Antisense oligodeoxynucleotides, both the phosphorothioate analogues and unmodified oligomers of the same sequence, inhibit replication and expression of human immunodeficiency virus already growing in tissue cultures of MOLT-3 cells with much greater efficacy than do mismatched ("random") oligomers and homooligomers of the same length and with the same internucleotide modification. This preferential inhibitory effect is elicited in as short a time as 4-24 hr postinfection. Likewise, antisense oligomers exhibit greater inhibitory effects on human immunodeficiency virus in chronically infected cells than do mismatched oligomers and homooligomers. Phosphorothioate antisense oligomers are up to 100 times more potent than unmodified oligomers of the same sequence in these inhibitory assays. These results, in major respects, confirm and extend those recently published by Matsukura et al. [Matsukura, M., Zon, G., Shinozuka, K., Robert-Guroff, M., Shimada, T., Stein, C. A., Mitsuza, H., Wong-Staal, F., Cohen, J. S. & Broder, S. (1989) Proc. Nati. Acad. Sci. USA 86,[4244][4245][4246][4247][4248]. They also point out the importance of computer analysis of sequences thought to be random but that in reality contain significant areas of likely hybridization, either to the viral genome or to the complementary DNA strand synthesized from it. They thus reinforce the concept that specific base pairing is a crucial feature of oligonucleotide inhibition of human immunodeficiency virus.Antisense oligodeoxynucleotides and their analogues have been used as tools for inhibiting viral replication (1-3), for blocking splicing and translation of mRNA (4, 5), and for regulating specific gene expression (6, 7). It has been found that an oligonucleotide complementary to a segment of a viral genome or an mRNA derived therefrom may interfere with the expression of that genetic segment by hybridization competition (1,2).In earlier reports, we demonstrated that replication of human immunodeficiency virus (HIV) could be inhibited by normal phosphodiester oligodeoxynucleotide sequences complementary to HIV RNA (4, 8). However, relatively short half-lives of normal oligonucleotides (9) in serum and in cells due to the presence of nucleases, and possibly the low permeability of these charged molecules into normal cells, limit their potential usefulness in vivo. To overcome this limitation, we and others (10-15) have studied internucleotide phosphate backbone-modified oligonucleotides, such as methylphosphonates (3, 10) as well as phosphorothioates and various phosphoramidates (11,12), for their antiviral activities against HIV.Here we report both the inhibition of HIV replication and the effect on cell growth of MOLT-3 cells that have been infected just 24 or 48 hr before addition of oligomers and also the effect on MOLT-3 cells chronically infected with HIV that were mixed with uninfected cells in the presence of oligodeoxynucleotides and their phosphorothioate analogues. MATERIALS AND METHODSOligonucleotide Synthesis. Oligonucleotides we...

DNA sequences of 496 somatic cell illegitimate crossing over regions were compiled and analyzed. Sites for non-homologous recombination on linear DNAs transfected into mammalian cells (Transfected Linear DNAs; TLD) were analyzed separately from the remaining illegitimate recombination regions (IRR). Trinucleotides that are preferentially cleaved by rat liver topoisomerase I in vitro (CAT, CTY, GTY, RAT where R = purine, Y = pyrimidine) were present in the 10 base pair (bp) vicinity of the cross-over sites in 92% of IRR and 93% of TLD. Multiple repeats of these trinucleotides have been observed in 39% of IRR and 38% of TLD. Runs of five or more contiguous purines (or pyrimidines on the complementary strand) were found in 26% of IRR and 14% of TLD. Adenine-Thymine rich regions of five or more bases were found in 14% of IRR and 21% of TLD. Alternating purine-pyrimidine tracks longer than four nucleotides in length were found in 11% of IRR, though only in 4% of TLD. I discuss the possible biological significance of these findings and present an appendix containing the sequences in the 10 bp vicinity of the non-homologous recombination sites analyzed.

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Prokaryotic, eukaryotic and mitochondrial DNA sequences of total Length 300000 nucleotides have been analyzed to find out whether stretches of alternating purines and pyrimidines are unusual in terms of occurrence, composition and base sequence. Alternating runs longer than 5 nucleotides are significantly underrepresented in the natural sequences as compared to random ones. Octanucleotides are the most deficient, occurring at only 60% of the frequency expected in random sequences. An unexpectedly high proportion of these octamers consists of alternating tetramers with the repeat structure (PuPyPuPy)2or (PyPuPyPu)2. DNA stretches containing such sequences can potentially form a Sl nuclease sensitive slippage (staggered loop) structure, which might serve as a locally unstacked intermediate in the B‐ to Z‐DNA conformational transition.