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1.
Figure 5

Figure 5. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

Representative MD structures of TBA containing 5FurU (red) bound to the thrombin protein (blue).

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

2.
Figure 2

Figure 2. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

Representative MD structure of the unbound TBA containing 5FurU at positions T3, T4, T7, T9, T12 or T13 (red).

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

3.
Figure 4

Figure 4. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

(A) Stacking interactions of the T4 base in the native (left) and modified (right) TBA. (B) Stacking interactions of the T13 base in the native (left) and modified (right) TBA.

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

4.
Figure 6

Figure 6. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

Nucleobase (green) and amino acid (blue) residues surrounding 5FurU at the T3, T4, T12 or T13 positions (red) at the DNA–protein interface in the modified TBA–thrombin complexes.

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

5.
Figure 7

Figure 7. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

Total number of contacts at the DNA–protein interface in the modified TBA–thrombin complexes. Experimental binding affinities of the TBA–thrombin complexes are indicated by the black dots.

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

6.
Figure 3

Figure 3. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

MD structures taken at 1 ns intervals of the unbound (left) and thrombin bound (right) TBA containing 5FurU at various positions (red) overlaid with respect to the aptamer backbone.

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

7.
Figure 1

Figure 1. From: Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations.

The thrombin-binding aptamer (TBA) antiparallel G-quadruplex, with T bases at six positions (3, 4, 7, 9, 12 and 13) highlighted in red and G-tetrads highlighted in blue (left), and the chemical structure of 5-furyl-2′-deoxyuridine (5FurU, right).

Preethi Seelam Prabhakar, et al. Molecules. 2019 Aug;24(16):2908.

CitationFull text

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