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Frequent occurrence of recognition site-like sequences in the restriction endonucleases.

Biro JC, Biro JM - BMC Bioinformatics (2004)

Bottom Line: It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7).A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA.We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Karolinska Institute, Stockholm, Sweden. jan.biro@sbcglobal.net

ABSTRACT

Background: There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while Crick argued that any connection between codons and amino acids is only the result of an "accident". This question is fundamental to understand the nature of specific protein-nucleic acid interactions.

Results: The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA. The average distance between the closest atoms in the codons and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the distance between the nitrogen and oxygen atoms of the co-localized molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15), when positively charged amino acids are involved. This is indicating that an interaction between the nucleic- and amino acids might occur.

Conclusion: We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

Show MeSH
Co-location of codon-like triplets and amino acids in RE-RS complexes. Examples are taken from Figure 6.
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Figure 7: Co-location of codon-like triplets and amino acids in RE-RS complexes. Examples are taken from Figure 6.

Mentions: Examples of the different kinds of codon-amino acid co-localizations are shown in Figure 7, 8. It was possible to find examples for 12 of 20 different amino acids. In many cases the nitrogen (N) or oxygen (O) atoms in the amino acid residue were within direct or indirect hydrogen bonding distance to an O or N atom in the first or second nucleotide residue of its codon-like triplet in the RS. These distances are short enough to indicate interactions (probably through H-bridges) between the molecules. We have found many examples where an amino acid was co-located with its codon-like triplet in the RS but without interaction with the nucleic acid bases. In these cases the amino acid residues were aligned along the phopho-deoxyribosil backbone of the DNA, close to the O atoms in the phosphate groups. A rather interesting example for this type of molecular alignment was found in EcoRI (part of Figure 7). In this example all the four theoretically possible overlappingly translated amino acids of the sequence CGAATT were co-located with the RS (GAATTC).


Frequent occurrence of recognition site-like sequences in the restriction endonucleases.

Biro JC, Biro JM - BMC Bioinformatics (2004)

Co-location of codon-like triplets and amino acids in RE-RS complexes. Examples are taken from Figure 6.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC394317&req=5

Figure 7: Co-location of codon-like triplets and amino acids in RE-RS complexes. Examples are taken from Figure 6.
Mentions: Examples of the different kinds of codon-amino acid co-localizations are shown in Figure 7, 8. It was possible to find examples for 12 of 20 different amino acids. In many cases the nitrogen (N) or oxygen (O) atoms in the amino acid residue were within direct or indirect hydrogen bonding distance to an O or N atom in the first or second nucleotide residue of its codon-like triplet in the RS. These distances are short enough to indicate interactions (probably through H-bridges) between the molecules. We have found many examples where an amino acid was co-located with its codon-like triplet in the RS but without interaction with the nucleic acid bases. In these cases the amino acid residues were aligned along the phopho-deoxyribosil backbone of the DNA, close to the O atoms in the phosphate groups. A rather interesting example for this type of molecular alignment was found in EcoRI (part of Figure 7). In this example all the four theoretically possible overlappingly translated amino acids of the sequence CGAATT were co-located with the RS (GAATTC).

Bottom Line: It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7).A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA.We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

View Article: PubMed Central - HTML - PubMed

Affiliation: Karolinska Institute, Stockholm, Sweden. jan.biro@sbcglobal.net

ABSTRACT

Background: There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while Crick argued that any connection between codons and amino acids is only the result of an "accident". This question is fundamental to understand the nature of specific protein-nucleic acid interactions.

Results: The nature of specific protein-nucleic acid interaction between restriction endonucleases (RE) and their recognition sequences (RS) was studied by bioinformatics methods. It was found that the frequency of 5-6 residue long RS-like oligonucleotides is unexpectedly high in the nucleic acid sequence of the corresponding RE (p < 0.05 and p < 0.001 respectively, n = 7). There is an extensive conservation of these RS-like sequences in RE isoschizomers. A review of the seven available crystallographic studies showed that the amino acids coded by codons that are subsets of recognition sequences were often closely located to the RS itself and they were in many cases directly adjacent to the codon-like triplets in the RS.Fifty-five examples of this codon-amino acid co-localization are found and analyzed, which represents 41.5% of total 132 amino acids which are localized within 8 A distance to the C1' atoms in the DNA. The average distance between the closest atoms in the codons and amino acids is 5.5 +/- 0.2 A (mean +/- S.E.M, n = 55), while the distance between the nitrogen and oxygen atoms of the co-localized molecules is significantly shorter, (3.4 +/- 0.2 A, p < 0.001, n = 15), when positively charged amino acids are involved. This is indicating that an interaction between the nucleic- and amino acids might occur.

Conclusion: We interpret these results in favor of Woese and suggest that the genetic code is "rational" and there is a stereospecific relationship between the codes and the amino acids.

Show MeSH