Denis A Malyshev

Synthorx

The polymerase chain reaction (PCR) is a universal and essential tool in molecular biology and biotechnology, but it is generally limited to the amplification of DNA with the four-letter genetic alphabet. Here, we describe PCR amplification with a six-letter alphabet that includes the two natural dA-dT and dG-dC base pairs and an unnatural base pai...

Ribosome assembly has been studied intensively using Förster resonance energy transfer (FRET) with fluorophore-labeled fragments of RNA produced by chemical synthesis. However, these studies are limited by the size of the accessible RNA fragments. We have developed a replicable unnatural base pair (UBP) formed between (d)5SICS and (d)MMO2 or (d)NaM...

All biological information, since the last common ancestor of all life on Earth, has been encoded by a genetic alphabet consisting of only four nucleotides that form two base pairs. Long-standing efforts to develop two synthetic nucleotides that form a third, unnatural base pair (UBP) have recently yielded three promising candidates, one based on a...

Seit dem letzten gemeinsamen Vorfahren allen Lebens auf der Erde wird die gesamte biologische Information durch ein genetisches Alphabet codiert, das aus nur vier Nucleotiden und den von ihnen gebildeten zwei Basenpaaren besteht. Aus langjährigen Versuchen, aus zwei synthetischen Nucleotiden ein drittes, nichtnatürliches Basenpaar (UBP) zu formen,...

We have developed a family of unnatural base pairs (UBPs), which rely on hydrophobic and packing interactions for pairing and which are well replicated and transcribed. While the pair formed between d5SICS and dNaM (d5SICS-dNaM) has received the most attention, and has been used to expand the genetic alphabet of a living organism, recent efforts ha...

Organisms are defined by the information encoded in their genomes, and since the evolution of life, this information has been encoded using a two base pair genetic alphabet (A-T and G-C). In vitro, the alphabet has been expanded to include several unnatural base pairs (UBPs)1–3. We have developed a class of UBPs formed between nucleotides bearing h...

The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it...

We synthesized a panel of unnatural base pairs whose pairing depends on hydrophobic and packing forces and identify dTPT3-dNaM, which is PCR amplified with a natural base pair-like efficiency and fidelity. In addition, the dTPT3 scaffold is uniquely tolerant of attaching a propargyl amine linker, resulting in the dTPT3(PA)-dNaM pair, which is ampli...

A class of replicable unnatural DNA base pairs formed between d5SICS and either dMMO2, dDMO, or dNaM were developed. To explore the use of these pairs to produce site-specifically labeled DNA, the synthesis of a variety of derivatives bearing propynyl groups, an analysis of their polymerase-mediated replication, and subsequent site-specific modific...

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventually in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs exemplified by d5SICS-dMMO2 and d5SICS-dNaM. When incorporated into DNA, the latter is replicated and transcribed with greater efficiency and fidelity than...

The natural four-letter genetic alphabet, comprised of just two base pairs (dA-dT and dG-dC), is conserved throughout all life, and its expansion by the development of a third, unnatural base pair has emerged as a central goal of chemical and synthetic biology. We recently developed a class of candidate unnatural base pairs, exemplified by the pair...

Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS,...

Expansion of the genetic alphabet with an unnatural base pair is a long-standing goal of synthetic biology. We have developed a class of unnatural base pairs, formed between d5SICS and analogues of dMMO2 that are efficiently and selectively replicated by the Klenow fragment (Kf) DNA polymerase. In an effort to further characterize and optimize repl...

Site-specific labeling of enzymatically synthesized DNA or RNA has many potential uses in basic and applied research, ranging from facilitating biophysical studies to the in vitro evolution of functional nucleic acids and the construction of various nanomaterials and biosensors. As part of our efforts to expand the genetic alphabet, we have develop...

As part of an ongoing effort to expand the genetic alphabet for in vitro and eventual in vivo applications, we have synthesized a wide variety of predominantly hydrophobic unnatural base pairs and evaluated their replication in DNA. Collectively, the results have led us to propose that these base pairs, which lack stabilizing edge-on interactions,...

Expansion of the genetic alphabet with a third base pair would lay the foundation for a semisynthetic organism with an expanded genetic code and also have immediate in vitro applications. Previously, the unnatural base pairs formed between d5SICS and either dNaM or dMMO2 were shown to be well-replicated by DNA polymerases under steady-state conditi...

Asymmetric V-catalyzed epoxidation of allylic alcohols can be carried out in water with chiral ligands, which incorporate sulfonamide and hydroxamic acid fragments. Furthermore, the reaction, notorious for its ligand-deceleration effect, in water turned into the ligand-accelerated process. By using this aqueous protocol, a range of allylic alcohols...

Leucinol and valinol have been identified as efficient organocatalysts for the aldol reaction of isatin and its derivatives (as examples of activated, non-enolizable ketones) with acetone. Uncommon mechanistic features were observed and used in the formulation of the transition state of the reaction.

The first example of sila-Morita-Bayis-Hillman reaction between 1-silylcyclopropenes and carbonyl compounds has been demonstrated. This novel phosphine-catalyzed transformation features a 1,3-Brook rearrangement/elimination cascade and provides convenient access to a variety of 1-(silyloxymethyl)cyclopropenes, which are not easily available via tra...

A novel homogeneous catalytic system has been developed for the regioselective hydrothiolation of alkynes based on CpNi(NHC)Cl complexes (NHC = N-heterocyclic carbene). The designed catalyst was efficient for the selective addition of a single ArS group to an alkyne and was suitable for the synthesis of vinylsulfides, without side reactions leading...

Regioselective Markovnikov-type addition of PhSH to alkynes (HC≡C-R) has been performed using easily available nickel complexes. The non-catalytic side reaction leading to anti-Markovnikov products was suppressed by addition of γ-terpinene to the catalytic system. The other side reaction leading to the bis(phenylthio)alkene was avoided by excluding...

A mechanistic study of the hydroselenation of alkynes catalyzed by Pd(PPh3)4 and Pt(PPh3)4 has shown that the palladium complex gives products of both Se-H and Se-Se bond addition to the triple bond of alkynes, while the platinum complex selectively catalyzes Se-H bond addition. The key intermediate of PhSeH addition to the metal center, namely Pt(...

Addition of benzeneselenol to terminal alkynes HCCR, catalyzed by Pd(0) complexes, leads to formation of mixtures of mono- and bis(phenylseleno)alkenes, depending on the nature of the R substituent. Electron-donor groups (R = Bu, CH2OH, CH2NMe2) give rise to addition according to the Markownikoff rule, whereas from alkynes with electron-acceptor gr...