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Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA - Nucleic Acids Res. (2012)

Bottom Line: However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences.Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules.Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

View Article: PubMed Central - PubMed

Affiliation: FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

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Experimental relationship between compositional diversity and template-directed ligation. (a) Fraction of DNA sequences having high compositional diversity (C3‚ÄČ>‚ÄČ0.95; analysis length‚ÄČ=‚ÄČ16) after template-directed ligation in a heterogeneous pool of degenerate oligonucleotides including four bases. A greater fraction of reaction products (yellow) have high C3 relative to the templates (red‚ÄČ=‚ÄČaverage C3 of 16-mers contained in sequenced 40-mer templates) and substrates (orange‚ÄČ=‚ÄČC3 of 16-mers from in silico non-templated, random concatenation of experimentally sequenced octamers). The fraction of high C3 sequences in a uniform random pool is shown in green. Error bars are SDs from replicate sequencing experiments. (b) Polyacrylamide gel showing higher molecular weight products of template-directed ligation for different single templates from a binary alphabet. Molecular weight markers are given in the left lane. ‚Äė√ė‚Äô indicates a reaction without template added. Template C3 increases from left (C3‚ÄČ=‚ÄČ0) to right (C3‚ÄČ=‚ÄČ0.97; see ‚ÄėMaterials and Methods‚Äô section for list of sequences).
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gks065-F3: Experimental relationship between compositional diversity and template-directed ligation. (a) Fraction of DNA sequences having high compositional diversity (C3‚ÄČ>‚ÄČ0.95; analysis length‚ÄČ=‚ÄČ16) after template-directed ligation in a heterogeneous pool of degenerate oligonucleotides including four bases. A greater fraction of reaction products (yellow) have high C3 relative to the templates (red‚ÄČ=‚ÄČaverage C3 of 16-mers contained in sequenced 40-mer templates) and substrates (orange‚ÄČ=‚ÄČC3 of 16-mers from in silico non-templated, random concatenation of experimentally sequenced octamers). The fraction of high C3 sequences in a uniform random pool is shown in green. Error bars are SDs from replicate sequencing experiments. (b) Polyacrylamide gel showing higher molecular weight products of template-directed ligation for different single templates from a binary alphabet. Molecular weight markers are given in the left lane. ‚Äė√ė‚Äô indicates a reaction without template added. Template C3 increases from left (C3‚ÄČ=‚ÄČ0) to right (C3‚ÄČ=‚ÄČ0.97; see ‚ÄėMaterials and Methods‚Äô section for list of sequences).

Mentions: Each reaction contained 1‚Äď2‚ÄȬĶM DNA template and 16‚ÄȬĶM random radiolabeled DNA octamers (Eurofins MWG Operon, Huntsville, AL, USA and Sigma-Aldrich, St Louis, MO, USA). In single-template reactions, the template oligonucleotides were composed of C and T while the octamers were composed of A and G. The templates used in the reactions of Figure 3b were:


Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences.

Derr J, Manapat ML, Rajamani S, Leu K, Xulvi-Brunet R, Joseph I, Nowak MA, Chen IA - Nucleic Acids Res. (2012)

Experimental relationship between compositional diversity and template-directed ligation. (a) Fraction of DNA sequences having high compositional diversity (C3‚ÄČ>‚ÄČ0.95; analysis length‚ÄČ=‚ÄČ16) after template-directed ligation in a heterogeneous pool of degenerate oligonucleotides including four bases. A greater fraction of reaction products (yellow) have high C3 relative to the templates (red‚ÄČ=‚ÄČaverage C3 of 16-mers contained in sequenced 40-mer templates) and substrates (orange‚ÄČ=‚ÄČC3 of 16-mers from in silico non-templated, random concatenation of experimentally sequenced octamers). The fraction of high C3 sequences in a uniform random pool is shown in green. Error bars are SDs from replicate sequencing experiments. (b) Polyacrylamide gel showing higher molecular weight products of template-directed ligation for different single templates from a binary alphabet. Molecular weight markers are given in the left lane. ‚Äė√ė‚Äô indicates a reaction without template added. Template C3 increases from left (C3‚ÄČ=‚ÄČ0) to right (C3‚ÄČ=‚ÄČ0.97; see ‚ÄėMaterials and Methods‚Äô section for list of sequences).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3378899&req=5

gks065-F3: Experimental relationship between compositional diversity and template-directed ligation. (a) Fraction of DNA sequences having high compositional diversity (C3‚ÄČ>‚ÄČ0.95; analysis length‚ÄČ=‚ÄČ16) after template-directed ligation in a heterogeneous pool of degenerate oligonucleotides including four bases. A greater fraction of reaction products (yellow) have high C3 relative to the templates (red‚ÄČ=‚ÄČaverage C3 of 16-mers contained in sequenced 40-mer templates) and substrates (orange‚ÄČ=‚ÄČC3 of 16-mers from in silico non-templated, random concatenation of experimentally sequenced octamers). The fraction of high C3 sequences in a uniform random pool is shown in green. Error bars are SDs from replicate sequencing experiments. (b) Polyacrylamide gel showing higher molecular weight products of template-directed ligation for different single templates from a binary alphabet. Molecular weight markers are given in the left lane. ‚Äė√ė‚Äô indicates a reaction without template added. Template C3 increases from left (C3‚ÄČ=‚ÄČ0) to right (C3‚ÄČ=‚ÄČ0.97; see ‚ÄėMaterials and Methods‚Äô section for list of sequences).
Mentions: Each reaction contained 1‚Äď2‚ÄȬĶM DNA template and 16‚ÄȬĶM random radiolabeled DNA octamers (Eurofins MWG Operon, Huntsville, AL, USA and Sigma-Aldrich, St Louis, MO, USA). In single-template reactions, the template oligonucleotides were composed of C and T while the octamers were composed of A and G. The templates used in the reactions of Figure 3b were:

Bottom Line: However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences.Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules.Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

View Article: PubMed Central - PubMed

Affiliation: FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA.

ABSTRACT
During the origin of life, the biological information of nucleic acid polymers must have increased to encode functional molecules (the RNA world). Ribozymes tend to be compositionally unbiased, as is the vast majority of possible sequence space. However, ribonucleotides vary greatly in synthetic yield, reactivity and degradation rate, and their non-enzymatic polymerization results in compositionally biased sequences. While natural selection could lead to complex sequences, molecules with some activity are required to begin this process. Was the emergence of compositionally diverse sequences a matter of chance, or could prebiotically plausible reactions counter chemical biases to increase the probability of finding a ribozyme? Our in silico simulations using a two-letter alphabet show that template-directed ligation and high concatenation rates counter compositional bias and shift the pool toward longer sequences, permitting greater exploration of sequence space and stable folding. We verified experimentally that unbiased DNA sequences are more efficient templates for ligation, thus increasing the compositional diversity of the pool. Our work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization and ligation could predispose toward a diverse pool of longer, potentially structured molecules. Such mechanisms could have set the stage for the appearance of functional activity very early in the emergence of life.

Show MeSH
Related in: MedlinePlus