Jump to main content
Jump to site search
Access to RSC content Close the message box

Continue to access RSC content when you are not at your institution. Follow our step-by-step guide.


Issue 1, 2009
Previous Article Next Article

Analysis of aptamer sequence activity relationships

Author affiliations

Abstract

DNA sequences that can bind selectively and specifically to target molecules are known as aptamers. Normally such binding analyses are performed using soluble aptamers. However, there is much to be gained by using an on-chip or microarray format, where a large number of aptameric DNA sequences can be interrogated simultaneously. To calibrate the system, known thrombin binding aptamers (TBAs) have been mutated systematically, producing large populations that allow exploration of key structural aspects of the overall binding motif. The ability to discriminate between background noise and low affinity binding aptamers can be problematic on arrays, and we use the mutated sequences to establish appropriate experimental conditions and their limitations for two commonly used fluorescence-based detection methods. Having optimized experimental conditions, high-density oligonucleotide microarrays were used to explore the entire loop–sequence–functionality relationship creating a detailed model based on over 40 000 analyses, describing key features for quadruplex-forming sequences.

Graphical abstract: Analysis of aptamer sequence activity relationships

Back to tab navigation

Supplementary files

Article information


Submitted
26 Aug 2008
Accepted
15 Oct 2008
First published
12 Nov 2008

Integr. Biol., 2009,1, 116-122
Article type
Paper

Search articles by author

Spotlight

Advertisements