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1.
Figure 4

Figure 4. Comparison of backbone torsion angles in rG4-substituted and unsubstituted Dickerson dodecamer NMR solution structures. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

Plot of the average differences in backbone torsion angles of the five best rG4-DNA and dd-DNA solution structures for each nucleotide. The differences were computed by subtracting the dd-DNA values from the rG4-DNA values.

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
2.
Figure 7

Figure 7. Effect of structural regularity on crystallization of ribonucleotide-containing DNA. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

Repetitive conformational regularity may result in better lattice contacts, providing a partial explanation for the crystallographic selectivity for minor but more regular solution conformations. The ribonucleotide-containing base pair is indicated as having an A' or A-like conformation.

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
3.
Figure 1

Figure 1. NOESY connectivities of base H6/H8 and H1'/H2',H2" protons in rG4-substituted Dickerson dodecamer. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

(a) Finger print region of the 100 ms mixing time NOESY spectrum of rG4-DNA, showing the aromatic to H1' intra-residue and sequential connectivities. (b) Finger print region of the 100 ms mixing time NOESY spectrum of rG4-DNA, showing the aromatic to H2'/2" intra-residue and sequential connectivities.

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
4.
Figure 6

Figure 6. Dependence of the minor groove width on ribonucleotide substitution. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

Plot of the average minor groove widths for each base-pair step. Results are presented for two NMR-derived conformations and four modeled structures, color-coded as in Figure 7. The blue and black curves correspond to the same rG4-DNA sequence. The progressive effect of ribonucleotide substitution level on the minor groove width is apparent.

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
5.
Figure 5

Figure 5. Structural parameters for NMR experimental and modeled rcDNA. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

Plots of average calculated values of the shear (a), stretch (b), opening (c), buckle (d), roll (e), and twist (f) for the two NMR-based structures, the dd-DNA (orange) and rG4-DNA (blue), and for four model rcDNA structures. The modeled structures correspond to: CGCrGAATTCGCG = rG4-DNA (black); CGCrGAArUTCGrCG (red); CrGCrGArAUrTCrGCrG (green); and Dickerson dodecamer sequence in an idealized A-DNA geometry (purple).

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
6.

Figure 2. Comparison of chemical shift and scalar coupling of rG4-substituted and unsubstituted Dickerson dodecamer. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

(a) Bar graph showing the differences between rG4-DNA and DNA H1' and H6/8 chemical shifts for each nucleotide. The differences were computed by subtracting the DNA value from the rG4-DNA value. The DNA chemical shifts are the values reported by Hare et al.30 (b) Bar graph showing the differences between rG4-DNA and DNA scalar coupling constants 3J1'2'3J1'2", and 3J3'(i)P(i+1). The differences were computed by subtracting the DNA value from the rG4-DNA value. The 3J1'2' and 3J1'2" scalar coupling values are from Bax and Lerner33 and the 3J3'(i)P(i+1) scalar coupling values are from Wu et al.34

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.
7.

Figure 3. Comparison of rG4-substituted and unsubstituted Dickerson dodecamer NMR solution structures. From: Solution Structure of the Dickerson DNA Dodecamer Containing a Single Ribonucleotide.

a) Stereo view of the superposition of the lowest energy rG4-DNA (red) and dd-DNA (blue) structures. The structures superimpose with an RMSD of 0.750 Å for all atoms. The rG4 ribonucleotide and its complement are highlighted as a stick rendering. The dd-DNA structures were computed using the same XPLOR-NIH simulated annealing calculation as the rG4-DNA with a similar set of experimental restraints as described in the text. The view is into the major groove along the major helical axis. 3b) A stereo view of nucleotides C3, rG4/G4, and A5 of the lowest energy rG4-DNA (cyan) and dd-DNA (coral) structures, showing the slight change in guanosine base position and sugar pucker from C2'-endo in the dd-DNA structure to C3'-endo in the rG4-DNA structure. The view is looking into the minor groove.

Eugene F. DeRose, et al. Biochemistry. ;51(12):2407-2416.

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