Efforts toward the Expansion of the Genetic Alphabet:  Information Storage and Replication with Unnatural Hydrophobic Base Pairs

Ogawa, Anthony K.; Wu, Yun; McMinn, Dustin L.; Liu, Jianquan; Schultz, and Peter G.; Romesberg, Floyd E.

doi:10.1021/ja9940064

Cited by 188 publications

(209 citation statements)

References 36 publications

(96 reference statements)

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“…8,9,11,14,15,20,22,[28][29][30][31][32][33][34] From these, 60 were collected ( Figure 2) and their phosphoramidites incorporated into the 3' end of a 24-mer primer oligonucleotide and at the 24 th position of a complementary 45-mer template oligonucleotide. Hybridization of any given primer strand with any template strand results in an unnatural primer terminus (dX:dY, where dX is the primer nucleobase and dY is the template nucleobase).…”

Section: Screening For Unnatural Base Pairsmentioning

confidence: 99%

“…Indeed, several nucleotides bearing predominantly hydrophobic nucleobase analogs have been shown to pair stably and selectively in duplex DNA. 13,14 We, 9,10,15,16 and others, 8,12,[17][18][19] have shown that hydrophobic forces are also sufficient for the enzymatic synthesis of an unnatural base pair by incorporation of an unnatural nucleoside triphosphate against a template unnatural nucleotide; however, synthesis beyond the unnatural base pair, i.e. extension, tends to be relatively inefficient and generally limits the utility of these base pairs.…”

Section: Introductionmentioning

confidence: 99%

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Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet

et al. 2008

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DNA is inherently limited by its four natural nucleotides. Efforts to expand the genetic alphabet, by addition of an unnatural base pair, promise to expand the biotechnological applications available for DNA as well as being an essential first step towards expansion of the genetic code. We have conducted two independent screens of hydrophobic unnatural nucleotides to identify novel candidate base pairs that are well recognized by a natural DNA polymerase. From a pool of 3600 candidate base pairs, both screens identified the same base pair, dSICS:dMMO2, which we report here. Using a series of related analogs, we performed a detailed structure-activity relationship analysis, which allowed us to identify the essential functional groups on each nucleobase. From the results of these studies, we designed an optimized base pair, d5SICS:dMMO2, which is efficiently and selectively synthesized by Kf within the context of natural DNA.

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Section: Screening For Unnatural Base Pairsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet

et al. 2008

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“…The creation of artificial nucleic acid motifs has relied on synthetic incorporation of nucleobases with altered hydrogen--bonding patterns 14,15 , or relying on hydrophobic interactions 16,17 and metal coordination 18--20 . Synthetic incorporation of unnatural bases which present more than one hydrogen--bonding 'face' in order to access higher--order DNA structures has been of great interest 21--25 .…”

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confidence: 99%

Reprogramming the assembly of unmodified DNA with a small molecule

et al. 2016

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The information storage and encoding ability of DNA arise from a remarkably simple 4--letter -A, T, G, C nucleobase code. Expanding this DNA 'alphabet' provides information about its function and evolution, and introduces new functionalities into nucleic acids and organisms. Previous efforts relied on the synthetically demanding incorporation of non--canonical bases into nucleosides. Here we report the discovery that a small molecule, cyanuric acid, with three thymine--like faces reprograms the assembly of unmodified poly(adenine) into stable, long and abundant fibers with a unique internal structure. Poly(A) DNA, RNA and PNA all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, bringing together poly(A) triplexes with subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen--bonding molecules can be used to induce the assembly of nucleic acids in water, leading to new structures from inexpensive and readily available materials.

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“…It has been possible to develop stable base pairs of this type, sometimes incorporated into DNA with high fidelity, but chain termination after insertion has been a significant problem (e.g. d3MN, dPICS and d7AI) [98,99]. Interestingly, the most efficient pairs have been "self-pairs," which is to say a base that elicits itself in DNA synthesis, which is perfectly reasonable for genetic code expansion.…”

Section: Recoding -Beyond Amber Suppressionmentioning

confidence: 99%

Unnatural Protein Engineering: Producing Proteins with Unnatural Amino Acids

Magliery¹

2005

MCRO

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Less than a decade ago, the ability to generate proteins with unnatural modifications was a Herculean task available only to specialty labs. Recent advances make it possible to generate reasonable quantities of protein with unnatural amino acids both in vitro and in vivo . The combination of solid-phase peptide synthesis and enzymatic or chemoselective ligation now permits construction of entirely-synthetic proteins as large as 25 kD. Incorporation of recombinant fragments (expressed protein ligation) allows unnatural modifications near protein termini in proteins of virtually any size. Site-specific modification of small quantities of protein at any position can be achieved using chemically-acylated tRNA. Microelectroporation now extends this method to cells like mammalian neurons, and combination with RNAdisplay makes unnatural proteins compatible with combinatorial methods. Widespread or residue-specific methods of amino acid replacement are especially suitable for the production of biomaterials, and bacteria have been engineered to expand the repertoire of amino acids available for this technique. Excitingly, the wholesale addition of engineered tRNAs and synthetases to bacteria and yeast now makes site-specific incorporation of unnatural amino acids possible in living cells with no chemical intervention. Methods of expanding the genetic code at the nucleic acid level, including 4-base codons and unnatural base pairs, are becoming useful for the addition of multiple amino acids to the genetic code. These recent advances in unnatural protein engineering are reviewed with an eye toward future challenges, including methods of creating nonpeptidic molecules using templated synthesis.

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Efforts toward the Expansion of the Genetic Alphabet: Information Storage and Replication with Unnatural Hydrophobic Base Pairs

Cited by 188 publications

References 36 publications

Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet

Discovery, Characterization, and Optimization of an Unnatural Base Pair for Expansion of the Genetic Alphabet

Reprogramming the assembly of unmodified DNA with a small molecule

Unnatural Protein Engineering: Producing Proteins with Unnatural Amino Acids

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