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The 24-mer DNA aptamer of Harada and Frankel (Harada, K,; Frankel, A. D. EMBO d. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem--loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Teachers can use a simple demonstration of how intermolecular forces make DNA helical in introductory classes when intermolecular forces are introduced. Students usually have heard that DNA is a double helix and the double helix is an elegant and easily understood example of how intermolecular forces determine macromolecular structure. A faculty member at Philadelphia College of Science and Pharmacy uses a model easily made from boxes and string to illustrate the principles involved. It works for more advanced classes to explain how intercalators unwind DNA.

The Holliday junction is a key intermediate in genetic recombination. The basis for the antiparallel orientation of the domains can either be of junction structure or the effect of electrostatic repulsion between domains. To distinguish between these two possibilities, an analogue called a bowtie junction was constructed and characterized. The analogue is such that one strand contains a 3',3' linkage at the branch point, the stand opposite contains a 5',5' linkage and the other two strands have the usual 3',5' linkages.

Focuses on the use of a spreadsheet to simulate enzyme kinetics. Details on spreadsheets with radioactive decay; Examination of a spreadsheet showing formulas to be entered into the cells; Reference to the use of the spreadsheets to determine the steady rate of gold formations.

The 24-mer DNA aptamer of Harada and Frankel (Harada, K.; Frankel,A. D.EMBOJ. 1995,14,5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands. [ABSTRACT FROM AUTHOR]

The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3' or 5' ends of the cytosine-repeats. Here, a series of oligomers d(XG i XC 5 X) and d(XC 5 XG i X) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs. Our data demonstrate that tetramolecular i-motif structure can tolerate specific flanking G-repeats. Assemblies of these oligonucleotides are polymorphic, but may be controlled by solution pH and counter ion species. Importantly, we find that the sequences d(TG i AC 5 ) can form the tetrameric i-motif in large quantities. This leads to the design of two oligonucleotides d(TG 4 AC 7 ) and d(TG Br GG Br GAC 7 ) that self-assemble to form quadruplex supramolecules under certain conditions. d(TG 4 AC 7 ) forms supramolecules under acidic conditions in the presence of K + that are mainly V-shaped or ring-like containing parallel G4s and antiparallel i-motifs. d(TG Br GG Br GAC 7 ) forms long linear quadruplex wires under acidic conditions in the presence of Na + that consist of both antiparallel G4s and i-motifs., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)