Efficient enzymatic synthesis of phosphoroselenoate RNA by using adenosine 5'-(alpha-P-seleno)triphosphate

Substrate Specificity of T7 RNA Polymerase toward Hypophosphoric Analogues of ATP

Modified nucleotides are commonly used in molecular biology as substrates or inhibitors for several enzymes but also as tools for the synthesis of modified DNA and RNA fragments. Introduction of modification into RNA, such as phosphorothioate (PS), has been demonstrated to provide higher stability, more effective transport, and enhanced activity of potential therapeutic molecules. Hence, in order to achieve widespread use of RNA molecules in medicine, it is crucial to continuously refine the techniques that enable the effective introduction of modifications into RNA strands. Numerous analogues of nucleotides have been tested for their substrate activity with the T7 RNA polymerase and therefore in the context of their utility for use in in vitro transcription. In the present studies, the substrate preferences of the T7 RNA polymerase toward β,γ-hypophospho-modified ATP derivatives for the synthesis of unmodified RNA and phosphorothioate RNA (PS) are presented. The performed studies revealed the stereoselectivity of this enzyme for α-thio-β,γ-hypo-ATP derivatives, similar to that for α-thio-ATP. Additionally, it is demonstrated herein that hypodiphosphoric acid may inhibit in vitro transcription catalyzed by T7 RNA polymerase.

Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA

In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.

Asymmetric Synthesis of Stereogenic Phosphorus P(V) Centers Using Chiral Nucleophilic Catalysis

Organophosphates have been widely used in agrochemistry, as reagents for organic synthesis, and in biochemistry. Phosphate mimics possessing four unique substituents, and thereby a chirality center, are useful in transition metal catalysis and as nucleotide therapeutics. The catalytic, stereocontrolled synthesis of phosphorus-stereogenic centers is challenging and traditionally depends on a resolution or use of stochiometric auxiliaries. Herein, enantioenriched phosphorus centers have been synthesized using chiral nucleophilic catalysis. Racemic H-phosphinate species were coupled with nucleophilic alcohols under halogenating conditions. Chiral phosphonate products were synthesized in acceptable yields (33-95%) and modest enantioselectivity (up to 62% ee) was observed after identification of an appropriate chiral catalyst and optimization of the solvent, base, and temperature. Nucleophilic catalysis has a tremendous potential to produce enantioenriched phosphate mimics that could be used as prodrugs or chemical biology probes.

Specificity Enhancement of Deoxyribonucleic Acid Polymerization for Sensitive Nucleic Acid Detection

Specificity of DNA polymerization plays a critical role in DNA replication and storage of genetic information. Likewise, biotechnological applications, such as nucleic acid detection, DNA amplification, and gene cloning, require high specificity in DNA synthesis catalyzed by DNA polymerases. However, errors in DNA polymerization (such as mis-incorporation and mis-priming) can significantly jeopardize the specificity. Herein, we report our discovery that the specificity of DNA enzymatic synthesis can be substantially enhanced (up to 100-fold higher) by attenuating DNA polymerase kinetics via the phosphorothioate dNTPs. This specificity enhancement allows convenient and sensitive nucleic acid detection, polymerization, PCR, and gene cloning with complex systems (such as human cDNA and genomic DNA). Further, we found that the specificity enhancement offered higher sensitivity (up to 50-fold better) for detecting nucleic acids, such as COVID-19 viral RNAs. Our findings have revealed a simple and convenient strategy for facilitating specificity and sensitivity of nucleic acid detection, amplification, and gene cloning.

High-quality RT-PCR with chemically modified RNA controls

In detecting infectious diseases, such as coronavirus 2019 (COVID-19), real-time reverse-transcription polymerase chain reaction (RT-PCR) is one of the most important technologies for RNA detection and disease diagnosis. To achieve high quality assurance, appropriate positive and negative controls are critical for disease detection using RT-PCR kits. In this study, we have found that commercial kits often adopt DNAs instead of RNAs as the positive controls, which can't report the kit problems in reverse transcription, thereby increasing risk of the false negative results when testing patient samples. To face the challenge, we have proposed and developed the chemically modified RNAs, such as phosphoroselenaote and phosphorothioate RNAs (Se-RNA and S-RNA), as the controls. We have found that while demonstrating the high thermostability, biostability, chemostability and exclusivity (or specificity), both Se-RNA and S-RNA can be fine templates for reverse transcription, indicating their potentials as both positive and negative controls for RT-PCR kits.

