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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
Expected (E) vs. Found (F) RS-like oligonucleotides in the REs. Expected and observed numbers (N) of RS-like nucleotides from 4 to 8 residues long are shown. Statistically significant E – F differences are indicated. NS: not significant, *: single value. For details see the Results.
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Figure 5: Expected (E) vs. Found (F) RS-like oligonucleotides in the REs. Expected and observed numbers (N) of RS-like nucleotides from 4 to 8 residues long are shown. Statistically significant E – F differences are indicated. NS: not significant, *: single value. For details see the Results.

Mentions: The statistical evaluation of the results was based on the calculation of the number of strings which are expected (E) to be found in a L residues long sequence only by chance and compare this number with the number of the same strings that are really found (F). The formula E = L/4n was used, where n is the number of residues in the string. The result of this statistical evaluation is shown in Figure 5.


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

Biro JC, Biro JM - BMC Bioinformatics (2004)

Expected (E) vs. Found (F) RS-like oligonucleotides in the REs. Expected and observed numbers (N) of RS-like nucleotides from 4 to 8 residues long are shown. Statistically significant E – F differences are indicated. NS: not significant, *: single value. For details see the Results.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: Expected (E) vs. Found (F) RS-like oligonucleotides in the REs. Expected and observed numbers (N) of RS-like nucleotides from 4 to 8 residues long are shown. Statistically significant E – F differences are indicated. NS: not significant, *: single value. For details see the Results.
Mentions: The statistical evaluation of the results was based on the calculation of the number of strings which are expected (E) to be found in a L residues long sequence only by chance and compare this number with the number of the same strings that are really found (F). The formula E = L/4n was used, where n is the number of residues in the string. The result of this statistical evaluation is shown in Figure 5.

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