with related theoretical and crystal structures.

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Section: Propellersupporting

confidence: 74%