Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet

  title={Enzymatic incorporation of a new base pair into DNA and RNA extends the genetic alphabet},
  author={Joseph A. Piccirilli and Steven A. Benner and Tilman Krauch and Simon E. Moroney},
A new Watson-Crick base pair, with a hydrogen bonding pattern different from that in the A·T and G·C base pairs, is incorporated into duplex DNA and RNA by DNA and RNA polymerases and expands the genetic alphabet from 4 to 6 letters. This expansion could lead to RNAs with greater diversity in functional groups and greater catalytic potential. 

Orthogonal base pairs continue to evolve.

Replacing the nucleobases in DNA with designer molecules.

  • E. Kool
  • Chemistry, Biology
    Accounts of chemical research
  • 2002
Molecular strategies in which the natural DNA bases on the sugar-phosphate backbone are replaced by other molecules are discussed, including fluorophores, ligands for metals, helix stabilizers, and DNA base shape mimics.

Alternative DNA base-pairs: from efforts to expand the genetic code to potential material applications.

This tutorial review highlights different approaches used to replace natural base-pairs with other molecular entities and equip them with novel function and discusses the advantages that non-natural base-Pairs convey with respect to practical applications.

Unnatural base pair systems for DNA/RNA-based biotechnology.

  • I. Hirao
  • Biology, Chemistry
    Current opinion in chemical biology
  • 2006

A New Molecular Encoding System

It is asked whether synthetic organic chemistry, enzymology, and molecular biology can be applied together to obtain an expanded molecular recognition system, modeled on nucleic acids, that is one-dimensional, and therefore is easy to synthesize.

A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate.

The artificial DNA exhibited almost the same characteristics as natural DNA, such as in regard to the stepwise duplex and triplex formation and the right-handed higher-order structure with an antiparallel alignment fashion.

Glucose-nucleobase pairs within DNA: impact of hydrophobicity, alternative linking unit and DNA polymerase nucleotide insertion studies† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04850e

Glucose-nucleobase pairs were designed, synthesized and incorporated into duplex DNA. Their stability, structure and polymerase replication was investigated.

Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair.

Structural insight is reported into the insertion of one of the most promising hydrophobic unnatural base pairs, the dDs-dPx pair, into a DNA strand by a DNA polymerase, and features that might hint at the mechanisms accounting for the lower incorporation efficiency observed when processing the unnatural substrates are identified.

Natural-like replication of an unnatural base pair for the expansion of the genetic alphabet and biotechnology applications.

The identification of dTPT3 represents significant progress toward developing an unnatural base pair for the in vivo expansion of an organism's genetic alphabet and for a variety of in vitro biotechnology applications, and it also demonstrates for the first time that hydrophobic and packing forces are sufficient to mediate natural-like replication.



Enzymatic incorporation of a new base pair into DNA and RNA

D-iso-G was found at the correct position in the product oligonucleotide by a “nearest-neighbor” analysis9 and by the “minus” sequencing method of Sanger to determine the specificity with which the new bases pair.

RNA-catalysed synthesis of complementary-strand RNA

The Tetrahymena ribozyme can splice together multiple oligonucleotides aligned on a template strand to yield a fully complementary product strand. This reaction demonstrates the feasibility of

A small catalytic oligoribonucleotide

A 19-nucleotide RNA fragment can cause rapid, highly specific cleavage of a 24-nucleotide RNA fragment under physiological conditions. Because each 19-mer can participate in many cleavage reactions,

Catalytic activity of an RNA molecule prepared by transcription in vitro.

The RNA moiety M1RNA of ribonuclease P from Escherichia coli and the unprocessed transcript prepared in vitro of the gene for M1 RNA can both perform the cleavage reactions of the canonical enzyme in the absence of the protein moiety.

The case for an ancestral genetic system involving simple analogues of the nucleotides.

It is proposed that RNA was preceded in the evolution of life by a polymer constructed from flexible, acyclic, probably prochiral nucleotide analogues that were synthesized readily on the primitive earth.

Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates.

A method is described to synthesize small RNAs of defined length and sequence using T7 RNA polymerase and templates of synthetic DNA which contain the T7 promoter to increase the variety of RNAs which can be made.

A general method for site-specific incorporation of unnatural amino acids into proteins.

The ability to selectively replace amino acids in a protein with a wide variety of structural and electronic variants should provide a more detailed understanding of protein structure and function.

RNA catalysis and the origins of life.

  • L. Orgel
  • Biology, Chemistry
    Journal of theoretical biology
  • 1986

Hydrolytic stability of helical RNA: a selective advantage for the natural 3',5'-bond.

  • D. A. UsherA. McHale
  • Chemistry
    Proceedings of the National Academy of Sciences of the United States of America
  • 1976
TheUse of the 3', 5'-bond, in combination with a right-handed helix, appears to have had a large selective advantage over the use of the 2', 5',bond for the storage of genetic information.

tRNA-like structures tag the 3' ends of genomic RNA molecules for replication: implications for the origin of protein synthesis.

  • A. WeinerN. Maizels
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1987
The CCA-adding activity was originally an RNA enzyme, that modern DNA telomeres with the repetitive structure CmAn are the direct descendants of the CCA terminus of tRNA, and that the precursor of the modern enzyme RNase P evolved to convert genomic RNA molecules by removing this 3'-terminal tRNA-like tag.