Sequence design

Occasionally, you may encounter the inverse of the structure predictions problem How do I design sequences with a particular structure Suppose, e. g., you have found a set of structural constraints necessary for a particular function, how do you know that these constraints are sufficient The most stringent test would be to design and test sequences that are as random as possible, given the constraints. 

Inverse folding can be viewed as an optimization problem that can be treated with simple heuristics. This is what the RNAinverse program does for you. Input for the RNAinverse program consists of an RNA secondary structure (the target) in bracket notation (on the first line), optionally followed by a sequence to be used as the starting point of the optimization (otherwise a random start sequence is used). 

Suppose we need sequences that fold into the structure 

The lower-case cca in the start sequence (second line of inverse.in) tells the program to keep these positions fixed all other positions are random. 

The 8 at the end of the line is the number of mutations done before a solution was found. Let us fold this sequence to check  

For hairpins, sodium concentration below 0.1 m is recommended to minimize bimolecular self-complementary internal loop formation (37). The predicted thermodynamics from RNA-MFOLD (28, 38) or DNA-MFOLD (39) programs are accurate enough to deduce if the putative internal loop will form in high population (to use MFOLD the two strands should be connected by the dummy sequence LLL (M. Zuker and J. SantaLucia, unpublished). Simulating the predicted populations of the hairpin and duplex forms by solving the simultaneous equilibria is also recommended (31, 36). 

For bimolecular structures (duplexes), it is generally recommended that self-complementary sequences be avoided, since they have high propensity to form competing hairpin structures. Even non-self-complementary duplexes can some- 

The design of more complex nucleic acid structures requires particular care. 

A general principle that has been appUed toward the synthesis of multi-branched loops (45) and novel structures (46) is to maximize orthogonality of the base pairing potential of different stems. The idea is to design the different stems with the lowest potential far forming alternative stem structures. If a complex structure requires a hairpin, the exceptionally stable UUCG (for RNA) or GNRA (for DNA or RNA) or GNA (for DNA) sequences are recommended (47, 

slow heating rates are recommended for these S5rstems. 

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The optimal sequence obtained, called FSD-1 for full sequence design, is shown in Table 17.2 and compared with the sequence of the template Zif 268. A search of the FSD-1 sequence against protein databases did not reveal a statistically significant similarity with any other protein, including zinc finger proteins. 

Standard nomenclature will be used for sequence designations and reaction probabilities. Thus, Pa, P are the Bemoullian probabilities of comonomers A and B, respectively, and the subscripts 1 and 2 correspond to conq>onents 1 and 2. 

In summary, these recently obtained results demonstrate that certain amphi-pathic peptoid sequences designed to mimic both the helical structure and approximate length of magainin helices are also capable of selective and biomimetic antibacterial activity. These antibacterial peptoids are helical in both aqueous buffer and in the presence of lipid vesicles. Ineffective (non-antibacterial) peptoids exhibit weak, random coil-like CD, with no spectral intensification in the presence of lipid vesicles. Selective peptoids exhibit stronger CD signals in bacterial-mimetic vesicles than in mammalian-mimetic vesicles. Non-selective peptoids exhibit intensely helical CD in both types of vesicles. 

Muelder and Shadoff (3) prepared C-2,3,7,8-Cl4-DBpD (0.9 mCi/ mmole) by chlorination of C-2,7-dichlorodibenzo-p-dioxin made from potassium C-2,4-dichlorophenate. The preparation of tritium-labeled 2,3,7,8-Cl4-DBpD is justified because the radiolabeled intermediates are less expensive and more accessible and because a higher specific activity is potentially attainable. Here, we consider the optimal conditions for the reaction sequence designed to obtain products of high chemical and radiochemical purity shown at the top of p. 8. 

Liang SD, Grishin NV. Effective scoring function for protein sequence design. Proteins 2004 54 271-81. 

Figure 5.15 (A) Pulse sequence designed for the combination of polarization...

Primers The primers are short (15-30) oligonucleotide sequences designed to base pair or anneal to complementary sequences that flank the DNA target sequence to be amplified. The primers are added at 0.1-1 qM in the assay. 