Synthesis of Selenium-Triphosphates (dNTPαSe) for More Specific DNA Polymerization

2'-Deoxynucleoside 5'-(alpha-P-seleno)-triphosphates (dNTPαSe) have been conveniently synthesized using a protection-free, one-pot strategy. One of two diastereomers of each dNTPαSe can be efficiently recognized by DNA polymerases, while the other is neither a substrate nor an inhibitor. Furthermore, this Se-atom modification can significantly inhibit non-specific DNA polymerization caused by mis-priming. Se-DNAs amplified with dNTPαSe via polymerase chain reaction have sequences identical to the corresponding native DNA. In conclusion, a simple strategy for more specific DNA polymerization has been established by replacing native dNTPs with dNTPαSe.

Heavy atom containing fluorescent ribonucleoside analog probe for the fluorescence detection of RNA-ligand binding

Although numerous biophysical tools have provided effective systems to study nucleic acids, our current knowledge on how RNA structure complements its function is limited. Therefore, development of robust tools to study the structure–function relationship of RNA is highly desired. Toward this endeavor, we have developed a new ribonucleoside analog, based on a (selenophen-2-yl)pyrimidine core, which could serve as a fluorescence probe to study the function of RNA in real time and as an anomalous scattering label (selenium atom) for the phase determination in X-ray crystallography. The fluorescent selenophene-modified uridine analog is minimally perturbing and exhibits probe-like properties such as sensitivity to microenvironment and conformation changes. Utilizing these properties and amicability of the corresponding ribonucleotide analog to enzymatic incorporation, we have synthesized a fluorescent bacterial ribosomal decoding site (A-site) RNA construct and have developed a fluorescence binding assay to effectively monitor the binding of aminoglycoside antibiotics to the A-site. Our results demonstrate that this simple approach of building a dual probe could provide new avenues to study the structure–function relationship of not only nucleic acids, but also other biomacromolecules.

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.

Se-derivatized RNAs for X-ray crystallography

Selenium derivatization of RNA is an important strategy for crystal structure determination and functional studies of noncoding RNAs and protein-RNA interactions. We describe here the synthesis of nucleoside 5'-(α-P-seleno)-triphosphate analogs (Se-NTPs) and their use in vitro transcription and purification of Se-derivatized RNA samples (phosphoroselenoate RNA, PSe-RNA).

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.

Protection-free one-pot synthesis of 2'-deoxynucleoside 5'-triphosphates and DNA polymerization

By differentiating the functional groups on nucleosides, we have designed and developed a one-pot synthesis of deoxyribonucleoside 5'-triphosphates without any protection on the nucleosides. A facile synthesis is achieved by generating an in situ phosphitylating reagent that reacts selectively with the 5'-hydroxyl groups of the unprotected nucleosides. The synthesized triphosphates are of high quality and can be effectively incorporated into DNAs by DNA polymerase. This novel approach is straightforward and cost-effective for triphosphate synthesis.

Stereocontrolled synthesis of oligonucleotide analogs containing chiral internucleotidic phosphorus atoms

Oligonucleotides, in which one of the two nonbridging oxygen atoms of internucleotidic phosphates is replaced by a different type of atom or a substituent, are useful as therapeutic agents and probes to elucidate mechanisms of enzymatic reactions. The internucleotidic phosphorus atoms of these oligonucleotides are chiral, and the properties of these oligonucleotides are affected by the absolute configuration of the chiral phosphorus atoms. In order to address the issue of chirality, various methods have been developed to synthesize these P-chiral oligonucleotide analogs in a stereocontrolled manner. This critical review focuses on the recent progress in this field (123 references).

Convenient synthesis of nucleoside 5'-triphosphates for RNA transcription

By generating a selective phosphitylating reagent in situ, nucleoside 5'-triphosphates can be conveniently synthesized in one pot. This novel strategy without nucleoside protection has been developed to largely simplify synthesis of the nucleoside triphosphates. This demonstrated principle can be applied to the 5'-triphosphate synthesis of both native and modified nucleosides.

