David G. Nickens

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Rhodospirillum centenum exhibited a number of general properties typically observed in nonsulfur purple bacteria, but also displayed a number of unusual characteristics that include: (1) conversion of the vibrioid/spiral cells to thick-walled cysts under certain growth conditions; (2) absence of O2 repression of photopigment synthesis; (3) synthesis of(More)
Although developments in small-molecule therapeutics for HIV-1 have been dramatic in recent years, the rapid selection of drug-resistant viral strains and the adverse side effects associated with long-term exposure to current treatments propel continued exploration of alternative anti-HIV-1 agents. Non-coding nucleic acids have emerged as potent inhibitors(More)
A better understanding of aptamer function in bacteria would help to establish simple model systems for screening RNA-protein interactions within an intracellular context. Escherichia coli DNA polymerase I mutants (Pol I(ts)) fail to grow at 37 degrees C unless an exogenous DNA polymerase such as HIV-1 reverse transcriptase (RT) is expressed within the(More)
The structural complexity required for substrate recognition within an active site constrains the evolution of novel catalytic functions. To evaluate those constraints within populations of incipient ribozymes, we performed a selection for kinase ribozymes under conditions that allowed competition for phosphorylation at nine candidate sites. Two candidate(More)
Alphavirus genome function is controlled by elements at both the 5' and 3' ends. The 5' 220 nt of the Sindbis virus genome is predicted to consist of four stem-loop structures the first of which has been demonstrated to be required for efficient minus-strand RNA synthesis. To understand the role of the structure of the first stem-loop (SL1) in regulating(More)
Assembly of a hepatitis B virus (HBV) virion begins with the formation of an RNA-filled core composed of a symmetrical capsid (built of core protein), viral pregenomic RNA, and viral reverse transcriptase. To generate the circular dsDNA genome of HBV, reverse transcription requires multiple template switches within the confines of the capsid. To date, most(More)
Small RNA molecules can participate in complex regulatory networks not merely through Watson-Crick interactions with other RNAs (as in anti-sense RNA), but also by forming discrete structures that bind protein or low-molecular weight targets. RNA aptamers derived from in vitro selections (SELEX) are being used inside cells for at least four purposes: (1) to(More)
Expression of the Rhodobacter capsulatus puc operon, which codes for structural polypeptides of the light-harvesting-II peripheral antenna complex, is highly regulated in response to alterations in oxygen tension and light intensity. To obtain an understanding of the puc promoter region we report the high-resolution 5' mapping of the puc mRNA(More)
The osmotic pressure within a living bacterium creates stresses in the peptidoglycan that stretch the sacculus. We measured the amount of stretch by monitoring the shrinkage of growing cells of Escherichia coli after removal of the osmotic pressure by disruption of the phospholipid membranes with sodium dodecyl sulfate. Because the rods of the wild type are(More)
Accommodation of donor and acceptor substrates is critical to the catalysis of (thio)phosphoryl group transfer, but there has been no systematic study of donor nucleotide recognition by kinase ribozymes, and there is relatively little known about the structural requirements for phosphorylating internal 2'OH. To address these questions, new(More)