E. M. Haacke, R. W. Brown, M. R. Thompson, R. Venkatesan 1999, Magnetic Resonance Imaging Physical Principles and Sequence Design, Wiley Sons, Chichester, 914 pp. Extensive textbook with focus on fundamentals, not on applications. 

Figure 4.1.1 CPMG pulse sequence designed for three-dimensional imaging. TE is echo time, and Gi, G2 and G3 represent the gradient magnetic fields along the directions of zlt z2 and z3, respectively.

The most promising types of biologic response modifiers are monoclonal antibodies, cytokines, and fusion proteins.1 Monoclonal antibodies may be chimeric (fused mouse and human segments designated -ximab ), humanized with intermittent murine sequences (designated -zumab ), human backbone with monkey sequences, or fully human.40... 

Pallitto MM, Ghanta J, Heizelman P, Kiessling LL, Murphy RM. Recognition sequence design for peptidyl modulators of beta-amyloid aggregation and toxicity. Biochemistry 1999 38 3570-3578. 

Figure 6. The c-mos negative regulatory element (NRE). Nucleotide positions of the NRE are shown relative to the spermatocyte transcription start site, taken as 280 base pairs upstream of the c-mos ATG (see Fig. 4). The endpoints of the NRE are defined by deletions that allow c-mos expression in NIH 3T3 and other somatic cells. Mutations of the sequences designated by boxes 1,2, and 3 also allow c-mos transcription in NIH 3T3 cells, indicating that these sequences represent functional elements within the NRE. Boxes 1 and 2 are similar to sequences upstream of the protamine (Prot) promoter that inhibit in vitro transcription in HeLa cell extracts. A sequence just upstream of box 2 is also similar to a putative repressor-binding site in the regulatory region of Pgk2.

The approach formulated in 1998 is based on the assumption that a copolymer obtained under some preparation conditions is able to remember features of its original conformation from which it was built and to store the corresponding information in the resulting sequence. Therefore, this approach may be called conformation-dependent sequence design. 

Most of the contributions collected in volumes 195 and 196 are dedicated to the review of the results obtained recently in this direction, i.e., dealing with the conformation-dependent sequence design of copolymers and the study of... 

One of the promising synthetic strategies of conformation-dependent sequence design is based on direct copolymerization under unusual conditions. 

All of the selected contributions that are present in these special volumes are good representatives for manifesting the importance of the concepts based on conformation-dependent sequence design. It has been our intention to provide the scientific and industrial polymer community with a comprehensive view of the current state of knowledge on designed polymers. Both volumes attempt to review what is currently known about these polymers in terms of their synthesis, chemical and physical properties, and applications. We will feel the volumes have been successful if some of the chapters presented here stimulate readers to become interested in and solve specific problems in this rapidly developing field of research. 

Keywords Biopolymers Copolymer sequences Globules Polymers Sequence design... 

An essential progress in this direction was achieved [69-71] with the following reformulation of the problem. Instead of trying to solve a very complex problem of real biological evolution, an attempt was made to find a way of preparing sequences ensuring certain properties of the synthesized heteropolymer. This problem is called polymer sequence design. Gen-... 

Polymers designed with this technique have a number of important aspects in common with proteins. First of all, the transition from a liquid-like globule into a frozen state occurs as a first order phase transition. Further, the frozen state itself has an essential stability margin, which is determined by the design parameters. As in real proteins, neither a large variation of temperature or other environmental conditions, nor a mutational substitution of several monomers leads to any change in basic state conformation. In this respect the ability of sequence design to capture certain essential characteristics of proteins seems quite plausible. 

Certain difficulties remain, however, with this approach. First, such an important feature as a secondary structure did not find its place in this theory. Second, the techniques of sequence design ensuring exact reproduction of the given conformation are well developed only for lattice models of polymers. The existing techniques for continuum models are complex, intricate, and inefficient. Yet another aspect of the problem is the necessity of reaching in some cases beyond the mean field approximation. The first steps in this direction were made in paper [84], where an analog of the Ginzburg number for the theory of heteropolymers was established. 

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