Special Issue "Nucleic Acid Derivatives in Emerging Technologies"
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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry, Molecular Biology and Biophysics".
Deadline for manuscript submissions: closed (28 February 2009)
Special Issue Editors
Guest Editor
Prof. Dr. Lajos Kovacs
Nucleic Acids Laboratory, Department of Medicinal Chemistry, Universtiy of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
Website: http://www.mdche.u-szeged.hu/~kovacs/nal.html
E-Mail: kovacs.lajos@med.u-szeged.hu
Phone: +36 62 54 51 45
Fax: +36 62 42 59 71
Interests: preparative organic chemistry of carbohydrates; nucleobases; nucleosides; C-nucleosides; peptide nucleic acids; indoles; alkaloids; polyamines; heterocycles; protecting groups; chemical information management
Editorial Advisor
Prof. Dr. Richard I. Gumport
Department of Biochemistry, University of Illinois, 419 Roger Adams Lab B-4, 600 S Mathews Ave, Urbana, IL 61801, USA
Website: http://www.life.uiuc.edu/biochem/f_gumport.html
E-Mail: gumport@uiuc.edu
Interests: nucleic acid biochemistry; enzymology; molecular biology
Special Issue Information
Submission
All papers should be submitted to ijms@mdpi.com. To be published continuously until the deadline and papers will be listed together at the special issue website.
Submitted papers should not have been published previously, nor be under consideration for publication elsewhere. All papers are refereed through a peer-review process. A guide for authors is available on the Instructions for Authors page. The International Journal of Molecular Sciences is an international peer-reviewed monthly journal published by MDPI.
Open Access publication fees are 800 CHF per paper. English correction fees and/or formatting fees (250 CHF) will be added in certain cases (1050 CHF per paper for those papers that require extensive additional formatting and/or English corrections).
Keywords
- nucleic acids
- nucleosides
- nucleotides
- polynucleotides
Published Papers (18 papers)
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Received: 18 April 2007; in revised form: 11 May 2007 / Accepted: 15 May 2007 / Published: 13 June 2007
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Abstract: Gold nanoparticles (AuNPs) have found widespread applications in lifesciences. While synthesis of monodispersed AuNPs has been fairly convenient by usingchemical reduction of chloroauric acid by sodium citrate, we found that AuNPs of highquality and high concentrations were not readily obtained via this method. As an example,we showed that monodispersed 13-nm AuNPs were readily synthesized at relatively lowconcentrations (e.g. 3.5 nM); in contrast, 13-nm AuNPs of 17 nM obtained by the directreduction method were irregularly shaped and not well dispersed. In this work, wedemonstrated that AuNPs of high concentration could be prepared by a two-step approach,i.e. chemical reduction at low concentrations and subsequent centrifugation. Compared tothe direct reduction method, this new two-step method led to AuNPs with high saltresistance and high stability, which are essential for the preparation of DNA-AuNPsconjugates for DNA biodetection.
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Received: 6 March 2007; in revised form: 6 June 2007 / Accepted: 14 June 2007 / Published: 4 July 2007
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Abstract: Two novel macrocyclic polyamine ligands and their dinuclear zinc (II)complexes were synthesized and characterized. Their interaction with plasmid DNA wasstudied by gel electrophoresis and fluorescence quenching experiment. The result showedthat these complexes could bind DNA efficiently under physiological conditions.
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Received: 31 May 2007; in revised form: 29 June 2007 / Accepted: 13 July 2007 / Published: 23 July 2007
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Abstract: Carbon nanotubes (CNTs) can be effectively dispersed and functionalized bywrapping with long single-stranded DNA (ssDNA) synthesized by asymmetric PCR. ThessDNA-CNTs attached on surface of glass carbon electrode made it possible forelectrochemical analysis and sensing, which was demonstrated by reduction of H2O2 onhemoglobin/ssDNA-CNTs modified electrodes. This research showed the potentialapplication of DNA-functionalised CNTs in construction of future electrochemicalbiosensors.
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Received: 3 December 2007; in revised form: 18 February 2008 / Accepted: 25 February 2008 / Published: 12 March 2008
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Abstract: 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.
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Received: 13 December 2007; in revised form: 29 February 2008 / Accepted: 29 February 2008 / Published: 12 March 2008
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Abstract: The discovery of siRNAs as the mediators of RNA interference has led to an increasing interest in their therapeutic applications. Chemical modifications are introduced into siRNAs to optimize the potency, the stability and the pharmacokinetic properties in vivo. Here, we synthesize and test the effects of RNA-3’-PNA chimeras on siRNA functioning and stability. We demonstrate that the chemical modifications are compatible with the siRNA machinery, because all the PNA-modified siRNAs can efficiently mediate specific gene silencing in mammalian cells. Furthermore, we find that the modification on the sense strand of siRNA results in an increased persistence of the activity, whereas modification on both strands results in enhanced nuclease resistance in serum.
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Received: 3 December 2007; in revised form: 15 February 2008 / Accepted: 29 February 2008 / Published: 12 March 2008
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Abstract: The electrochemical behavior of o-nitrophenol was studied in detail with a glassy carbon electrode (GCE). The dependence of peak potential on pH indicated that equivalent electrons and protons were involved in the process of o-nitrophenol reduction. The interaction of o-nitrophenol with calf thymus DNA was investigated by adding DNA to the o-nitrophenol solution and by immobilizing DNA on GCE, respectively. The peak current decrement and peak potential shift in presence of DNA indicated that o-nitrophenol could interact with DNA. The result was demonstrated that the in situ DNA damage was detected by differential pulse voltammetry after the o-nitrophenol was electrochemically reduced.
