Internal 32P-labeling of L-deoxyoligonucleotides

Probing the Conformational Restraints of DNA Damage Recognition with β-L-Nucleotides

The DNA building blocks 2'-deoxynucleotides are enantiomeric, with their natural β-D-configuration dictated by the sugar moiety. Their synthetic β-L-enantiomers (βLdNs) can be used to obtain L-DNA, which, when fully substituted, is resistant to nucleases and is finding use in many biosensing and nanotechnology applications. However, much less is known about the enzymatic recognition and processing of individual βLdNs embedded in D-DNA. Here, we address the template properties of βLdNs for several DNA polymerases and the ability of base excision repair enzymes to remove these modifications from DNA. The Klenow fragment was fully blocked by βLdNs, whereas DNA polymerase κ bypassed them in an error-free manner. Phage RB69 DNA polymerase and DNA polymerase β treated βLdNs as non-instructive but the latter enzyme shifted towards error-free incorporation on a gapped DNA substrate. DNA glycosylases and AP endonucleases did not process βLdNs. DNA glycosylases sensitive to the base opposite their cognate lesions also did not recognize βLdNs as a correct pairing partner. Nevertheless, when placed in a reporter plasmid, pyrimidine βLdNs were resistant to repair in human cells, whereas purine βLdNs appear to be partly repaired. Overall, βLdNs are unique modifications that are mostly non-instructive but have dual non-instructive/instructive properties in special cases.

Highly specific fluorescence detection of T4 polynucleotide kinase activity via photo-induced electron transfer

Sensitive and reliable study of the activity of polynucleotide kinase (PNK) and its potential inhibitors is of great importance for biochemical interaction related to DNA phosphorylation as well as development of kinase-targeted drug discovery. To achieve facile and reliable detection of PNK activity, we report here a novel fluorescence method for PNK assay based on a combination of exonuclease cleavage reaction and photo-induced electron transfer (PIET) by using T4 PNK as a model target. The fluorescence of 3'-carboxyfluorescein-labeled DNA probe (FDNA) is effectively quenched by deoxyguanosines at the 5' end of its complementary DNA (cDNA) due to an effective PIET between deoxyguanosines and fluorophore. Whereas FDNA/cDNA hybrid is phosphorylated by PNK and then immediately cleaved by lambda exonuclease (λ exo), fluorescence is greatly restored due to the break of PIET. This homogeneous PNK activity assay does not require a complex design by taking advantage of the quenching ability of deoxyguanosines, making the proposed strategy facile and cost-effective. The activity of PNK can be sensitively detected in the range of 0.005 to 10 U mL(-1) with a detection limit of 2.1×10(-3) U mL(-1). Research on inhibition efficiency of different inhibitors demonstrated that it can be explored to evaluate inhibition capacity of inhibitors. The application for detection of PNK activity in complex matrix achieved satisfactory results. Therefore, this PIET strategy opens a promising avenue for studying T4 PNK activity as well as evaluating PNK inhibitors, which is of great importance for discovering kinase-targeted drugs.

Aptamers as a novel tool for diagnostics and therapy

Aptamers are short single-stranded DNA or RNA oligonucleotides that are capable of binding small molecules, proteins, or nucleotides with high specificity. They show a stable conformation and high binding affinity for their target molecules. There are numerous applications for aptamers in biotechnology, molecular diagnostics and targeted therapy of diseases. Their production is cheap, and they generally display lower immunogenicity than monoclonal antibodies. In the present review, we give an introduction to the preparation of aptamers and provide examples for their use in biotechnology, diagnostics and therapy of diseases.

An amplified fluorescence detection of T4 polynucleotide kinase activity based on coupled exonuclease III reaction and a graphene oxide platform

A novel amplified fluorescence graphene oxide (GO) sensing system for sensitive detection of T4 polynucleotide kinase (PNK) activity and inhibition was developed based on the exonuclease III (ExoIII) reaction.

A sensitive immobilization-free electrochemical assay for T4PNK activity based on exonuclease III-assisted recycling

This work develops a novel, immobilization-free, simple and sensitive electrochemical platform for the detection of T4PNK activity based on λ-exo and exonuclease III-assisted signal amplification.

A WS2 nanosheet based sensing platform for highly sensitive detection of T4 polynucleotide kinase and its inhibitors

DNA phosphorylation, catalyzed by polynucleotide kinase (PNK), plays significant regulatory roles in many biological events. Here, a novel fluorescent nanosensor based on phosphorylation-specific exonuclease reaction and efficient fluorescence quenching of single-stranded DNA (ssDNA) by a WS2 nanosheet has been developed for monitoring the activity of PNK using T4 polynucleotide kinase (T4 PNK) as a model target. The fluorescent dye-labeled double-stranded DNA (dsDNA) remains highly fluorescent when mixed with WS2 nanosheets because of the weak adsorption of dsDNA on WS2 nanosheets. While dsDNA is phosphorylated by T4 PNK, it can be specifically degraded by λ exonuclease, producing ssDNA strongly adsorbed on WS2 nanosheets with greatly quenched fluorescence. Because of the high quenching efficiency of WS2 nanosheets, the developed platform presents excellent performance with a wide linear range, low detection limit and high signal-to-background ratio. Additionally, inhibition effects from adenosine diphosphate, ammonium sulfate, and sodium chloride have been investigated. The method may provide a universal platform for PNK activity monitoring and inhibitor screening in drug discovery and clinic diagnostics.

