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Potential protein-encoded synthesis of DNA and RNA
The central dogma of molecular biology, as proposed by Francis Crick in 1958 () and later formulated in 1970 (), is based on extensive genetic and biochemical studies on living organisms and is fundamental to life sciences. It follows that the sequence information of DNA can be self-replicated or transferred residue by residue to RNA and then to protein (). However, the sequence information encoded by protein cannot be transferred back to nucleic acids. In some special cases, DNA can also serve as a template in directing in vitro protein synthesis in the presence of antibiotics such as neomycin (). In addition, regarding the origin of the central dogma, it is widely believed that the codon-amino acid stereochemical pairing occurred during early evolution and played a crucial role in the current ribosome-mediated translation process, which does not involve the direct interaction between codons and corresponding amino acids ().
Nevertheless, the specific amino acid-nucleotide interaction between TALE and DNA, or between PUF and RNA, may provide new insights into the origin of the central dogma. For instance, regarding the origin of the ribosome-mediated translation from mRNA to protein, a direct codon-amino acid stereochemical pairing was suggested to occur during evolution (), which later evolved to the current translation form that does not involve such direct pairing. It was proposed recently () that the third characteristic residue of the PUF repeat, which stacks on and sandwiches successive bound RNA bases (), may have played a role during the evolution of such pairing. Therefore, it is of interest to further investigate the evolutionary significance of the other two characteristic residues of the PUF repeat that make hydrogen bonds or Van der Waals interactions with RNA. H
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In this article, I suggest the possibility that the sequence information encoded by protein can be artificially transferred residue by residue directly to DNA and RNA, respectively, based on transcription activator-like effectors (TALE) and Pumilio/fem-3 mRNA-binding factors (PUF). This hypothesis, if proved experimentally, suggests a new strategy for the synthesis of short DNA/RNA molecules.
TALE proteins are secreted by bacterial plant pathogens and specifically recognize host DNA sequences via their modular DNA-binding domain of tandem repeats (). Each repeat comprises around 34 conserved amino acids and targets a specific base pair by using repeat variable diresidues (RVDs) at positions 12 and 13 () (). Structural studies have revealed that multiple TALE repeats form a superhelical structure to track along the sense strand of the DNA duplex within its internal layer and that the 12th residue in each repeat stabilizes the RVD loop while the 13th residue makes a nucleotide-specific contact (). Since the DNA specificity can be designed by customizable assembly of TALE repeats, TALEN (a TALE protein fused with a nuclease protein) is being deployed as a powerful DNA targeting tool utilized in different organisms ().
The genetic material is stored in the form of DNA in most organisms
In summary, it is proposed that sequence-specific DNA and RNA molecules can possibly be synthesized according to the characteristic amino acid sequences of designed TALE and PUF proteins, respectively. In terms of thermodynamics, TALE and PUF proteins arrange or fix the free mono- or dinucleotides, leading to a reduction in the entropy of the nucleotides and thus facilitating the subsequent ligation or condensation. This hypothesis is clearly experimentally testable. If proved, it is of interest to further examine whether Trp RNA-binding attenuation proteins () and pentatricopeptide repeat proteins (), both interacting with RNA in a sequence-specific manner, can serve a similar purpose as PUF. More importantly, proving these possibilities by rational design of experiments suggests a new protein-based strategy for synthesizing DNA/RNA molecules, which is of interest in life science research and biotechnology.
This process of DNA-directed protein synthesis occurs in two stages: 1) transcription (messenger RNA synthesis: copying the genetic information from DNA to RNA) and 2) translation (polypeptide synthesis: using the genetic information in RNA to make a specific chain of amino acids).
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Stages of transcription (article) | Khan Academy
As stated by the central dogma of molecular biology, in living organisms the sequence information of DNA is transferred to RNA and then to protein, but such information cannot be transferred back from protein to nucleic acids. In this article, it is proposed that the sequence information encoded by protein can be artificially transferred back to DNA and RNA, respectively, based on transcription activator-like effectors (TALE) and Pumilio/fem-3 mRNA-binding factors (PUF). Specifically, mono- and/or dinucleotides are assumed to be arranged along the characteristic amino acids of TALE and PUF, and then assembled as oligonucleotides by ligase or condensation agents. This hypothesis suggests a new protein-based strategy for synthesizing DNA and RNA molecules.
Nucleotide Metabolism: Nucleic Acid Synthesis
| Illustration of the modified central dogma from potential synthesis of DNA and RNA encoded by protein. A Sequence information transfer (from DNA to RNA to protein) takes place in nature and is summarized by the central dogma of molecular biology (black). Sequence information transfer from protein (e.g., TALE or PUF) to DNA or RNA is illustrated (highlighted in red or blue). B Schematic illustration of the synthesis of a DNA duplex by DNA ligase or condensation agents from mono- or dideoxyribonucleotide base pairs that are arranged in a sequence-specific manner along the characteristic residues of TALE repeats in a designed TALE protein. The amino acid code of DNA sequence specificity was adopted from Bogdanove et al. (). C Schematic illustration of the synthesis of RNA by RNA ligase or condensation agents from mono- or diribonucleotides that are arranged in a sequence-specific manner along the characteristic residues of multiple PUF repeats. The amino acid code of RNA base specificity was adopted from earlier studies ().
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