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.

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.

Synthesis of the first tellurium-derivatized oligonucleotides for structural and functional studies

We report here the first synthesis of Te-nucleoside phosphoramidites and Te-modified oligonucleotides. We protected the 2'-tellurium functionality by alkylation and found that the Te functionality is compatible with solid-phase synthesis and that the Te oligonucleotides are stable during deprotection and purification. In addition, the redox properties of the Te functionalities have been explored. We found that the telluride and telluoxide DNAs are interchangeable by redox reactions. At elevated temperature, the Te-DNA can also be site-specifically fragmented oxidatively or reductively when 2'-TePh functionality is present, whereas elimination of the nucleobase is observed in the presence of 2'-TeMe. Moreover, the stability of the DNA duplexes derivatized with the Te functionalities has been investigated. Our Te derivatization of nucleic acids provides a novel approach for investigating DNA damage as well as for structure and function studies of nucleic acids and their protein complexes.

Synthesis of a 4-selenothymidine phosphoramidite and incorporation into oligonucleotides

The detailed synthetic protocol for a 4-selenothymidine phosphoramidite and its use to prepare modified oligonucleotides is described here. The Se-phosphoramidite synthesis was achieved by developing a useful protection and deprotection system for the selenium functionality. The coupling reaction of the Se-phosphoramidite during solid-phase oligonucleotide synthesis is quantitative, and the oligonucleotides containing the Se-modification are stable. Based on crystal structure analysis, the selenium-modified oligonucleotides retain base-pairing like their native counterparts, and the derivatized DNA structure is virtually identical to the native structure. This achievement will present a novel opportunity for structural studies of nucleic acids and their protein complexes, because selenium can resolve the phase problem in macromolecular X-ray crystallography. In addition, this atom-specific replacement of oxygen with selenium will provide a useful tool for investigating biochemical and biophysical properties of nucleic acids and their protein complexes.

Biochemistry of selenium-derivatized naturally occurring and unnatural nucleic acids

Selenium (Se) can provide unique biochemical and biological functions, and properties to macromolecules, including protein and RNA. Although Se has not yet been found in DNA, identification of the presence of Se in natural tRNAs has led to discovery of the naturally occurring 2-selenouridine and 5-[(methylamino)methyl]-2-selenouridine (mnm(5)se(2)U). The Se-atoms at C(2) of the modified uridines are introduced by 2-selenouridine synthase via displacement of the S-atoms in the corresponding 2-thiouridine nucleotides of the tRNAs, and selenophosphate is used as the Se donor. The research indicated that mnm(5)se(2)U is located at the first or wobble position of the anticodons in several bacterial tRNAs, including tRNA(Lys), tRNA(Glu), and tRNA(Gln). The 2-seleno functionality on this modified nucleotide probably improves the translation accuracy and/or efficiency. These observations in vivo suggest that the presence of Se can provide natural RNAs with useful properties to better function and survival. To further investigate the biochemical and structural properties of Se-derivatized nucleic acids (SeNA), we have pioneered chemical and enzymatic synthesis of Se-derivatized nucleic acids, and introduced Se into both RNA and DNA at a variety of positions by atom-specific replacement of oxygen. This review outlines the recent advancements in chemical and biochemical syntheses, and studies of SeNAs, and their potential applications in structural and functional investigation of nucleic acids and their protein complexes.

Selenium derivatization of nucleic acids for phase and structure determination in nucleic acid X-ray crystallography

Selenium derivatization (via selenomethionine) of proteins for crystal structure determination via MAD phasing has revolutionized protein X-ray crystallography. It is estimated that over two thirds of all new crystal structures of proteins have been determined via Se-Met derivatization. Similarly, selenium functionalities have also been successfully incorporated into nucleic acids to facilitate their structure studies and it has been proved that this Se-derivatization has advantages over halogen strategy, which was usually used as a traditional method in this field. This review reports the development of site-specific selenium derivatization of nucleic acids for phase determination since the year of 2001 (mainly focus on the 2'-position of the ribose). All the synthesis of 2'-SeMe modified phosphoramidite building blocks (U, C, T, A, G) and the according oligonucleotides are included. In addition, several structures of selenium contained nucleic acid are also described in this paper.

