Examining Cultural Structures and Functions in Biology.

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods.

Thermodynamic examination of pH and magnesium effect on U6 RNA internal loop.

U6 RNA contains a 1 × 2-nt internal loop that folds and unfold during spliceosomal assembly and activation. The 1 × 2 loop consists of a C•A base pair that forms an additional hydrogen bond upon protonation, C•A, and uracil (U80) that coordinates the catalytically essential magnesium ions. We designed a series of RNA and DNA constructs with a 1 × 2 loop sequence contained in the ISL, and its modifications, to measure the thermodynamic effects of protonation and magnesium binding using UV-visible thermal denaturation experiments.

Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs.

Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl(2) or 1 M KCl.

On using magnesium and potassium ions in RNA experiments.

RNA is a dynamic molecule that can adopt different conformations under different conditions. In the cell, the negatively charged RNA is expected to interact with potassium and magnesium ions. The role of magnesium ions has been extensively studied in RNA, as it is necessary for proper folding of RNA and acts as a nucleophile in many reactions catalyzed by RNA.

Metal ion binding to RNA.

RNA crystal structures have provided a wealth of information on localized metal ions that are bound to specific sites, such as the RNA deep groove, the Hoogsteen face of guanine nucleotides and anionic phosphate oxygens. With a number of crystal structures being solved with heavy metal derivatives and other "reporter" ions, sufficient information is available to estimate global similarities and differences in ion binding properties and to begin determining the influence of RNA and ions on each other. Here we will discuss the ions that are observed bound to RNA, their coordination properties, and the roles they play in RNA structural studies.

Thermodynamic examination of the pyrophosphate sensor helix in the thiamine pyrophosphate riboswitch.

Riboswitches are functional mRNA that control gene expression. Thiamine pyrophosphate (TPP) binds to thi-box riboswitch RNA and allosterically inhibits genes that code for proteins involved in the biosynthesis and transport of thiamine. Thiamine binding to the pyrimidine sensor helix and pyrophosphate binding to the pyrophosphate sensor helix cause changes in RNA conformation that regulate gene expression.

Thermodynamic examination of trinucleotide bulged RNA in the context of HIV-1 TAR RNA.

RNA structures contain many bulges and loops that are expected to be sites for inter- and intra-molecular interactions. Nucleotides in the bulge are expected to influence the structure and recognition of RNA. The same stability is assigned to all trinucleotide bulged RNA in the current secondary structure prediction models.

How to create successful discussions in science classrooms.

Professors often expect students to have the skills that are necessary to participate in discussions. Students, on the other hand, have been trained to glean information from the lecture format; their prior experiences in discussions are likely to be limited to personal opinions on topics such as stem-cell research or evolution. Sudden changes in expectations are jarring and unwelcome at any stage of life but especially when it affects our performance.

Introductory course based on a single problem: Learning nucleic acid biochemistry from AIDS research.

In departure from the standard approach of using several problems to cover specific topics in a class, I use a single problem to cover the contents of the entire semester-equivalent biochemistry classes. I have developed a problem-based service-learning (PBSL) problem on HIV/AIDS to cover nucleic acid concepts that are typically taught in the second semester of a biochemistry class. Use of research articles on a specific topic allows developing problems such as one discussed here.

Steric interference modification of the hammerhead ribozyme.

Although the structure of the hammerhead ribozyme is well characterized, many questions remain about its catalytic mechanism. Extensive evidence suggests the necessity of a conformational change en route to the transition state. We report a steric interference modification approach for investigating this change.