Vinay Bachu, Lazmy Deware, Ayush Kumar, Pooja Rani Kuri, Malaya Mili, Naveen Kumar Singh, & Pranab Goswami . Aptabase: An aptamer database, October 24 (2021).
Biosensors and Biofuel cell Lab, IIT Guwahati, Pin: 781039, Assam, India
APTABASE is a database, an effort from our lab to collect and group all available aptamer data. The vision behind the construction of aptabase is to create a one-click all aptamer data for researchers worldwide. The site contains aptamer data of more than 600 aptamers, which is constantly updated and scouted for any errors. We have also made efforts to make the site interactive by allowing interested aptamer scientists worldwide to include their aptamer's data in our site with an update form. Other add-ons include plugins to calculate GC content from both RNA and DNA aptamers. We are constantly updating the APTABASE in different aspects to ensure to make the site user-friendly.
Aptamers are single-stranded nucleic acid molecules that bind to a specific target molecule with high affinity and specificity (Advance Mater. & Tech. for Biosensors and Bioanalytical applications, 2020, CRC press). They are closer to monoclonal antibodies in functions. Aptamer-target binding is achieved mainly through electrostatic interactions, hydrogen bonding, van der Waals forces, and hydrophobic interactions, so the variability in aptamer sequences is what gives them their versatility(BBA General Subject 1861, 3289-3299 (2017). The way aptamers fold into the tertiary structure depends on several factors like the nucleic acid sequence and the conditions of the matrix they are in and the GC content. All this contributes to binding a target with high selectivity. Aptamers are of different lengths, generally ranging from 20 - 90 nucleotides. However, aptamers as small as 8 nucleotides to as lengthy as 230 are also reported.
To bind to a small molecule, it is common for an aptamer to engulf the target. This type of binding will cause a structural switch, changing the aptamer's structure. This feature can be utilized for detection methods. When binding to a large molecule, an aptamer usually only interacts with an external surface. In addition to small and large molecules, aptamers have been successfully identified as binding molecules for whole cells, viruses, tissues, and non-biological targets like small organic molecules, and metal ions. This range of potential targets makes them ideal for many applications. Uses for aptamers mostly include biomarker and drug discovery diagnostics, therapeutics, and biosensors.
Vinay Bachu, Lazmy Deware, Ayush Kumar, Pooja Rani Kuri, Malaya Mili, Naveen Kumar Singh, & Pranab Goswami . Aptabase: An aptamer database, October 24 (2021): www.iitg.ac.in/proj/aptabase
For all correspondence: pgoswami@iitg.ac.in (P.Goswami).