Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add additional functional groups, not found in natural DNA but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1′-β-D-2′-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1′-β-D-2′-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to pair via strict Watson-Crick geometry. These were added to lies in a ibrarlaboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection systems, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Z’s and P’s. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system, and that GACTZP libraries are richer reservoir of functionality than standard libraries.

The first general method for the selection of boronic acid-based aptamers that allow for glycan substructure focusing is described. Using fibrinogen as a model, we have selected boronic acid-modified DNA aptamers that have high affinities (low nM K d ) and the ability to recognize changes in the glycosylation site. The method developed should also be applicable to the development of aptamers for other glyco-products, such as glycolipids and glycopeptides. E-mail: wang@gsu.edu Supporting Information Available: Description of the experimental procedure and detailed results. This material is available free of charge via the Internet at http://pubs.acs.org. Glycosylation profoundly affects the function and activities of many proteins. 1,2 However, detecting and differentiating variations in glycosylation as an integral part of a glycoprotein is not a trivial matter, mostly due to a lack of good tools. Two most powerful methods exist for developing "binders" for glycoproteins: antibody production and nucleic acid-based aptamer selection. 2 However, none of these methods has the intrinsic ability to specifically focus on the glycosylation site, which include both the glycan and the surrounding structures, in epitope selection. We are interested in examining the possibility of directing the selection of aptamers to preferentially go after the glycosylation site of a glycoprotein (the sweet spot). By taking advantage of many published methods on incorporating modified nucleotide into DNA/RNA for aptamer selection, 3 we decided to incorporate a boronic acid-modified thymidine-5′-triphosphate (B-TTP, Figure 1) into DNA for aptamer selection. Because of the intrinsic ability for the boronic acid moiety to interact with diols 4 and single hydroxyl groups, 5 we hypothesized that the incorporation of the boronic acid moiety into DNA would allow the selection to gravitate toward the glycosylation site and therefore for the specific recognition of the glycosylation site. When necessary, counter selection can be used to eliminate unwanted cross-reactivity for binders as described in literatures. 3, 6 Herein, we report our work that demonstrates the feasibility by using a model protein, fibrinogen, which was chosen because of its commercial availability in large quantities and its known glycan structures. NIH Public AccessWe used the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) approach for aptamer selection. 2,3 Introduction of the boronic acid moiety was accomplished through tethering to the 5-position of TTP ( Figure 1) because (1) modification at this position has long been known to have minimal effect on polymerase-catalyzed incorporation; 3 (2) 5-position modified TTP has been widely used in aptamer selections to tune their affinity and bestow novel properties, 3 and (3) we have demonstrated that the B-TTP can be successfully incorporated into DNA using DNA polymerases, and the synthesized boronic acid-modified DNA (B-DNA) can serve as templates for further amplification. 7For the aptamer sel...