Inhibition of 5'-UTR RNA conformational switching in HIV-1 using antisense PNAs

BACKGROUND

The genome of retroviruses, including HIV-1, is packaged as two homologous (+) strand RNA molecules, noncovalently associated close to their 5'-end in a region called dimer linkage structure (DLS). Retroviral HIV-1 genomic RNAs dimerize through complex interactions between dimerization initiation sites (DIS) within the (5'-UTR). Dimer formation is prevented by so calledLong Distance Interaction (LDI) conformation, whereas Branched Multiple Hairpin (BMH) conformation leads to spontaneous dimerization.

METHODS AND RESULTS

We evaluated the role of SL1 (DIS), PolyA Hairpin signal and a long distance U5-AUG interaction by in-vitro dimerization, conformer assay and coupled dimerization and template-switching assays using antisense PNAs. Our data suggests evidence that PNAs targeted against SL1 produced severe inhibitory effect on dimerization and template-switching processes while PNAs targeted against U5 region do not show significant effect on dimerization and template switching, while PNAs targeted against AUG region showed strong inhibition of dimerization and template switching processes.

CONCLUSIONS

Our results demonstrate that PNA can be used successfully as an antisense to inhibit dimerization and template switching process in HIV -1 and both of the processes are closely linked to each other. Different PNA oligomers have ability of switching between two thermodynamically stable forms. PNA targeted against DIS and SL1 switch, LDI conformer to more dimerization friendly BMH form. PNAs targeted against PolyA haipin configuration did not show a significant change in dimerization and template switching process. The PNA oligomer directed against the AUG strand of U5-AUG duplex structure also showed a significant reduction in RNA dimerization as well as template- switching efficiency.The antisense PNA oligomers can be used to regulate the shift in the LDI/BMH equilibrium.

Role of body surface cultures in prediction of sepsis in a neonatal intensive care unit

An analysis of surface cultures of 35 preterm infants of less than 33 weeks gestational age hospitalized in a neonatal intensive care unit was made. The babies had received neither antiseptic nor antibiotic therapy prior to collection of specimens. Surface cultures were collected on the 4th or 5th day of life from 16 skin or mucosal sites. At the onset of a febrile episode within 14 days of collection of surface swabs, a blood culture was done on 31 infants (four did not develop fever) and the results were compared with the surface cultures. Sepsis was diagnosed by positive blood culture in twenty neonates (57.1%). With this frequency of sepsis, the optimum sensitivity, specificity and positive predictive values of surface cultures were 60%, 27% and 60%, respectively. These values did not improve substantially for any anatomic site cultured or for any pathogen recovered. We conclude that surface cultures are of limited value in predicting the aetiology of sepsis in neonates.

Evaluation of histological appearance of tissues removed by cavitron ultrasonic surgical aspirator (CUSA)

Histological appearances of the tissue fragments obtained by cavitron ultrasonic surgical aspirator (CUSA) were studied in 25 cases to determine whether the aspirated tissue could be used for diagnosis. It was found that a definite diagnosis could be made on the tissue removed by this method.