Secondary structure - general

See also Secondary Structure (General), Secondary Structure (Terms), Secondary Structures (Specific examples). Factors Determining Secondary and Tertiary Structure, Sheet, Keratin,... 

See also Ramachandran Plots, Secondary Structure (General), Secondary Structure (Terms)... 

Escherichia coli assignments, secondary structure, general fold, and backbone dynamics. Biochemistry 34, 13 858-13 870. 

Plenary 2. S A Asher et al, e-mail address asher ,vms.cis.pitt.edu/asher+ (RRS, TRRRS). UV RRS is used to probe methodically the secondary structure of proteins and to follow unfolding dynamics. Developing a library based approach to generalize the mediod to any protein. 

Ribosomes, the supramolecular assemblies where protein synthesis occurs, are about 65% RNA of the ribosomal RNA type. Ribosomal RNA (rRNA) molecules fold into characteristic secondary structures as a consequence of intramolecular hydrogen bond interactions (marginal figure). The different species of rRNA are generally referred to according to their sedimentation coefficients (see the Appendix to Chapter 5), which are a rough measure of their relative size (Table 11.2 and Figure 11.25). 

Primer design is one of the most important aspects of a robust PCR assay. In general, primers should be designed such that they are not able to form secondary structures such as stemloop or hairpin configurations. A primer must not be complementary at the 3 end, as this will cause primer dimers to form. All primers should have similar melting temperatures and should not contain stretches of individual nucleotides. There are software programs available to assist in primer design, but it is crucial that primers are tested in the assay, especially in a multiplex system. 

Yoda T, Sugita Y, Okamoto Y (2004) Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations. Chem Phys 307 269... 

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