The secondary structure model

The secondary structure model, proposed by Templeton et al., relates the secondary structures of novolacs [see Figs. 11.36(a) and (b)] to their dissolution behavior. The authors distinguished between structures where intermolecular bonds between novolac molecules predominate and those with predominantly intramolecular hydrogen bonds and they correlated these to dissolution behavior. They found that, for example, for novolacs made from p-cresol, the secondary structure of the resin brings the OH groups of the phenols together to such an extent that 

Szmanda, and R.L. Fischer, Jr., Resist dissolution kinetics and submicron process control, Proc. SPIE 920, 321 (1988). 

Templeton, C.R. Szamanda, and A. Zampini, Dissolution kinetics of positive photoresists the secondary structure model, Proc. SPIE 771, 136 (1987). 

Reiser, Photoreactive Polymers The Science and Technology of Resists, p. 217, John Wiley Sons, Hoboken, NJ (1989). 

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Recall that the secondary-structure model for RNA is a model - and a crude one at that. It neglects pseudo knots and other tertiary interactions, does not take deviations from the additive nearest neighbor energy model into account, and is based on thermodynamic parameters extracted from melting experiments by means of multidimensional fitting procedures. Thus, you cannot expect perfect predictions for each individual sequence. Rather, the accuracy is on the order of 50% of the base pairs for the minimum free energy structure. 

Figure 4.2 The hammerhead and hairpin ribozymes. Secondary structures for both the hammerhead and hairpin ribozymes are depicted. N=any nucleotide, R=Purine and Y=Pyrimidine. A diagram of the tertiary structure of the hammerhead ribozyme is depicted above the secondary structure model. The corresponding stems I, II and III in both structures are shown. In the hammerhead ribozyme H=A, C or U at the cleavage site. In the hairpin ribozymes HI, H2, etc. refer to the helical regions of the RNA structure.

Examples of models that have been proposed in an attempt to link the above steps into a coherent mechanism include the membrane model, the secondary structure model, the critical deprotonation model, the percolation model, the critical ionization model, and the stone wall model, to mention but a few. In the following sections, we briefly review the aspects of these models. 

Hanabata, Y. Uetani, and A. Furuta, Novolak design for high resolution positive photoresists. II. stone wall model for positive photoresist development, Proc. SPIE 920, 349 482 (1990). C.G. Willson, R. Miller, D. McKean, N. Clecak, T. Tompkins, D. Hofer, J. Michl, and J. Downing, Design of a positive resist for projection lithography in the mid UV, Polym. Sci. Eng. 23, 1004 (1983) M.K. Templeton, C.R. Szamanda, and A. Zampini, Dissolution kinetics of positive photo resists the secondary structure model, Proc. SPIE 771, 136 (1987). 

As discussed earlier in the secondary structure model, Templeton et al. have shown that the steric arrangement of the methylene links in the novolac resin can have a profound effect on its dissolution rate and on lithographic performance. Using molecular mechanics, these authors have calculated the equilibrium secondary structures of cresol-formaldehyde oligomers. They found that the secondary structure of these molecules determines the relative positions of the hydroxyl groups in the novolac matrix, and hence the possibility of intramolecular hydrogen bonding. ... 

The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

The cylinder model is used to characterize the helices in the secondary structure of proteins (see the helices in Figure 2-124c),... 

Nlng Q and T J Sejnowsld 1988. Predicting the Secondary Structure of Globular Proteins Using Neural Network Models. Journal of Molecular Biology 202 865-888. 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

N Qian, TJ Sejnowski. Predicting the secondary structure of globular proteins using neural network models. J Mol Biol 202 865-884, 1988. 

In 1953, James Watson and Francis Crick made their classic proposal for the secondary structure of DNA. According to the Watson-Crick model, DNA under physiological conditions consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix like the handrails on a spiral staircase. The two strands are complementary rather than identical and are held together by hydrogen bonds between specific pairs of... 

The secondary structure of DNA is shown in Figure B. This "double helix" model was first proposed in 1953 by James Watson and Francis Crick, who used the x-ray crystallographic data of Rosalind Franklin and Maurice Wilkins. Beyond that, they were intrigued by the results of analyses that showed that in DNA the ratio of adenine to thymine molecules is almost exactly 1 1, as is the ratio of cytosine to guanine ... 

In another study, ATPase reconstituted into liposomes was analyzed by infrared attenuated total reflection spectroscopy and the secondary-structure elements of the molecule were determined from the spectra obtained by Fourier self-deconvolution [42]. Gratifyingly, essentially identical secondary-structure estimates for the ATPase were obtained by this entirely different approach, suggesting quite strongly that these secondary-structure estimates are reasonably accurate. Thus, any future models for the structure of the H -ATPase must take this information into account. 

In proteins in particular the peptide bonds contribute to the CD-spectra of the macromolecule. Here, CD-spectra reflect the secondary structure of proteins, which are derived from CD-spectra of model macromolecules with only one defined secondary structure (like poly-L-lysine at given pH values) or based on spectra of proteins with known structures (e.g.,from X-ray crystallography). The amount of a-helices or -sheets in the unknown structure is calculated by linear combination of the reference spectra [150,151]. 

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