DNA aptamer folding on gold nanoparticles: from colloid chemistry to biosensors

We have investigated the effect of the folding of DNA aptamers on the colloidal stability of gold nanoparticles (AuNPs) to which an aptamer is tethered. On the basis of the studies of two different aptamers (adenosine aptamer and K+ aptamer), we discovered a unique colloidal stabilization effect associated with aptamer folding: AuNPs to which folded aptamer structures are attached are more stable toward salt-induced aggregation than those tethered to unfolded aptamers. This colloidal stabilization effect is more significant when a DNA spacer was incorporated between AuNP and the aptamer or when lower aptamer surface graft densities were used. The conformation that aptamers adopt on the surface appears to be a key factor that determines the relative stability of different AuNPs. Dynamic light scattering experiments revealed that the sizes of AuNPs modified with folded aptamers were larger than those of AuNPs modified with unfolded (but largely collapsed) aptamers in salt solution. From both the electrostatic and steric stabilization points of view, the folded aptamers that are more extended from the surface have a higher stabilization effect on AuNP than the unfolded aptamers. On the basis of this unique phenomenon, colorimetric biosensors have been developed for the detection of adenosine, K+, adenosine deaminase, and its inhibitors. Moreover, distinct AuNP aggregation and redispersion stages can be readily operated by controlling aptamer folding and unfolding states with the addition of adenosine and adenosine deaminase.

A DNA-gold nanoparticle-based colorimetric competition assay for the detection of cysteine

We report the development of a highly sensitive and selective colorimetric detection method for cysteine based upon oligonucleotide-functionalized gold nanoparticle probes that contain strategically placed thymidine-thymidine (T-T) mismatches complexed with Hg2+. This assay relies upon the distance-dependent optical properties of gold nanoparticles, the sharp melting transition of oligonucleotide-linked nanoparticle aggregates, and the very selective coordination of Hg2+ with cysteine. The concentration of cysteine can be determined by monitoring with the naked eye or a UV-vis spectrometer the temperature at which the purple-to-red color change associated with aggregate dissociation takes place. This assay does not utilize organic cosolvents, enzymatic reactions, light-sensitive dye molecules, lengthy protocols, or sophisticated instrumentation thereby overcoming some of the limitations of more conventional methods.

Facile synthesis of oligonucleotide phosphoroselenoates

Se-(2-cyanoethyl)phthalimide was synthesized from di-(2-cyanoethyl) diselenide. This reagent was found to be an efficient selenium transfer reagent in the synthesis of selenophosphates. Thus, nucleotide H-phosphonate diesters that are formed in situ through the H-phosphonate chemistry undergo quantitative reaction with Se-(2-cyanoethyl)phthalamide. The resulting Se-(2-cyanoethyl) oligonucleotide phosphoroselenoate triesters are subsequently deprotected to give oligonucleotide phosphoroselenoate diesters in excellent yields.

Blue-to-red chromatic sensor composed of gold nanoparticles conjugated with thermoresponsive copolymer for Thiol sensing

We describe the first determination of thiol compounds with gold nanocomposites composed of gold nanoparticles and thermoresponsive copolymers having polyamino groups. The gold nanocomposites, which are used as a chromatic sensor, reveal chromatic change from blue to red with thermal stimuli, heating followed by cooling the solution. The blue-to-red chromatic change results from disassembly of the gold nanocomposites, which arises from shrinkage of the thermoresponsive copolymers bound to the gold nanoparticle surfaces due to the phase transition induced by thermal stimuli. The disassembly is inhibited by addition of thiol compounds through displacement of the adhered thermoresponsive copolymers. The detached copolymers no longer influence morphological change of the gold nanocomposites. Corresponding with increase of concentration of the thiol compounds, a solution of the gold nanocomposites after the thermal stimuli shows chromatic change, which was quantified with the a* value in L*a*b* chromatic coordinates. A linear relationship between the a* value and concentration of cysteine, examined as a bio-important thiol, is obtained below 7x10(-6) mol dm(-3), estimating a detection limit defined as 3sigma of the blank to be 2.8x10(-7) mol dm(-3). The chromatic sensor of the gold nanocomposites is applied to the determination of cysteine in commercial supplements containing ascorbic acid, which seriously interferes with redox-based determination of cysteine. Analytical results obtained with the chromatic sensor are identical to those obtained with HPLC.

