Halogenated Bases - Introduction

Introduction to Halogenated Bases

Halogenated nucleotides, for example, 5-Br-dC, 5-I-dU, are modified with a halogen on the base (NOT the ribose). Halogenated nucleotides are incorporated into oligonucleotides for determining DNA/RNA structural characteristics by X-ray crystallography (1). In addition, because they are photo-labile, oligonucleotides modified with halogenated bases can be UV cross-linked with other molecules, for example proteins, in order to investigate the structure and function of complexes between DNA and the other molecules (2). This property of photo-lability can also be taken advantage of in aptamer development, where halogenated bases can be incorporated into an aptamer, post-SELEX, to create a photo-aptamer. Such photo-aptamers still retain essentially the same binding affinity for their target, but are now capable of being UV cross-linked to those targets (3).