Toward rules for 1:1 polyamide:DNA recognition

Polyamides composed of four amino acids, imidazole (Im), pyrrole (Py), hydroxypyrrole (Hp), and β-alanine (β), are synthetic ligands that form highly stable complexes in the minor groove of DNA. Although specific pairing rules within the 2:1 motif can be used to distinguish the four Watson⋅Crick base pairs, a comparable recognition code for 1:1 polyamide:DNA complexes had not been described. To set a quantitative baseline for the field, the sequence specificities of Im, Py, Hp, and β for the four Watson⋅Crick base pairs were determined for two polyamides, Im-β-ImPy-β-Im-β-ImPy-β-Dp (1, for Im, Py, and β) and Im-β-ImHp-β-Im-β-ImPy-β-Dp (2, for Hp), in a 1:1 complex within the DNA sequence context 5′-AAAGAGAAGAG-3′. Im residues do not distinguish G,C from A,T but bind all four base pairs with high affinity. Py and β residues exhibit ≥10-fold preference for A,T over G,C base pairs. The Hp residue displays a unique preference for a single A⋅T base pair with an energetic penalty.

A Computer-Assisted Personalized Approach in an Undergraduate Plant Physiology Class1

We used Computer-Assisted Personalized Approach (CAPA), a networked teaching and learning tool that generates computer individualized homework problem sets, in our large-enrollment introductory plant physiology course. We saw significant improvement in student examination performance with regular homework assignments, with CAPA being an effective and efficient substitute for hand-graded homework. Using CAPA, each student received a printed set of similar but individualized problems of a conceptual (qualitative) and/or quantitative nature with quality graphics. Because each set of problems is unique, students were encouraged to work together to clarify concepts but were required to do their own work for credit. Students could enter answers multiple times without penalty, and they were able to obtain immediate feedback and hints until the due date. These features increased student time on task, allowing higher course standards and student achievement in a diverse student population. CAPA handles routine tasks such as grading, recording, summarizing, and posting grades. In anonymous surveys, students indicated an overwhelming preference for homework in CAPA format, citing several features such as immediate feedback, multiple tries, and on-line accessibility as reasons for their preference. We wrote and used more than 170 problems on 17 topics in introductory plant physiology, cataloging them in a computer library for general access. Representative problems are compared and discussed.

Coupling the folding of homologous proteins

The empirical observation that homologous proteins fold to similar structures is used to enhance the capabilities of an ab initio algorithm to predict protein conformations. A penalty function that forces homologous proteins to look alike is added to the potential and is employed in the coupled energy optimization of several homologous proteins. Significant improvement in the quality of the computed structures (as compared with the computational folding of a single protein) is demonstrated and discussed.

Prediction of the stability of DNA triplexes.

We present rules that allow one to predict the stability of DNA pyrimidine.purine.pyrimidine (Y.R.Y) triple helices on the basis of the sequence. The rules were derived from van't Hoff analysis of 23 oligonucleotide triplexes tested at a variety of pH values. To predict the enthalpy of triplex formation (delta H degrees), a simple nearest-neighbor model was found to be sufficient. However, to accurately predict the free energy of the triplex (delta G degrees), a combination model consisting of five parameters was needed. These parameters were (i) the delta G degrees for helix initiation, (ii) the delta G degrees for adding a T-A.T triple, (iii) the delta G degrees for adding a C(+)-G.C triple, (iv) the penalty for adjacent C bases, and (v) the pH dependence of the C(+)-G.C triple's stability. The fitted parameters are highly consistent with thermodynamic data from the basis set, generally predicting both delta H degrees and delta G degrees to within the experimental error. Examination of the parameters points out several interesting features. The combination model predicts that C(+) -G.C. triples are much more stabilizing than T-A.T triples below pH 7.0 and that the stability of the former increases approximately equal to 1 kcal/mol per pH unit as the pH is decreased. Surprisingly though, the most stable sequence is predicted to be a CT repeat, as adjacent C bases partially cancel the stability of one another. The parameters successfully predict tm values from other laboratories, with some interesting exceptions.