Nucleic acid sequence evolution

MO Dayhoff, WC Barker, PJ McLaughlin. Inferences from protein and nucleic acid sequences Early molecular evolution, divergence of kingdoms and rates of change. Orig Life 5 311-330, 1974. 

Li, W.-H., and Gouy, M. (1990). Statistical tests of molecular phylogenies. In Molecular Evolution Computer Analysis of Protein and Nucleic Acid Sequences. (Doolittle, R. F., ed.) Methods Enzymol. 183, 645-659. 

A somewhat different view of biological evolution has arisen from a comparison of nucleic acid sequences in different organisms. The best-known sequences for such stud-... 

Volume 183. Molecular Evolution Computer Analysis of Protein and Nucleic Acid Sequences... 

Doolittle, R.F. 1990. Molecular evolution Computer analysis of protein and nucleic acid sequences. In Methods in Enzymology, Vol. 183, R. F. Doolittle, Ed. Academic Press, Inc. San Diego, Chapter 6. 

RNA has three basic roles in the cell. First, it serves as the intermediate in the flow of information from DNA to protein, the primary functional molecules of the cell. The DNA is copied, or transcribed, into messenger RNA (mRNA), and the mRNA is translated into protein. Second, RNA molecules serve as adaptors that translate the information in the nucleic acid sequence of mRNA into information designating the sequence of constituents that make up a protein. Finally, RNA molecules are important functional components of the molecular machinery, called ribosomes, that carries out the translation process. As will be discussed in Chapter 2, the unique position of RNA between the storage of genetic information in DNA and the functional expression of this information as protein as well as its potential to combine genetic and catalytic capabilities are indications that RNA played an important role in the evolution of life. 

The last theme to be considered is the interrupted character of most eukaryotic genes, which are mosaics of nucleic acid sequences called introns and exons. Both are transcribed, but introns are cut out of newly synthesized RNA molecules, leaving mature RNA molecules with continuous exons. The existence of introns and exons has crucial implications for the evolution of proteins. 

This models the relationship between repertoire size and repertoire completeness, and shows that at least 108-1010 different antibodies are needed in the repertoire if a threshold Kd of 10 8-10 10 is required, depending of the probability selected (Fig. 8.3).3 Therefore, for one initial or starting sequence, the first step in the directed evolution cycle must be capable of generating 108-1010 nucleic acid sequences that code for different proteins. This library or repertoire size is needed for directed evolution according to this model. However, good results have been obtained experimentally (mainly with enzymes) using smaller libraries, of 104 members.6 7... 

This flow of information depends on the genetic code, which defines the relation between the sequence of bases in DNA (or its mRNA transcript) and the sequence of amino acids in a protein. The code is nearly the same in all organisms a sequence of three bases, called a codon, specifies an amino acid. There is another step, between transcription and translation, in the expression of most eukaryotic genes, which are mosaics of nucleic acid sequences called introns and exons. Both are transcribed, but introns are cut out of newly synthesized RNA molecules, leaving mature RNA molecules with continuous exons. The existence of introns and exons has crucial Implications for the evolution of proteins. 

Evolution of nucleic acid sequence Phylogenetic analyses often examine whether nucleotide substitutions are synonymous (not altering encoded amino acid) or nonsynonymous, and trace the history of gene- TABLE 18.6 Phylogenetic databases and utilities ... 

Aptamers are nucleic acid sequences that specifically bind proteins or low molecular-weight substrates. Aptamers are selected from a combinatorial library of lO -lO DNAs, using the Systematic Evolution of Ligands by Exponential Enrichment Process (SELEX). Numerous aptamers that specifically bind proteins or low molecular-weight substrates have been elicited in recent years. Also, their recognition properties have been used extensively to develop electrochemical [162,163] or optical... 

Dayhoff, M. O., Barker, W. C., and Schwartz, R. M., 1978, Evolution of the mammalian genome, a view based on protein and nucleic acid sequence data. Fed. Proc. 37 1419. 

Wong, T.S., Tee, K.L., Hauer, B. and Schwaneberg, U. (2004) Sequence saturation mutagenesis (SeSaM) a novel method for directed evolution. Nucleic Acids Research, 32, e26. 

Eisen JA, Sweder KS, Hanawalt PC (1995) Evolution of the SNF2 family of proteins subfamilies with distinct sequences and functions. Nucleic Acids Res 23 2715-2723 Falbo KB, Shen X (2006) Chromatin remodeling in DNA replication. J Cell Biochem 97 684-689 Fazzio TG, Gelbart ME, Tsukiyama T (2005) Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo. Mol Cell Biol 25 9165-9174... 

Some time after the evolution of this primitive protein-synthesizing system, there was a further development DNA molecules with sequences complementary to the self-replicating RNA molecules took over the function of conserving the genetic information, and RNA molecules evolved to play roles in protein synthesis. (We explain in Chapter 8 why DNA is a more stable molecule than RNA and thus a better repository of inheritable information.) Proteins proved to be versatile catalysts and, over time, took over that function. Lipidlike compounds in the primordial soup formed relatively impermeable layers around self-replicating collections of molecules. The concentration of proteins and nucleic acids within these lipid enclosures favored the molecular interactions required in self-replication. 

Aptamers are nucleic acids which exhibit a defined structure due to their nucleotide sequence and therefore, are able to specifically bind selected targets [1] (aptus [lat.] = fitting, sticking to). Aptamers and likewise, ribozymes [2] and deoxyribozymes [3] are selected in vitro by screening nucleic acid libraries. Here we describe in detail the selection of aptamers by a process called SELEX (Systematic Evolution of Ligands by Exponential enrichment) [4]. 

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