Label-free and reagentless aptamer-based sensors for small molecules

A label free, reagentless aptasensor for adenosine is developed on an ISFET device. The separation of an aptamer/nucleic acid duplex by adenosine leads to the aptamer/adenosine complex that alters the gate potential of the ISFET. The sensitivity limit of the device is 5 x 10-5 M. Also, the immobilization of the aptamer/nucleic acid duplex on an Au-electrode and the separation of the duplex by adenosine mono-phosphate (AMP) enable the electrochemical detection of adenosine by faradaic impedance spectroscopy. The separation of the aptamer/nucleic acid duplex by adenosine and the formation of the aptamer/adenosine complex results in a decrease in the interfacial electron-transfer resistance in the presence of [Fe(CN)6]3-/4- as redox active substrate.

Ultrasensitive electrochemical detection of proteins by amplification of aptamer-nanoparticle bio bar codes

An ultrasensitive label-free bioelectrochemical method for rapid determination of thrombin has been developed by directly detecting the redox activity of adenine (A) nucleobases of anti-thrombin aptamer using a pyrolytic graphite electrode. The bioelectrochemical protocol involves a sandwich format. Thrombin, captured by immobilzed anti-thrombin antibody on microtiter plates, is detected by anti-thrombin aptamer-Au nanoparticle bio bar codes. A systematic optimization of the parameters has been carried out via ELAA (enzyme linked aptamer assay) performance. The adenine nucleobases were released by acid or nuclease from Au nanoparticles bound on microtiter plates. Differential pulse voltammetry was employed to investigate the electrochemical behaviors of the purine nucleobases. Well-defined adenine signal was observed at about 0.85 V in pH 5.9 acetate buffer. Because the nanoparticle carries a large number of aptamers per thrombin binding event, there is substantial amplification and thrombin can be detected at a very low level of detection (0.1 ng/mL). This method has been used to detect thrombin in complex matrix such as fetal calf serum with minimum background interference.

Silver nanoparticle-oligonucleotide conjugates based on DNA with triple cyclic disulfide moieties

We report a new strategy for preparing silver nanoparticle-oligonucleotide conjugates that are based upon DNA with cyclic disulfide-anchoring groups. These particles are extremely stable and can withstand NaCl concentrations up to 1.0 M. When silver nanoparticles functionalized with complementary sequences are combined, they assemble to form DNA-linked nanoparticle networks. This assembly process is reversible with heating and is associated with a red shifting of the particle surface plasmon resonance and a concomitant color change from yellow to pale red. Analogous to the oligonucleotide-functionalized gold nanoparticles, these particles also exhibit highly cooperative binding properties with extremely sharp melting transitions. This work is an important step toward using silver nanoparticle-oligonucleotide conjugates for a variety of purposes, including molecular diagnostic labels, synthons in programmable materials synthesis approaches, and functional components for nanoelectronic and plasmonic devices.

Non-base pairing DNA provides a new dimension for controlling aptamer-linked nanoparticles and sensors

DNA aptamers have been recently applied as simple and fast colorimetric sensors for a wide range of molecules. A unique feature of these systems is the presence of non-base pairing oligonucleotides in both DNA aptamers and spacers on DNA-functionalized nanoparticles. We report here a systematic investigation on an adenosine aptamer-linked gold nanoparticle system. When the aptamer overhang and the spacer were aligned on the same side, adenosine-responsive disassembly was inhibited. This inhibition effect increased with the length of the spacer, and fully inhibited activity was observed with the spacer containing more than three nucleotides. In contrast to a linear relationship between the spacer length and melting temperature in double-stranded DNA systems without overhangs, the aptamer system displayed a nonlinear relationship, with the melting temperature decreasing exponentially with spacer length. Control experiments suggested that this inhibition effect was due to thermodynamic factors rather than kinetic traps. A comparison with aptamer beacon systems indicated that nanoparticles may play an important role in this inhibition effect, and no specific interactions between the aptamer overhang and spacer were detected. The identity of nucleotides in the spacer did not affect the conclusions. Furthermore, the rate of disassembly or color change was slower at lower temperature or higher ionic strength, but was little affected by pH from 5.2 to 9.2. Therefore, non-base pairing DNA provided another dimension for controlling DNA-linked nanoparticles in addition to pH, temperature, or ionic strength, and this knowledge has resulted in the most optimal construct for sensing applications.

