Nudeotide sequence

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

Codons are usually presented in the messenger RNA language of adenine (A), guanine (G), cytosine (C), and uracil (U). Their nudeotide sequences are always written from the 5 -end to the 3 -end. The four nucleotide bases are used to produce the three-base codons. There are, therefore, 64 different combinations of bases, taken three at a time as shown in Figure 31.2. 

Combinatorial libraries are limited by the number of sequences that can be synthesized. For example, a library consisting of one molecule each of a 60-nudeotide sequence randomized at each position, would have a mass of >1014 g, well beyond the capacity for synthesis and manipulation. Thus, even if nucleotide addition is random at all the steps during synthesis of the oligonudeotide only a minority of the sequences can be present in the output from a laboratory-scale chemical DNA synthesis reaction. In analyzing these random but incomplete libraries, the protocol is efficient enough to allow selection of aptamers of lowest dissociation constants (Kd) from the mixture after a small number of repetitive selection and amplification cycles. Once a smaller population of oligonucleotides is amplified, the aptamer sequences can be used as the basis for constructing a less complex library for further selection. 

PCR is a versatile technique that can be used for applications other than simply detecting or quantitating DNA or RNA sequences. Figure 5-19 summarises some of its important uses it can be used to introduce mutations by use of mismatch primers to tag a DNA sequence dther radioactively or with a range of different labels to introduce restriction sites for sub-doning and to isolate unknown nudeotide sequences provided that partial sequence information is available. 

Naito E, Ozasa H, Ikeda Y, Tanaka K. Molecular cloning and nudeotide sequence of complementary DNAs encoding human short chain acyl-coenzyme A dehydrogenase and the study of the molecular basis of human short chain acyl-coenzyme A dehydrogenase defidency. J Clin Invest. 1989 May 83(5) 1605-13. PubMed dtation... 

The transfer of genetic information from the level of the nudeic add sequence of a gene to the level of the amino acid sequence of a protein or to the nudeotide sequence of RNA is termed gene expression. The entire process of gene expression in eucaryotes includes the following steps ... 

The ros genes appear to resemble those of erbB and also the insulin receptor. They encode transmembrane proteins, and their nudeotide sequences suggest they have a number of structural features in common (Wang, 1988). c-Ros is a receptor-like protein kinase with an extracellular domain of about 2000 amino... 

Figure 21.29. Li t-genmited array (riigooucleotides. The surface is ligbt-actimed lo react wtt die added nudeotides, sequence to the synthesized at each position in dm array. From Ref. 60.

Repeat expansion Nudeotide repeats are short DNA sequences that are repeated a number of times in a row. For example, a trinudeotide repeat is made up of 3-base-pair sequences, and a tetranudeotide repeat is made up of 4-base-pair sequences. A repeat expansion is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly. 

Prakash, The Sacdiaromyces cerevisiae RAD 18 gene encodes a protein that contains potential zinc finger domains for nudeic acid binding and a putative nudeotide binding sequence. Nucleic Acids Res, 1988, 16(14B), 7119-31. 

Frameshift A type of mutation which causes out-of-phase transcription of the base sequence such mutations arise from the addition or delection of nudeotide(s) in numbers other than 3 or multiples of 3. [NIH]... 

Fig. 8. A simplified combinatorial approach to identify the binding sequence for a (O) protein of interest, within 4096 sequences where ( ) represents the PCR primers, N a nudeotide, ie, A, G, C, or T. An essential aspect of this experiment is the ability to separate protein-bound from free DNA prior to...

By similar logic, protein affinity libraries have been constructed to identify protein—protein combining sites, as in antibody—antigen interaction (19) and recombinant libraries have been made which produce a repertoire of antibodies in E. coli (20). In another case, a potential DNA-based therapeutic strategy has been studied (21). DNAs from a partially randomized library were sdected to bind thrombin in vitro. Oligonucleotides, termed aptamers that bound thrombin shared a conserved sequence 14—17 nudeotides long. 

Walker, J.E., Saraste, M., Runswick, M.J., and Gay, N.J. (1982) Distanfly related sequences in fhe alpha- and beta-subunits of ATP synfhase, myosin, kinases and ofher ATP-requiring enzymes and a common nudeotide binding fold. 

Loo, T.W., Bartlett, M.C., and Clarke, D.M. (2002) The LSGGQ motif in each nudeotide-binding domain of human P-glycoprotein is adjacent to the opposing Walker A sequence. The Journal of Bio-logical Chemistry, 277 (44), 41303—41306. 

Lader, J., Malkani, B., Amin, S., et al. (2007) Sequence context-and temperature-dependent nudeotide exdsion repair of a benzo[a]pyrene diol epoxide-guanine DNA adduct catalyzed by thermophilic UvrABC proteins. Biochemistry, 46, 7006-7015. 

Babij P, Kelly C, Periasamy M (1991) Characterization of a mammalian smooth musde myosin heavy-chain gene complete nudeotide and protdn coding sequence and analysis of the 5 end of the gene. Proc Natl Acad Sd U S A 88 10676-10680... 

It is not necessary and would be enormously expensive to obtain a person s entire genome. Single-nudeotide polymorphisms (SNPs snips) are specific DNA sequences. Single nucleotides—A, T, C, or G—are what make up the genes. For example, two DNA sequences, such as AAGCCTAoi AAGCTTA, differ only in a single nucleotide. 

Detection of single nudeotide polymorphisms (SNPs) in genomic sequences. 

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