Synthesis and crystallographic analysis of 5-Se-thymidine DNAs

Syntheses of Pyrimidine-Modified Seleno-DNAs as Stable Antisense Molecules

Chemically modified antisense oligonucleotides (ASO) currently in pre-clinical and clinical experiments mainly focus on the 2'-position derivatizations to enhance stability and targeting affinity. Considering the possible incompatibility of 2'-modifications with RNase H stimulation and activity, we have hypothesized that the atom specific modifications on nucleobases can retain the complex structure and RNase H activity, while enhancing ASO's binding affinity, specificity, and stability against nucleases. Herein we report a novel strategy to explore our hypothesis by synthesizing the deoxynucleoside phosphoramidite building block with the seleno-modification at 5-position of thymidine, as well as its Se-oligonucleotides. Via X-ray crystal structural study, we found that the Se-modification was located in the major groove of nucleic acid duplex and didn't cause the thermal and structural perturbations. Surprisingly, our nucleobase-modified Se-DNAs were exceptionally resistant to nuclease digestion, while compatible with RNase H activity. This affords a novel avenue for potential antisense modification in the form of Se-antisense oligonucleotides (Se-ASO).

Modifications at the C(5) position of pyrimidine nucleosides

This review summarizes the state of knowledge on the chemical methods of C(5)-modifications of uridine and cytidine derivatives and may serve as a useful tool for synthetic chemists to choose an appropriate reaction protocol. The synthesis of 5-substituted uracil derivatives is gaining an increasing interest because of their possible applications in medicine and pharmacy. Modifications at the C(5) position of pyrimidine nucleosides can enhance their biostability, bioavailability or(and) biological activity. Among the C(5)-modified nucleosides, 5-halopyrimidines exhibit anticancer, antiviral, radio- and photosensitizing properties. Besides 5-halo-substituted derivatives, there are other examples of nucleosides with confirmed biological activity containing a C–C bond at the C(5) position in the pyrimidine ring. In recent decades, scientists have achieved great progress in the field of cross-coupling reactions. Among them, nickel-catalyzed processes provide a broad spectrum of synthetic methods that are based on less toxic and cheaper starting materials. This review summarizes the synthetic approaches based on the coupling or halogenation reactions, which enable 5-substituted pyrimidine nucleosides to be obtained. Moreover, the importance of the systems considered for medicine and pharmacy is briefly discussed.

The bibliography includes 197 references.

Copper-mediated arylsulfanylations and arylselanylations of pyrimidine or 7-deazapurine nucleosides and nucleotides

The syntheses of 5-arylsulfanyl- or 5-arylselanylpyrimidine and 7-arylsulfanyl- or 7-arylselanyl-7-deazapurine nucleosides and nucleotides were developed by the Cu-mediated sulfanylations or selanylations of the corresponding 5-iodopyrimidine or 7-iodo-7-deazapurine nucleosides or nucleotides with diaryldisulfides or -diselenides. The reactions were also applicable for direct modifications of 2'-deoxycytidine triphosphate and the resulting 5-arylsulfanyl or 5-arylselanyl-dCTP served as substrates for the polymerase synthesis of modified DNA bearing arylsulfanyl or arylselanyl groups in the major groove.

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

The foundational goal of structural DNA nanotechnology-the field that uses oligonucleotides as a molecular building block for the programmable self-assembly of nanostructured systems-was to use DNA to construct three-dimensional (3D) lattices for solving macromolecular structures. The programmable nature of DNA makes it an ideal system for rationally constructing self-assembled crystals and immobilizing guest molecules in a repeating 3D array through their specific stereospatial interactions with the scaffold. In this work, we have extended a previously described motif (4 × 5) by expanding the structure to a system that links four double-helical layers; we use a central weaving oligonucleotide containing a sequence of four six-base repeats (4 × 6), forming a matrix of layers that are organized and dictated by a series of Holliday junctions. In addition, we have assembled mirror image crystals (l-DNA) with the identical sequence that are completely resistant to nucleases. Bromine and selenium derivatives were obtained for the l- and d-DNA forms, respectively, allowing phase determination for both forms and solution of the resulting structures to 3.0 and 3.05 Å resolution. Both right- and left-handed forms crystallized in the trigonal space groups with mirror image 3-fold helical screw axes P3₂ and P3₁ for each motif, respectively. The structures reveal a highly organized array of discrete and well-defined cavities that are suitable for hosting guest molecules and allow us to dictate a priori the assembly of guest-DNA conjugates with a specified crystalline hand.

