Recognition nucleic acid sequences

S. Kwakye and A. Baeumner, A microfluidic biosensor based on nucleic acid sequence recognition, A7iaZ. Bioanal. Chem., 376 (2003) 1062-1068. 

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... 

The increasing numbers of stored protein and nucleic acid sequences, and the recognition that functionally related proteins often had similar sequences, catalyzed the development of statistical techniques for sequence comparison which underlie many of the core bioinformatic methods used in proteomics today. Nucleic acid sequences are stored in three primary sequence databases - GenBank, the EMBL nucleotide sequence database, and the DNA database of Japan (DDBJ) - which exchange data every day. These databases also contain protein sequences that have been translated from DNA sequences. A dedicated protein sequence database, SWISS-PROT, was founded in 1986 and contains highly curated data concerning over 70 000 proteins. A related database, TrEMBL, contains automatic translations of the nucleotide sequences in the EMBL database and is not manually curated. 

Palindrome a nucleic acid sequence that is identical to its complementary strand (when both are read in the same 5 -3 direction). In the region of a P. there is therefore a twofold rotational symmetry. Perfect P, e.g. GAATTC, often occur as recognition sites for restriction enzymes. Imperfect palindromes, e.g. TACCrCTGGCGTGATA, often act as binding sites for proteins such as repressors. Interrupted P, e.g. GGTTXXXXXAACC, make possible the for-... 

Gierer (23) had proposed palindromic structures as recognition sites for DNA-protein interactions and, specifically for operon-repressor interactions. As will be seen below, certain nucleic acid sequences in such sites are, effectively, palindromes. 

Seeman, N.C., Rosenberg, J.M., Rich, A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73 804-809, 1976. 

N. T., Lhomme J., Helene C. Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[alpha]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 1987 15 7749-7760. 

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