We report experiments in the rat demonstrating the feasibility of intraventricular administration of oligodeoxynucleotides (ODNs) as a regional treatment approach to disorders within the central nervous system (CNS). Although we fmd little intrinsic nuclease activity in cerebrospinal fluid (CSF), phosphodiester ODNs are rapidly degraded by brainassociated a-exonuclease activity. Phosphorothioate ODNs, however, appear resistant to degradation in the CNS and, after intraventricular administration, we fmd they are cleared in a manner consistent with CSF bulk flow. To avoid obstacles associated with systemic administration, we and others have focused on regional therapeutic strategies to evaluate ODN actions in vivo (5, 6). We now describe the stability, disposition, and clearance of ODNs within a clinically important, physiologically well-defined biologic compartment-namely, the cerebrospinal fluid (CSF) space of the rat. We report that potentially therapeutic concentrations of intact phosphorothioate ODN can be maintained within the CSF without gross toxicity to the animal. Extensive penetration into brain parenchyma can be demonstrated. These findings support the feasibility of ODNbased therapeutic approaches to viral and neoplastic disorders within the central nervous system (CNS).MATERIALS AND METHODS ODN Synthesis, Modification, and Purification. Lyophilized preparations of several unmodified 15-base phosphodiester ODNs were obtained from Gilead Sciences (Foster City, CA) or Synthecell (Gaithersburg, MD). The sequences used in this study were as follows: 5'-ATG CCG AGC TGC TCC-3' (ODN 1) and 5'-GGA GCA GCT CGG CAT-3' (ODN 2). Both ODNs were used interchangeably and behaved identically in all cases. These ODNs were synthesized by standard cyanoethyl phosphoramidite chemistry and were chromatographically purified. Corresponding 15-base phosphorothioate ODNs were prepared on an Applied Biosystems 380B automated synthesizer by using phosphoramidite chemistry and Beaucage sulfurization reagent (Glen Research, Sterling, VA) in the oxidation step (7).The 5' radiolabeling of phosphodiester ODNs was performed with polynucleotide kinase (BRL) according to the manufacturer's instructions. The 3' radiolabeling of sequences was performed with terminal deoxynucleotidyltransferase (BRL) according to the manufacturer's instructions. Labeled material was added as tracer (1-5 x 107 cpm per ,umol of total DNA) to ODN infusions.Internal fluorescein labeling of both phosphodiester and phosphorothioate ODNs (ODN 1) was accomplished at the 8th base position (from the 3' end) during automated synthesis with a fluorescein amidite reagent (Glen Research). Fluorescein-labeled ODNs were used either undiluted or diluted up to 1:3 with nonlabeled ODN of the same sequence.Analysis of ODN Stability in Vitro. Solutions of 20 ,uM fluoresceinated ODN (both phosphodiester and phosphorothioate) were prepared in human CSF containing 100 units of penicillin per ml and 100 ,ug of streptomycin per ml (Biofluids, Rockville, MD). A vol of 0.75 ...