Evolution of functional six-nucleotide DNA

Axiomatically, the density of information stored in DNA, with just four nucleotides (GACT), is higher than in a binary code, but less than it might be if synthetic biologists succeed in adding independently replicating nucleotides to genetic systems. Such addition could also add functional groups not found in natural DNA, but useful for molecular performance. Here, we consider two new nucleotides (Z and P, 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribo-furanosyl)-2(1H)-pyridone and 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one). These are designed to pair via complete Watson-Crick geometry. These were added to a library of oligonucleotides used in a laboratory in vitro evolution (LIVE) experiment; the GACTZP library was challenged to deliver molecules that bind selectively to liver cancer cells, but not to untransformed liver cells. Unlike in classical in vitro selection, low levels of mutation allow this system to evolve to create binding molecules not necessarily present in the original library. Over a dozen binding species were recovered. The best had Z and/or P in their sequences. Several had multiple, nearby, and adjacent Zs and Ps. Only the weaker binders contained no Z or P at all. This suggests that this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries.

Synthesis and optical behaviors of 6-seleno-deoxyguanosine

We have developed a simple method to synthesize 6-seleno-2'-deoxyguanosine (^SedG) by selectively replacing the 6-oxygen atom with selenium. This selenium-atom-specific modification (SAM) alters the optical properties of the naturally occurring 2'-deoxyguanosine (dG). Unlike the native dG, the UVabsorption of ^SedG is significantly influenced by the pH of the aqueous solution. Moreover, ^SedG is fluorescent at the physiological pH and exhibits pH-dependent fluorescence in aqueous solutions. Furthermore, ^SedG has noticeable fluorescence in non-aqueous solutions, indicating its sensitivity to environmental changes. This is the first time a fluorescent nucleoside by single-atom alteration has been observed. Fluorescent nucleosides modified by a single atom have great potential as molecular probes with minimal perturbations to investigate nucleoside interactions with proteins, such as membrane-transporter proteins.

Use of a novel 5'-regioselective phosphitylating reagent for one-pot synthesis of nucleoside 5'-triphosphates from unprotected nucleosides

5'-Triphosphates are building blocks for enzymatic synthesis of DNA and RNA. This unit presents a protocol for convenient synthesis of 2'-deoxyribo- and ribonucleoside 5'-triphosphates (dNTPs and NTPs) from any natural or modified base. This one-pot synthesis can also be employed to prepare triphosphate analogs with a sulfur or selenium atom in place of a non-bridging oxygen atom of the α-phosphate. These S- or Se-modified dNTPs and NTPs can be used to prepare diastereomerically pure phosphorothioate or phosphoroselenoate nucleic acids. Even without extensive purification, the dNTPs or NTPs synthesized by this method are of high quality and can be used directly in DNA polymerization or RNA transcription. Synthesis and purification of the 5'-triphosphates, as well as analysis and confirmation of natural and sulfur- or selenium-modified nucleic acids, are described in this protocol unit.

Synthesis of novel di-Se-containing thymidine and Se-DNAs for structure and function studies

The selenium derivatization of nucleic acids and nucleic acid-protein complexes has provided a powerful tool to solve phase problem in X-ray crystallography. Selenium atoms in the nucleotides can serve as fine scattering centers in crystal diffraction. Towards the synthesis of multiple selenium atom-containing nucleotides, which offers strong phasing power to facilitate crystal structure determination, we report here the synthesis of the thymidine analogue containing two Se atoms in one nucleobase. The novel Se-containing nucleoside and oligonucleotide DNAs were synthesized and found with the red-shifted UV spectrum and yellow color. Their unique properties are useful in phase determination, nucleic acid-based detection as well as spectroscopic studies of nucleic acids and nucleic acid-protein complexes.

Synthesis of the tellurium-derivatized phosphoramidites and their incorporation into DNA oligonucleotides

In this unit, an efficient method for the synthesis of 2'-tellerium-modified phosphoramidite and its incorporation into oligonucleotide are presented. We choose 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine nucleosides (S.1, S.2) as starting materials due to their easy preparation. The 5'-O-DMTr-2,2'-anhydro-uridine and -thymidine can be converted to the corresponding 2'-tellerium-derivatized nucleosides by treating with the telluride nucleophiles. Subsequently, the 2'-Te-nucleosides can be transformed into 3'-phosphoramidites, which are the building blocks for DNA/RNA synthesis. The DNA synthesis, purification, and applications of oligonucleotides containing 2'-Te-U or 2'-Te-T are described in the protocol.

Hydrogen bond formation between the naturally modified nucleobase and phosphate backbone

Natural RNAs, especially tRNAs, are extensively modified to tailor structure and function diversities. Uracil is the most modified nucleobase among all natural nucleobases. Interestingly, >76% of uracil modifications are located on its 5-position. We have investigated the natural 5-methoxy (5-O-CH₃) modification of uracil in the context of A-form oligonucleotide duplex. Our X-ray crystal structure indicates first a H-bond formation between the uracil 5-O-CH₃ and its 5′-phosphate. This novel H-bond is not observed when the oxygen of 5-O-CH₃ is replaced with a larger atom (selenium or sulfur). The 5-O-CH₃ modification does not cause significant structure and stability alterations. Moreover, our computational study is consistent with the experimental observation. The investigation on the uracil 5-position demonstrates the importance of this RNA modification at the atomic level. Our finding suggests a general interaction between the nucleobase and backbone and reveals a plausible function of the tRNA 5-O-CH₃ modification, which might potentially rigidify the local conformation and facilitates translation.

