Opening Image: Van der Waals surface of d(GCGAATTCG)₂. The model shows seven magnesium ions and one chloride ion, and 152 ordered water molecules. Although many of the hydrogen atoms of the water molecules cannot be located in the electron density map, the DNA hydrogens have been located in the model.

At 0.9-angstrom resolution, this model of a self-complementary DNA is the best crystallographic structure of the right-handed B-DNA double helix to date; we'll return to this DNA molecule in a later tutorial on the role of water in protein-nucleic acid interactions. However, our focus here is the flexibility of the sugar-phosphate backbone, with an emphasis on the structure and function of aptamers.

Aptamers are short (<100 nt) single-stranded oligonucleotides (ssDNA or ssRNA) with the ability to fold into a stable three-dimensional structure, thus creating a specific binding site for target ligands. Aptamers are selected by an automated technique which allows the simultaneous screening of more than 10¹⁵ individual nucleic acid molecules for a few sequences with the desired binding specificity. This method is commonly known as "in vitro evolution" or SELEX (Systematic Evolution of Ligands by Exponential Enrichment). Basic steps of the SELEX procedure are presented in Figure 1. The same approach can also be used to select aptamers with catalytic activity, either an RNA enzyme (ribozyme) or DNA enzyme (deoxyribozyme). There does not appear to be any systematic differences between RNA and DNA aptamers, save the greater intrinsic chemical stability of DNA.

Based on their three-dimensional structures, aptamers can bind to a wide variety of targets from single molecules to living cells. Aptamers bind to their targets by a combination of complementarity in shape, van der Waals interactions, stacking interactions between aromatic compounds and the bases of the aptamer, electrostatic interactions between charged groups, and hydrogen bonding.

Anti-VEGF aptamer. Age-related macular degeneration (AMD) is the leading cause of blindness in the United States, affecting approximately 15 million people. Pegaptanib, a 28-mer RNA directed against a specific isoform of vascular endothelial growth factor (VEGF-165), was approved by the Food and Drug Administration in 2004 for the treatment of AMD.

Detection of Cancer Cells Using DNA Aptamers

Burkitt's lymphoma, an acute blood cell cancer, is one of the most progressive of all human cancers. Early diagnosis and targeted therapy are crucial for treating its victims. However, Burkitt's lymphoma is immunologically indistinguishable from many other large B-cell lymphomas and is usually diagnosed by inspecting the morphology of blood cells and the patient's symptoms. The lack of effective molecular probes to recognize cell surface biomarkers prevents early diagnosis of Burkitt's lymphoma and makes early detection difficult or even impossible. Recently Weihong Tan and colleagues have selected DNA aptamers for the specific recognition of Burkitt's lymphoma cells. The aptamers lost their binding to the target cells if the cells were incubated with a proteolytic enzyme. This result clearly suggests that the targets of the aptamers are most likely membrane proteins or proteins tightly associated with them.