Results: 4

1.
Figure 2

Figure 2. From: A crystallographic map of the transition from B-DNA to A-DNA.

The 13 unique conformations (a to m) seen in the single-crystal structures of d(GGCGCC)2, d(GGm5CGCC)2, d(GGBr5CGCC)2, d(GGCGm5CC)2, and d(GGCGBr5CC)2 arranged as described in the text and Table 2. Each structure is viewed down the helix axis (purple dot), and into the helix axis (purple line). Conformations ad are B-type helices (green labels), e and f are composite helices (blue labels), g and h are extended intermediates (purple labels), im are A-DNA allomorphs, starting with A/B-intermediates (red labels) and progressing continuously to standard A-DNA (orange labels). The overall transition through each structure is shown in Movie 1, which is published as supplemental data on the PNAS web site, www.pnas.org.

Jeffrey M. Vargason, et al. Proc Natl Acad Sci U S A. 2001 June 19;98(13):7265-7270.
2.
Figure 4

Figure 4. From: A crystallographic map of the transition from B-DNA to A-DNA.

Stereoview of the individual steps of the B- to A-DNA transition at the central base pairs of the double helix. A–D show the view into the major groove of the three base pairs (G2-C11, C3-G10, and G4-C9) from each conformational class superimposed on base pairs from the next conformational class along the transition pathway. The atoms of G4-C9 (lower base pairs) serve as the common reference to superimpose the structures. The carbons and phosphorus atoms of the base pairs are colored to distinguish between the conformations. (A) The transformation of standard B-DNA structure (d, green) to the composite intermediate (e, blue) shows the effect of changing half the sugars from C2′-endo to C3′-endo. (B) The transformation from e to the extended intermediate (g, purple) involves the complete conversion of the sugar puckers, resulting in the increase in the rise, slide, and unwinding of base pairs. (C) The transition to an A/B intermediate (j, red) results in the reduction of the rise and slide, but with very little inclination of the base pairs. (D) The final conversion to canonical A-DNA (m, orange) shows the compression of the major groove resulting from the inclination of the base pairs. These details for the individual base pairs are shown in Movie 2, which is published as supplemental data on the PNAS web site, www.pnas.org.

Jeffrey M. Vargason, et al. Proc Natl Acad Sci U S A. 2001 June 19;98(13):7265-7270.
3.
Figure 1

Figure 1. From: A crystallographic map of the transition from B-DNA to A-DNA.

Single-crystal structures of d(GGBr5CGCC)2 and d(GGm5CGCC)2. (A) Experimental electron density map derived from the 1.6-Å multiwavelength anomalous diffraction phased x-ray diffraction data of d(GGBr5CGCC)2. The electron density, after density modification, of one base pair is shown with the final refined model of this GC base pair included for reference [figure created with bobscript (21)]. (B) Comparison of the δ- and χ-torsion angles and the sugar conformations of the nucleotides in d(GGBr5CGCC)2 (open symbols) and d(GGm5CGCC)2 (closed symbols). Nucleotides with C2′-endo type sugars are indicated by circles, with the C3′-endo sugars by squares, and those with intermediate O4′-endo sugars by diamonds. Nucleotides in the two structures are numbered 1–6 for one strand and 7–12 for the complementary strand (both in the 5′ to 3′ directions). The values of δ and χ for previous single-crystal structures [comprising high resolution—better than 2 Å—crystal structures deposited in the Nucleic Acid Database (22)] of B-DNA are defined by the hashed oval, and those of A-DNA are defined by the open oval [adapted from Lu et al. (23)].

Jeffrey M. Vargason, et al. Proc Natl Acad Sci U S A. 2001 June 19;98(13):7265-7270.
4.
Figure 3

Figure 3. From: A crystallographic map of the transition from B-DNA to A-DNA.

Helical parameters of the crystal structures of d(GGCGCC)2 and its methylated and brominated analogs. The x-displacement, inclination of the base pairs, pseudorotation phase angle, base-pair slide, and zP are plotted, from top to bottom, for the 13 unique helical conformations (a–m) arranged along a common transition pathway according to their x-displacement. Helical parameters were calculated with curves 5.2 (30), with the exception of zP, which was calculated by X3DNA (23). The average values for the parameters are shown for each structure, with the bars extending above and below the average reflecting the values for the individual base pairs or dinucleotide steps. Values for ideal B- and A-DNA in each plot are labeled B and A, respectively. Negative x-displacements reflect shifts of the base pairs away from the helix axis toward the minor groove; negative inclination angles arise from base pairs being tipped away from perpendicular of the helix axis and toward the 3′-end of each strand, and slide has the stacked base pairs displaced relative to each other along their long axes (30). Pseudorotation phase angles reflect the conformation of the deoxyribose sugars (labeled according to their respective endo-type families), with open circles representing the pseudorotation angle of the end nucleotides and closed circles the internal nucleotides of each strand. The parameter zP measures the displacement of the phosphates along each strand away from the midpoint between two stacked base pairs (31).

Jeffrey M. Vargason, et al. Proc Natl Acad Sci U S A. 2001 June 19;98(13):7265-7270.

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk