Find the parts that we added to the registry and a description of them below. You can also click on the link to take you to the parts page on the parts registry
| Name | Type | Description | Designers | Length |
|---|---|---|---|---|
| BBa_K4397000 | RNA | β55: Amyloid-Beta Aptamer | Rashik Chand | 66 bp |
| BBa_K4397001 | RNA | E22P-AbD43: Amyloid-Beta Aptamer | Rashik Chand | 77 bp |
| BBa_K4397002 | DNA | T-SO508: Amyloid-Beta Aptamer | Rashik Chand | 24 bp |
| BBa_K4397003 | DNA | RNV95: Amyloid-Beta Aptamer | Rashik Chand | 39 bp |
| BBa_K4397004 | DNA | Aβ7-92-1H1: Amyloid-Beta Aptamer | Rashik Chand | 44 bp |
| BBa_K4397005 | DNA | ssDNA1: Tau Aptamer | Rashik Chand | 15 bp |
| BBa_K4397006 | DNA | 3146: Tau Aptamer | Rashik Chand | 29 bp |
| BBa_K4397007 | DNA | IT2: Tau Aptamer | Rashik Chand | 30 bp |
β55 is a novel RNA aptamer generated from a SELEX screen against monomeric Aβ1–40 was previously shown to bind synthetic amyloid fibrils [1]. Despite that SELEX screens have been used against covalently stabilized Aβ trimmers, Aβ1–40 conjugated to colloidal gold nanoparticles as well as DNA aptamer selected against α-synuclein, no ex vivo stains of human AD brain tissues have been performed with aptamer probes [1]. Therefore, the novel ability of β55 to bind amyloid plaques in ex vivo human AD brain tissue and in live transgenic mouse models of AD is of great importance [1]. The main idea behind this aptamer is that β55 binds Aβ oligomers and is able to visualize the oligomeric halo surrounding the dense cores of amyloid plaques [1].
E22P–Aβ42 is RNA aptamer obtained from a preincubated dimer model of E22P–Aβ42, which is dimerized via a linker located at Val-40, as the target of in vitro selection [2]. E22P–AbD43 has preferential affinity toward PFs due to its higher affinity for the toxic dimer unit (KD = 20 ± 6.0 nm) of Aβ42 than for less-toxic Aβ40 aggregates [2]. Preferential binding of E22P–AbD43 toward the dimer might be related to the formation of a G-quadruplex structure [2]. E22P–AbD43 significantly inhibited the nucleation phase of the dimer and its associated neurotoxicity in SH-SY5Y human neuroblastoma cells [2]. Furthermore, in an AD mouse model, E22P–AbD43 preferentially recognized diffuse aggregates, which likely originated from PFs or higher-order oligomers with curvilinear structures, compared with senile plaques formed from fibrils [2].
T-SO508 is a DNA aptamer specific for Aβ oligomer, suggesting that the G-quadruplex form of DNA aptamer tends to preferentially bind to the β-structures of Aβ oligomer [3]. Presently, aptamer T-SO508 has been the most commonly used recognition molecule in Aβ40 oligomers detection [3]. T-SO508 is suitable for the construction of Aβ sensing platforms, however the distinction between Aβ40 oligomer and Aβ42 oligomer is limited [3]. T-SO508’s high affinity for Aβ is beneficial to improve detection sensitivity and inhibition efficiency for further applications in clinical diagnosis and treatment of AD. However, compared to α-synuclein oligomers, affinity of T-SO508 aptamer to Aβ40 oligomers was slightly lower (Kd value of 25nM) [3].
RNV95 is a DNA aptamer with ability to detect tetrameric/pentameric low-molecular-weight Aβ aggregates [4]. During Western Blot analysis, both RNV95 and anti-Aβ antibodies detect a high-molecular-weight aggregate between 75 and 100 kDa in low yields, RNV95 shows higher intensities in detecting Aβ band than the anti-Aβ antibody [4]. Moreover, RNV95 does not show the ∼15 kDa band corresponding tetrameric/pentameric Aβ aggregates in healthy control brain tissue samples which is indicative of the binding specificity of RNV95 to AD [4]. Therefore, according to this research RNV95 could be a better alternative to the characterized monoclonal anti-Aβ antibody to detect low-molecular-weight aggregates of Aβ in AD brain tissue by western blot [4].
Aβ7-92-1H1 is a DNA aptamer with a length of 44 bases containing a stem-loop structure. Aβ7-92-1H1 Kd value of 63.4 nM indicated high specificity of this aptamer for Aβ42 monomer [3]. It has been shown that Aβ7-92-1H1 could not bind to Aβ40 monomer, but it recognizes Aβ42 and Aβ40 aggregates (oligomer and fibril) with various affinities [3]. This indicates that the selectivity of Aβ7-92-1H1 for Aβ40 monomer needs to be improved. Still, its ability to recognize Aβ monomers and aggregates is very suitable for the development of inhibitors for regulating Aβ aggregation [3].
Data shows that with growing concentration of tau in the equilibrium mixture, the peak of tau–ssDNA1 complex increases, while that of free ssDNA1 decreases [5]. Secondly, when investigated using NECEEM, the complexes of tau with ssDNA2 were present in the amount much lower than those of tau with ssDNA1 and similarly, the complexes of tau with ssDNA3 were undetectable with the used concentration of tau [5]. The Kd value of the tau–ssDNA1 complex is lower than those of the tau–ssDNA2 and the tau–ssDNA3 complexes by more than two orders of magnitude [5]. The difference in the affinity for the three ssDNA molecules indicates that tau binds ssDNA in a sequence-specific fashion [5].
DNA aptamer 3146 is obtained from a 5 × 1012 DNA oligonucleotide library in only three rounds that can be performed within one day [8]. Target of 3146 aptamer is 2N4R-Tau, with selectivity for a monomer and with the Kd value of 13 nM (SPR) [2]. Aptamer 3146 bound tau isoforms in the following order: 2N4R (KD = 13 nM) > 0N4R (49 nM) > 0N3R (84 nM) > 1N3R (116 nM) [2].
Sequence IT2 demonstrates a unique binding profile on three of the peptides (T231, T231P, and S202) [6]. IT2 was at first truncated to IT2a based on an evident stem–loop motif observed in the predicted secondary structure, and IT2a demonstrated binding ability equal to IT2 for targets T231, T231P, and S202 [6]. However, IT2b failed to maintain the properties of the original aptamer. Sequence IT2c presented binding ability similar to IT2a, but a gradual loss of binding ability was observed by further truncating the stem of IT2c into IT2d and IT2e, suggesting the importance of a stable stem for binding of aptamer IT2c to its targets [6].