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NU172
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The crystal structure of NU172 is shown in Fig 8A. This DNA aptamer was designed to bind Thrombin and has a high potency as an anticoagulant [58]. NU172 contains two of the top predictive 6-mers GGT TGG and TGG TGG. This structure has a chair-like anti-parallel fold, where the 6-mer GGT TGG forms G-tetrad type I and II. The second 6-mer TGG TGG is part of a TGT loop that surrounds the G-tetrad. This TGT loop is highly flexible and different from other TGT loops found in another DNA aptamer sequences. |
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AMP
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The NMR structure of AMP is shown in Fig 8B. This DNA aptamer binds AMP as well as adenosine with an affinity shown to be 6 μM [10]. It has the 6-mer sequence TGG GGG, as one of two highly conserved guanine-rich regions. The TGG GGG sequence is part of two AMP-binding sites, which are located in the minor groove of the DNA helix. The TGG GGG also adapts a complex with the major groove centered about the adjacently bound AMP molecules. |
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V7t1
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The NMR structure of V7t1 is shown in Fig 8C. This DNA aptamer binds to VEGF165 and VEGF121, the two most abundant VEGF isoforms, with KD values at a very low nanomolar concentration [64]. V7t1 comprises several G-rich regions and folds into a G-quadruplex. It contains the top predictive 6-mers GGG GTG and TGG GGG that overlap in the sequence GTGGGGGTG. These nucleotides are numbered as G2–G10. Loop regions comprise a non-residue propeller-type loop between G6 and G7, a T9-G10 D-shaped loop connecting outermost residues G8 and G11 within the same strand. The DNA backbone is in an extended conformation in the G6-G8 tract, which causes displacement of G6 and G8 from what is considered their ideal stacking position. The DNA strand is connecting residues G8 and G11 of the outer G-quartets within the same column of a G-quadruplex core. G11 adopts anti-conformation along with its glycosidic bond, and G7-G8 and G11 segments can be considered parts of two DNA strands oriented in a parallel fashion. |
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HD22
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The crystal structure of HD22 is shown in Fig 8D. This DNA aptamer also binds to Thrombin and exhibits a substantially high negative charge density compared to other thrombin’s aptamers, thus strengthening its specificity for target recognition [61]. It is also a bimodular aptamer with respect to a double helix and a G-quadruplex. This aptamer has the top predictive 6-mers GGG GTG and GGT TGG that overlap in a single sequence as GGTTGGGGTG. Its bases are numbered as G17–G25. This region of the aptamer is part of the duplex structure, and it is organized into a G-tetrad capped by the Thy18-Thy19 on one side. Interaction between HD22-27 and Thrombin involves numerous residues, including molecules such as Thy18, Thy19, Gua20, Gua23, Thy24, of the aptamer and segments 89–101, 230–245 of Thrombin. Hydrophobic contacts, mainly involving loop residues Thy18 and Thy19, also contribute to the stability of the complex. A further anchorage is produced by Thy24, which bulges from the duplex region of the nucleotide into a protein pocket where it is mainly involved in polar contacts. |
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HIV-1 RT
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The crystal structure of HIV-1 RT is shown in Fig 8E. This DNA aptamer binds to HIV-1 reverse transcriptase with ultra-high affinity [62]. It has two repeats of the 6-mer GGG GGG, numbered as G27–G32, as part of the primer duplex strand. The conformational analysis of this aptamer suggest that base pairs conformation conforms into a B-form geometry. Nucleotides 28–33 can interact with crucial amino acid residues located in the p66 finger as well as in the palm and thumb subdomains of HIV-1 reverse transcriptase. |