Aptamer-functionalized gold nanoparticles for turn-on light switch detection of platelet-derived growth factor

An aptamer modified gold nanoparticles (Apt-AuNPs) based molecular light switching sensor has been demonstrated for the analysis of breast cancer markers (platelet-derived growth factors (PDGFs) and their receptors) in homogeneous solutions. The PDGF binding aptamer has a unique structure with triple-helix conformation that allows N,N-dimethyl-2,7-diazapyrenium dication (DMDAP) and PDGF bindings. The fluorescence of DMDAP is almost completely quenched by Apt-AuNPs when it intercalates with the aptamers. Owing to high magnitudes of increases (up to 40-fold) in the turn-on fluorescence signals of DMDAP/Apt-AuNP upon PDGFs binding, the approach is highly sensitive for the detection of PDGFs. The DMDAP/Apt-AuNP probe specifically and sensitively detected PDGFs under optimal concentrations of salts and DMDAP. We also demonstrated that the Apt-AuNPs are effective selectors for enrichment of PDGF-AA from large-volume samples. The approach allows detection of PDGF-AA at a concentration down to 8 pM, showing better sensitivity than other signal aptamers. By conducting a competitive assay, we demonstrated the determination of PDGF receptor-alpha with LOD of 0.25 nM when using the DMDAP/Apt-AuNP as a probe.

Quantum dot encoding of aptamer-linked nanostructures for one-pot simultaneous detection of multiple analytes

One major challenge in analytical chemistry is multiplex sensing of a number of analytes with each analyte displaying a different signal. To meet such a challenge, quantum dots that emit at 525 and 585 nm are used to encode aptamer-linked nanostructures sensitive to adenosine and cocaine, respectively. In addition to quantum dots, the nanostructures also contain gold nanoparticles that serve as quenchers. Addition of target analytes disassembles the nanostructures and results in increased emission from quantum dots. Simultaneous colorimetric and fluorescent detection and quantification of both molecules in one pot is demonstrated.

Glyconanoparticles for the colorimetric detection of cholera toxin

Cholera continues to represent a major threat to human health, particularly in developing countries. Death can be readily avoided when medical treatment is rapidly administered. In order to provide a means of detecting the bacterially secreted toxin, we have developed a simple, yet rapid, bioassay for the cholera toxin. The colorimetric bioassay is based on a specifically synthesized lactose derivative that is self-assembled onto gold nanoparticles of 16 nm diameter. In solution the lactose-stabilized nanoparticles are red in color due to the intense surface plasmon absorption band centered at 524 nm. Cholera toxin (added as the B-subunit) (CTB) binds to the lactose derivative and induces aggregation of the nanoparticles. Upon aggregation, the surface plasmon absorption band broadens and red shifts such that the nanoparticle solution appears a deep purple color. The selectivity of the bioassay stems from the thiolated lactose derivative that mimics the GM(1) ganglioside--the receptor to which cholera toxin binds in the small intestine. Consequently, added metal ions, anions, and a protein, at relevant concentrations, do not induce nonspecific aggregation of the nanoparticles. The simple color change of the bioassay provides a selective means to detect and quantify the cholera toxin within 10 min. The theoretical limit of detection of the bioassay was determined to be 54 nM (3 microg/mL) for CTB. The stability of the lactose-stabilized nanoparticles was established by freeze-drying and then resuspending the particles in water and subsequently measuring CTB in biologically relevant electrolyte solutions. This colorimetric bioassay provides a new tool for the direct measurement of cholera toxin.

Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures

This protocol describes a simplified means of introducing an anomalously scattering atom into oligonucleotides by conventional solid-phase synthesis. Replacement of a nonbridging phosphate oxygen in the backbone with selenium is practically suitable for any nucleic acid. The resulting oligonucleotide P-diastereomers can be separated using anion exchange HPLC to yield diastereomerically pure phosphoroselenoates (PSes). The total time for the synthesis and ion-exchange HPLC separation of pure PSe is approximately 60 h.

Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study

[reaction: see text] To investigate nucleic acids with selenium derivatization for crystallography, we report the first synthesis of 2'-methylseleno-thymidine phosphoramidite and its incorporation into DNAs and RNAs by solid-phase synthesis with over 99% coupling yield. The d(GT(Se)GTACAC)2 crystal structure was also determined at 1.40 A resolution using Se phasing, revealing that this Se derivatization did not cause significant structure perturbation, consistent with our UV melting study. In addition, we observed that the Se modification largely facilitated the crystallization.

Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography

Because oxygen and selenium are in the same group (Family VI) in the periodic table, the site-specific mutagenesis at the atomic level by replacing RNA oxygen with selenium can provide insights on the structure and function of catalytic RNAs. We report here the first Se-derivatized ribozymes transcribed with all nucleoside 5'-(alpha-P-seleno)triphosphates (NTPalphaSe, including A, C, G, and U). We found that T7 RNA polymerase recognizes NTPalphaSe Sp diastereomers as well as the natural NTPs, whereas NTPalphaSe Rp diastereomers are neither substrates nor inhibitors. We also demonstrated the catalytic activity of these Se-derivatized hammerhead ribozymes by cleaving the RNA substrate, and we found that these phosphoroselenoate ribozymes can be as active as the native one. These hammerhead ribozymes site-specifically mutagenized by selenium reveal the close relationship between the catalytic activities and the replaced oxygen atoms, which provides insight on the participation of oxygen in catalysis or intramolecular interaction. This demonstrates a convenient strategy for the mechanistic study of functional RNAs. In addition, the active ribozymes site-specifically derivatized by selenium will allow for convenient MAD phasing in X-ray crystal structure studies.

Silver and gold glyconanoparticles for colorimetric bioassays

The color changes associated with the aggregation of metal nanoparticles has led to the development of colorimetric-based assays for a variety of target species. We have examined both silver- and gold-based nanoparticles in order to establish whether either metal exhibits optimal characteristics for bioassay development. These silver and gold nanoparticles have been stabilized with a self-assembled monolayer of a mannose derivative (2-mercaptoethyl alpha-d-mannopyranoside) with the aim of inducing aggregation by exploiting the well-known interaction between mannose and the lectin Concanavalin A (Con A). Both metal glyconanoparticles were determined to be ca. 16 nm in diameter (using TEM measurements). Aggregation was observed on addition of Con A to both silver and gold nanoparticles resulting in a shift in the surface plasmon absorption band and a consequent color change of the solution, which was monitored using UV-visible spectrophotometry. Mannose-stabilized silver nanoparticles at a concentration of 3 nM provide an assay for Con A with the largest linear range (between 0.08 and 0.26 microM). Additionally, the kinetic rate of aggregation of the silver-nanoparticle-based bioassay was significantly greater than that of the gold-nanoparticle system. However, in terms of sensitivity, the mannose-stabilized gold-nanoparticle-based assay was optimum with a limit of detection of 0.04 microM Con A, as compared with a value of 0.1 microM obtained for the mannose-stabilized silver nanoparticles. Additionally, a lactose derivative (11-mercapto-3,6,9-trioxaundecyl beta-D-lactoside) was used to stabilize gold nanoparticles to induce aggregation upon addition of the galactose specific lectin Ricinus communis agglutinin (RCA(120)). To examine the specificity of the bioassay, lactose-stabilized gold nanoparticles were mixed with a solution of mannose-stabilized silver nanoparticles to give an aggregation assay capable of detecting two different lectins. When either Con A or RCA(120) was added to the mixed glyconanoparticles, selective recognition of the respective natural ligand was shown by aggregation of a single metal nanoparticle. Centrifugation and removal of the aggregated species enabled further bioassay measurements using the second glyconanoparticle system.