Amplified detection of T4 polynucleotide kinase activity by the coupled λ exonuclease cleavage reaction and catalytic assembly of bimolecular beacons

The phosphorylation of nucleic acid catalyzed by polynucleotide kinase is an indispensible procedure involved in many vital cellular activities such as DNA recombination and DNA repair. Herein, a novel strategy for the sensitive determination of T4 polynucleotide kinase (PNK) activity and inhibition was proposed, which combined exonuclease enzyme reaction and bimolecular beacons (bi-MBs)-based signal amplification. A hairpin probe (HP) with 5'-hydroxyl termini and two different types of molecular beacons (MBs), MB1 and MB2, is designed. Taking advantage of the efficient enzyme reactions, namely the phosphorylation of HP by PNK and the λ exonuclease cleavage reaction, the trigger DNA fragment can be released from HP and is used to trigger the catalytic assembly of bimolecular beacons, resulting in a remarkably amplified fluorescence signal toward PNK activity detection. The detection limit of this method toward PNK was obtained as 1 mU/mL, which was superior or comparable with the reported methods. Furthermore, the facile and sensitive method can also be used to screen the inhibition effects toward several common inhibitors. It provides a promising platform for sensitive determination of nucleotide kinase activity and inhibition, and also shows great potential for biological process research, drug discovery, and clinic diagnostics.

Exploring the role of chirality in nucleic acid recognition

The study of the base-pairing properties of nucleic acids with sugar moieties in the backbone belonging to the L-series (β-L-DNA, β-L-RNA, and their analogs) are reviewed. The major structural factors underlying the formation of stable heterochiral complexes obtained by incorporation of modified nucleotides into natural duplexes, or by hybridization between homochiral strands of opposite sense of chirality are highlighted. In addition, the perspective use of L-nucleic acids as candidates for various therapeutic applications, or as tools for both synthetic biology and etiology-oriented investigations on the structure and stereochemistry of natural nucleic acids is discussed.

Biodistribution of antisense nanoparticles in mammary carcinoma rat model

Efficient and specific delivery of antisenses (ASs) and protection of the sequences from degradation are critical factors for effective therapy. Sustained release nanoparticles (NP) offer increased resistance to nuclease degradation, increased amounts of AS uptake, and the possibility of control in dosing and sustained duration of AS administration. The biodegradable and biocompatible poly(D,L-lactic-co-glycolic acid) copolymer (PLGA) was utilized to encapsulate AS directed against osteopontin (OPN), which is a promising therapeutic target in mammary carcinoma. Whole body biodistribution of OPN AS NP was evaluated in comparison to naked AS, in intact and mammary carcinoma metastasis model bearing rats. Naked and NP encapsulated AS exhibited different biodistribution profiles. AS NP, in contrast to naked AS, tended to accumulate mostly in the spleen, liver, and at the tumor inoculation site. Drug levels in intact organs were negligible. The elimination of naked AS was faster, due to rapid degradation of the unprotected sequence. It is concluded that AS NP protect the AS from degradation, provide efficient AS delivery to the tumor tissue, and minimize AS accumulation in intact organs due to the AS sustained release profile as well as the favorable NP physicochemical properties.

Advances in aptamers

Aptamers are nucleic acid sequences synthesized through in vitro selection and amplification technique, possessing a broader range of applications in therapeutics, biosensing, diagnostics, and research. Aptamers offer a number of advantages over their antibodies counterpart, one of them is their ability to undergo chemical derivatization to increase their life in the body fluids and bioavailability in animals. Although aptamers were discovered in 1990s, they have become one of the most widely investigated molecules, with a huge number of publications in the last decade. This article presents an overview of the advancements that have been made in aptamers. We mainly focused on articles published since 2005.

Real-time monitoring of the activity and kinetics of T4 polynucleotide kinase by a singly labeled DNA-hairpin smart probe coupled with lambda exonuclease cleavage

We describe a novel method for real-time monitoring of the activity and kinetics of T4 polynucleotide kinase (PNK) by use of a singly fluorophore-labeled DNA-hairpin smart probe (SP) coupled with lambda exonuclease (lambda exo) cleavage. The method was performed in a sealed reaction tube and offered more sensitive, fast, high-throughput, and cost-effective detection. The SP was designed with a fluorophore at the 3'-end, and the fluorescence was quenched by a GGG-triplet at the 5'-end without any other additional quenchers. The 5'-hydroxyl group of the SP was phosphorylated by T4 PNK in the presence of ATP, and the resulting 5'-phosphoryl end product was promptly cleaved by lambda exo, which caused significant enhancement of fluorescence. A fast and accurate method for assaying the kinase activity of T4 PNK was developed with a wide linear detection range from 0.022 to 5.6 nM s(-1). The phosphorylation reaction was monitored at varying substrate concentrations at the molecular level, and K(m), V(max), and K(cat) values were all calculated. Furthermore, the effects of ATP concentration and salts were investigated. The developed method can be easily adapted to the detection of many other nucleic acid enzymes and may find widespread applications.

Stereoselective synthesis using immobilized Diels-Alderase ribozymes

Development of artificial ribozymes by in vitro selection has so far, mostly been addressed from the viewpoint of fundamental research. However, such ribozymes also have high potential as selective catalysts in practical syntheses. Immobilization of an active and selective ribozyme is an important step towards this end. A 49-nucleotide RNA molecule that was previously found to stereoselectively catalyze Diels-Alder reactions between various anthracene dienes and maleimide dienophiles was quantitatively immobilized on an agarose matrix by periodate oxidation of the 3'-terminal ribose and coupling to a hydrazide moiety. Typical loadings were 45 pmol microL(-1) gel. The specific activity was comparable to that of soluble ribozyme, and high enantioselectivities were obtained in catalyzed cycloadditions. The catalytic matrix was found to be stable and could be regenerated about 40 times with only minimal reduction of catalytic activity. Like the soluble ribozyme, the immobilized catalyst stereoselectively converts various diene and dienophile substrates. By using either natural D-RNA or enantiomeric L-RNA, both product enantiomers were made synthetically accessible with similar selectivities.