1. Volume 95, Issue 7, Pages 3340-3348 (October 2008)
Metallic Nanoparticles Used to Estimate the Structural Integrity of DNA Motifs 
Jiwen Zheng, Philip S. Lukeman, William B. Sherman, Christine Micheel, A. Paul Alivisatos, Pamela E. Constantinou, Nadrian C. Seeman 
Biophysical Journal 
Volume 95, Issue 7, Pages (October 2008)
DOI: /biophysj
Copyright © 2008 The Biophysical Society Terms and Conditions

2. Figure 1
The sequences of the molecules used here. (a) The parallelogram. (b) The bulged-junction triangle. (c) The DX triangle. “C6-S-” indicates the particle site of attachment.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

3. Figure 2
DNA parallelograms with gold nanoparticles. The expected angles between the edges of the parallelograms are shown in the circles in the schematics at left and are indicated on the TEM pictures at right. The circles are scaled to indicate nanoparticle size. (a) Four 5nm gold nanoparticles. For clarity, some angles are displaced in the TEM picture. (b) Three 5nm nanoparticles and one 10nm nanoparticle near an acute angle. Note the second parallelogram from the bottom, where the 10nm particle flanks an obtuse angle. (c) Three 5nm nanoparticles and one 10nm nanoparticle near an obtuse angle. Note the bottom image, where the 10nm particle flanks an acute angle.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

4. Figure 3
DNA parallelograms with two 5nm particles and two 10nm particles. The same conventions apply as in Fig. 2. (a) The 10nm particles flank acute angles. The bottom image is nearly ideal, but the other images are distorted significantly. (b) The 10nm particles flank obtuse angles. Distortions are seen in several of the parallelograms, most prominently in the bottom image, where the expected distribution is reversed.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

5. Figure 4
3D-DX triangles with two or three particles attached. (a) Three 5nm particles attached. Note that the triangles are not significantly distorted from ideality. (b) Two 5nm particles and one 10nm particle attached. Only minor distortions are seen. (c) Two 5nm particles attached. This asymmetric distribution of particles produces separations close to the expected values. (d) Two 10nm particles attached. Even 10nm particles attached asymmetrically do not produce separations indicative of motif distortion.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

6. Figure 5
Bulged-junction triangles with three particles attached. (a) Three 5nm particles. (b) Two 5nm particles and one 10nm particle. In each case, a triangle can be seen that is near the expected shape, but most triangles are highly distorted.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

7. Figure 6
Angular distributions observed and fit by a Gaussian function. The parallelogram distributions (a) and (b) are very broad, as is the distribution of the single domain triangle with three 5nm particles (e). The distribution of the triangle with a 10nm particle is narrower but is badly fit by a single Gaussian (f). The 3D-DX distributions are very narrow (c) and (d). The parameters describing the distributions are listed in Table 1.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions