RNA-based drugs are an emerging class of therapeutics. They have the potential to regulate proteins, chromatin, as well as bind to specific proteins of interest in the form of aptamers. These aptamers are protected from nuclease attack by chemical modifications that enhance their stability for in vivo usage. However, nucleases are ubiquitous, and as we have yet to characterize the entire human microbiome it is likely that many nucleases are yet to be identified. Any novel, unusual enzymes present in vivo might reduce the efficacy of RNA-based therapeutics, even when they are chemically modified. We have previously identified an RNA-based aptamer capable of neutralizing a broad spectrum of clinical HIV-1 isolates and are developing it as a vaginal and rectal microbicide candidate. As a first step we addressed aptamer stability in the milieu of proteins present in these environments. Here we uncover a number of different nucleases that are able to rapidly degrade 2-F-modified RNA. We demonstrate that the aptamer can be protected from the nuclease(s) present in the vaginal setting, without affecting its antiviral activity, by replacement of key positions with 2-O-Me-modified nucleotides. Finally, we show that the aptamer can be protected from all nucleases present in both vaginal and rectal compartments using Zn 2؉ cations. In conclusion we have derived a stable, antiviral RNA-based aptamer that could form the basis of a pre-exposure microbicide or be a valuable addition to the current tenofovir-based microbicide candidate undergoing clinical trials.Since the discovery of protein regulation by RNA interference (RNAi), RNA, as both a target and effector molecule has been widely researched for therapeutic purposes (1, 2). To the original exogenous small interfering RNAs (siRNA), microRNA, non-coding RNA, and long non-coding RNA have been added; all of which are capable of fine regulation of their target protein(s), and thereby cellular processes (3). This has opened up the possibility of managing both genetic and acquired diseases by modifying the levels of the important disease-associated proteins or essential pathogen-associated proteins using RNA-based technologies (4, 5). Moreover, RNA has the ability to fold into complex tertiary structures that rival antibodies in their potential diversity (provided by the sequence context of the RNA)(6). This conformational heterogeneity makes RNA an ideal effector molecule to bind to and inactivate proteins in a structure-specific manner, similar to the antibody-antigen interaction. Such RNA molecules are called aptamers and have been used both in the laboratory, e.g. to distinguish diseased from wild-type prion protein conformations (7), and in the clinic, e.g. to treat age-related macular degeneration (Macugen). Additionally, our laboratory has recently been developing a clinically relevant RNA-based aptamer to prevent HIV-1 infection (8, 9).The "RNA world" hypothesis states that life originated using RNA as the inherited genetic molecule, which was superseded by DNA due to...