Nucleic acid X-ray crystallography via direct selenium derivatization

X-ray crystallography has proven to be an essential tool for structural studies of bio-macromolecules at the atomic level. There are two major bottle-neck problems in the macromolecular crystal structure determination: phasing and crystallization. Although the selenium derivatization is routinely used for solving novel protein structures through the MAD phasing technique, the phase problem is still a critical issue in nucleic acid crystallography. The background and current progress of using direct selenium-derivatization of nucleic acids (SeNA) to solve the phase problem and to facilitate nucleic acid crystallization for X-ray crystallography are summarized in this tutorial review.

Synthesis of the 5'-Se-thymidine phosphoramidite and convenient labeling of DNA oligonucleotide

The synthesis of the 5'-Se-derivatized thymidine and phosphoramidite is reported, and the Se-phosphoramidite was incorporated into DNA. Because of its high nucleophilicity, this 5'-Se-moiety permits convenient postsynthetic modification of oligonucleotides. The proof of principle was successfully demonstrated by incorporating fluorescein into DNA. It was also found that the 5'-dye-labeled Se-DNA can be recognized by DNA polymerase as an efficient primer. This novel strategy opens a new avenue for nucleic acid probe preparation and detection.

Electrophilic aromatic selenylation: new OPRT inhibitors

2-Ethoxyethaneseleninic acid reacts with electron-rich aromatic substrates to deliver, by way of the selenoxides, the (2-ethoxyethyl)seleno ethers, which can in turn be transformed into a diverse set of aryl-selenylated products. Among these, a family of 5-uridinyl derivatives shows submicromolar inhibition of human and malarial orotate phosphoribosyltransferase.

Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies

It is estimated that over two thirds of all new crystal structures of proteins are determined via the protein selenium derivatization (selenomethionine (Se-Met) strategy). This selenium derivatization strategy via MAD (multi-wavelength anomalous dispersion) phasing has revolutionized protein X-ray crystallography. Through our pioneer research, similarly, Se has also been successfully incorporated into nucleic acids to facilitate the X-ray crystal-structure and function studies of nucleic acids. Currently, Se has been stably introduced into nucleic acids by replacing nucleotide O-atom at the positions 2', 4', 5', and in nucleobases and non-bridging phosphates. The Se derivatization of nucleic acids can be achieved through solid-phase chemical synthesis and enzymatic methods, and the Se-derivatized nucleic acids (SeNA) can be easily purified by HPLC, FPLC, and gel electrophoresis to obtain high purity. It has also been demonstrated that the Se derivatization of nucleic acids facilitates the phase determination via MAD phasing without significant perturbation. A growing number of structures of DNAs, RNAs, and protein-nucleic acid complexes have been determined by the Se derivatization and MAD phasing. Furthermore, it was observed that the Se derivatization can facilitate crystallization, especially when it is introduced to the 2'-position. In addition, this novel derivatization strategy has many advantages over the conventional halogen derivatization, such as more choices of the modification sites via the atom-specific substitution of the nucleotide O-atom, better stability under X-ray radiation, and structure isomorphism. Therefore, our Se-derivatization strategy has great potentials to provide rational solutions for both phase determination and high-quality crystal growth in nucleic-acid crystallography. Moreover, the Se derivatization generates the nucleic acids with many new properties and creates a new paradigm of nucleic acids. This review summarizes the recent developments of the atomic site-specific Se derivatization of nucleic acids for structure determination and function study. Several applications of this Se-derivatization strategy in nucleic acid and protein research are also described in this review.

The many twists and turns of DNA: template, telomere, tool, and target

If any proof were needed of DNA's versatile roles and use, it is certainly provided by the numerous depositions of new three-dimensional (3D) structures to the coordinate databanks (PDB, NDB) over the last two years. Quadruplex motifs involving G-repeats, adducted sequences and oligo-2'-deoxynucleotides (ODNs) with bound ligands are particularly well represented. In addition, structures of chemically modified DNAs (CNAs) and artificial analogs are yielding insight into stability, pairing properties, and dynamics, including those of the native nucleic acids. Besides being of significance for establishing diagnostic tools and in the analysis of protein-DNA interactions, chemical modification in conjunction with investigations of the structural consequences may yield novel nucleic acid-based therapeutics. DNA's predictable and highly specific pairing behavior makes it the material of choice for constructing 3D-nanostructures of defined architecture. Recently the first examples of DNA nanoparticle and self-assembled 3D-crystals were reported. Although the structures discussed in this review are all based either on X-ray crystallography or solution NMR, small angle X-ray scattering (SAXS), and cryoEM are proving to be useful approaches for the characterization of nanoscale DNA architecture.