PubMed · 9537907
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R Sikorski, R Peters. 1998-03-20. CPU by DNA?. https://pubmed.ncbi.nlm.nih.gov/9537907/
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The G-tetrad-forming oligonucleotides and have been identified as potent inhibitors of human immunodeficiency virus type 1 integrase (HIV-1 IN) activity (Rando, R. F., Ojwang, J., Elbaggari, A., Reyes, G. R., Tinder, R., McGrath, M. S., and Hogan, M. E. (1995) J. Biol. Chem. 270, 1754-1760; Mazumder, A., Neamati, N., Ojwang, J. O., Sunder, S., Rando, R. F., and Pommier, Y. (1996) Biochemistry 35, 13762-13771; Jing, N., and Hogan, M. E. (1998) J. Biol. Chem. 273, 34992-34999). To understand the inhibition of HIV-1 IN activity by the G-quartet inhibitors, we have designed the oligonucleotides and, composed of three and four G-quartets with stem lengths of 19 and 24 A, respectively. The fact that increasing the G-quartet stem length from 15 to 24 A kept inhibition of HIV-1 IN activity unchanged suggests that the binding interaction occurs between a GTGT loop domain of the G-quartet inhibitors and a catalytic site of HIV-1 IN, referred to as a face-to-face interaction. Docking the NMR structure of (Jing and Hogan (1998)) into the x-ray structure of the core domain of HIV-1 IN, HIV-1 IN-(51-209) (Maignan, S., Guilloteau, J.-P. , Qing, Z.-L., Clement-Mella, C., and Mikol, V. (1998) J. Mol. Biol. 282, 359-368), was performed using the GRAMM program. The statistical distributions of hydrogen bonding between HIV-1 IN and were obtained from the analyses of 1000 random docking structures. The docking results show a high probability of interaction between the GTGT loop residues of the G-quartet inhibitors and the catalytic site of HIV-1 IN, in agreement with the experimental observation.
We calculated correlations of the nucleotide distributions along the E. coli genome. Subsequent cluster analysis of the correlation distributions showed that the genome was composed of two qualitatively different types of nucleotide sequences. The first type exhibited strong correlations of the genomic distributions of A with T and G with C, and high anticorrelations of A with C and G with T. In contrast, the second type was characterized by weak or negligible correlations typical of randomized sequences. Both types of sequences were almost equally abundant in the E. coli genome and their length varied from several hundred nucleotides to about 70 kilobases. They were not disjunct with respect to their (G + C) content but the high correlations and anticorrelations were rather characteristic for (A + T)-rich genomic segments. We offer possible explanations of the mosaic structure of the E. coli genome.
DNA.RNA hybrid duplexes are substrates of RNase H and reverse transcriptase. The crystal structure of a hybrid duplex, d(5'-CTCTTCTTC-3').r(5'-gaagaagag-3') (the uppercase letters indicate DNA and lowercase letters RNA), with a polypurine RNA strand and a complementary DNA strand has been determined at 1.8 A resolution. The structure was refined first at 1.9 A by XPLOR and subsequently by CNS at 1.8 A. The hybrid is found in a standard A-form conformation with all the sugars in the C3'-endo puckering. The 5'-terminal base dC of the DNA strand was clearly visible in the electron density map of the present structure, in contrast to the previously reported structure d(TTCTTBr(5)CTTC).r(gaagaagaa) where the 5'-terminal base dT was not visible, leaving the terminal rA unpaired. Thus, the comparison of the terminal base pairs, C.g versus T.a, in the two hybrid crystal structures provides information on the stability of these base pairs in hydrogen bonding (three versus two) and base stacking interactions. The differences in the terminal base pairs produce different kinks in the two structures. Minor groove widening is observed in the present structure at a distinctive kink in the lower half of the duplex, in contrast to the small widening of the minor groove and a very slight bend in the upper half of the T.a structure.