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The unusual and dynamic character of PX-DNA.

Niu D, Jiang H, Sha R, Canary JW, Seeman NC - Nucleic Acids Res. (2015)

Bottom Line: Some of the structural features of the molecule have been noted previously, but the structure requires further characterization.In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure.Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

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Angular titration experiments to establish the best positions to place the labels. (A) Schemes of moving the labels on the zigzag PX-DNA: top: side view; bottom: front view (red arrow: 3′ direction, blue arrow: 5′ direction). (B) A matrix of the selected AFM images from each of the variants in the titration experiments.
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Figure 3: Angular titration experiments to establish the best positions to place the labels. (A) Schemes of moving the labels on the zigzag PX-DNA: top: side view; bottom: front view (red arrow: 3′ direction, blue arrow: 5′ direction). (B) A matrix of the selected AFM images from each of the variants in the titration experiments.

Mentions: If the structure of PX-DNA were inconsistent with the B-form DNA conformation, the labeling sites chosen above might not be optimal. One solution to this problem is moving all the labels in either the 3′ or 5′ direction by a fixed small number of nucleotides so as to rotate them by a few nucleotide twist intervals. The rotation is expected eventually to place the conjugates at sites where a clear zigzag could form. Figure 3A illustrates the idea behind this experiment. Considering the rotation per base pair in B-form DNA is roughly equal to 34–36°, moving the labels by a maximum of 3 nt should be sufficient to titrate the required angular range. We have made and tested six different systems, and the AFM results are summarized in Figure 3B. Among all the results, only moving the labels by 2 nt in the 5′ direction sometimes generates a zigzag PX-DNA pattern (32%), whereas all the other five variants largely produce linear PX-DNA streptavidin patterns. Although a small number of barely zigzag molecules were also observed from each of the other variants, the percentages of the absolutely linear patterns from them are all higher than 90%.


The unusual and dynamic character of PX-DNA.

Niu D, Jiang H, Sha R, Canary JW, Seeman NC - Nucleic Acids Res. (2015)

Angular titration experiments to establish the best positions to place the labels. (A) Schemes of moving the labels on the zigzag PX-DNA: top: side view; bottom: front view (red arrow: 3′ direction, blue arrow: 5′ direction). (B) A matrix of the selected AFM images from each of the variants in the titration experiments.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4551946&req=5

Figure 3: Angular titration experiments to establish the best positions to place the labels. (A) Schemes of moving the labels on the zigzag PX-DNA: top: side view; bottom: front view (red arrow: 3′ direction, blue arrow: 5′ direction). (B) A matrix of the selected AFM images from each of the variants in the titration experiments.
Mentions: If the structure of PX-DNA were inconsistent with the B-form DNA conformation, the labeling sites chosen above might not be optimal. One solution to this problem is moving all the labels in either the 3′ or 5′ direction by a fixed small number of nucleotides so as to rotate them by a few nucleotide twist intervals. The rotation is expected eventually to place the conjugates at sites where a clear zigzag could form. Figure 3A illustrates the idea behind this experiment. Considering the rotation per base pair in B-form DNA is roughly equal to 34–36°, moving the labels by a maximum of 3 nt should be sufficient to titrate the required angular range. We have made and tested six different systems, and the AFM results are summarized in Figure 3B. Among all the results, only moving the labels by 2 nt in the 5′ direction sometimes generates a zigzag PX-DNA pattern (32%), whereas all the other five variants largely produce linear PX-DNA streptavidin patterns. Although a small number of barely zigzag molecules were also observed from each of the other variants, the percentages of the absolutely linear patterns from them are all higher than 90%.

Bottom Line: Some of the structural features of the molecule have been noted previously, but the structure requires further characterization.In comparison with conventional double stranded DNA and with antiparallel DNA double crossover molecules, it is clear that PX-DNA is a more dynamic structure.Furthermore, the spacing between the nucleotide pairs along the helix axis is shorter, suggesting a mixed B/A structure.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.

Show MeSH