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Received: 23 January 2008; in revised form: 17 March 2008 / Accepted: 18 March 2008 / Published: 24 March 2008
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Abstract: Here we tested the ability to augment the biological activity of the thrombin aptamer, d(GGTTGGTGTGGTTGG), by using locked nucleic acid (LNA) to influence its G-quadruplex structure. Compared to un-substituted control aptamer, LNA-containing aptamers displayed varying degrees of thrombin inhibition. Aptamers with LNA substituted in either positions G5, T7, or G8 showed decreased thrombin inhibition, whereas LNA at position G2 displayed activity comparable to un-substituted control aptamer. Interestingly, the thermal stability of the substituted aptamers does not correlate to activity – the more stable aptamers with LNA in position G5, T7, or G8 showed the least thrombin inhibition, while a less stable aptamer with LNA at G2 was as active as the un-substituted aptamer. These results suggest that LNA substitution at sites G5, T7, and G8 directly perturbs aptamer-thrombin affinity. This further implies that for the thrombin aptamer, activity is not dictated solely by the stability of the G-quadruplex structure, but by specific interactions between the central TGT loop and thrombin and that LNA can be tolerated in a biologically active nucleic acid structure albeit in a position dependent fashion.
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Received: 21 December 2007; in revised form: 22 April 2008 / Accepted: 23 April 2008 / Published: 24 April 2008
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Abstract: The structural damage of double-stranded DNA under UV radiation was examined using single-molecule fluorescence microscopy. Compared to undamaged DNA, the diffusion coefficient of λ-DNA was significantly increased with 12 min or 20 min of radiation but remained unchanged for 40 min of exposure possibly due to strand crosslinking. The structural damage of DNA was further examined using transmission electron microscopy which revealed kinks and sharp bends along the DNA backbone.
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Received: 18 December 2007; in revised form: 3 April 2008 / Accepted: 24 April 2008 / Published: 24 April 2008
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Abstract: Aptamers, single stranded DNA or RNA molecules, generated by a method called SELEX (systematic evolution of ligands by exponential enrichment) have been widely used in various biomedical applications. The newly developed Cell-SELEX (cell based-SELEX) targeting whole living cells has raised great expectations for cancer biology, -therapy and regenerative medicine. Combining nanobiotechnology with aptamers, this technology opens the way to more sophisticated applications in molecular diagnosis. This paper gives a review of recent developments in SELEX technologies and new applications of aptamers.
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Received: 25 April 2008; in revised form: 15 May 2008 / Accepted: 16 May 2008 / Published: 20 May 2008
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Abstract: Although cellular RNA is subjected to the same oxidative insults as DNA and other cellular macromolecules, oxidative damage to RNA has not been a major focus in investigations of the biological consequences of free radical damage. In fact, because it is largely single-stranded and its bases lack the protection of hydrogen bonding and binding by specific proteins, RNA may be more susceptible to oxidative insults than is DNA. Oxidative damage to protein-coding RNA or non-coding RNA will, in turn, potentially cause errors in proteins and/or dysregulation of gene expression. While less lethal than mutations in the genome, such sublethal insults to cells might be associated with underlying mechanisms of several chronic diseases, including neurodegenerative disease. Recently, oxidative RNA damage has been described in several neurodegenerative diseases including Alzheimer disease, Parkinson disease, dementia with Lewy bodies, and prion diseases. Of particular interest, oxidative RNA damage can be demonstrated in vulnerable neurons early in disease, suggesting that RNA oxidation may actively contribute to the onset of the disease. An increasing body of evidence suggests that, mechanistically speaking, the detrimental effects of oxidative RNA damage to protein synthesis are attenuated, at least in part, by the existence of protective mechanisms that prevent the incorporation of the damaged ribonucleotides into the translational machinery. Further investigations aimed at understanding the processing mechanisms related to oxidative RNA damage and its consequences may provide significant insights into the pathogenesis of neurodegenerative and other degenerative diseases and lead to better therapeutic strategies.
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Received: 7 April 2008; in revised form: 16 May 2008 / Accepted: 27 May 2008 / Published: 13 June 2008
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Abstract: MicroRNAs (miRNAs) are a class of short non-coding RNAs with posttranscriptional regulatory functions. To date, more than 600 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs. Accumulating evidence has linked the dysregulated expression patterns of miRNAs to a variety of diseases, such as cancer, neurodegenerative diseases, cardiovascular diseases and viral infections. MiRNAs provide its particular layer of network for gene regulation, thus possessing the great potential both as a novel class of therapeutic targets and as a powerful intervention tool. In this regard, synthetic RNAs that contain the binding sites of miRNA have been shown to work as a “decoy” or “miRNA sponge” to inhibit the function of specific miRNAs. On the other hand, miRNA expression vectors have been used to restore or overexpress specific miRNAs to achieve a long-term effect. Further, double-stranded miRNA mimetics for transient replacement have been experimentally validated. Endogenous precursor miRNAs have also been used as scaffolds for the induction of RNA interference. This article reviews the recent progress on this emerging technology as a powerful tool for gene regulation studies and particularly as a rationale strategy for design of therapeutics.
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Received: 5 May 2008; in revised form: 6 June 2008 / Accepted: 10 June 2008 / Published: 20 June 2008
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Abstract: Cathepsin G (CatG) is a chymotrypsin-like protease released upon degranulation of neutrophils. In several inflammatory and ischaemic diseases the impaired balance between CatG and its physiological inhibitors leads to tissue destruction and platelet aggregation. Inhibitors of CatG are suitable for the treatment of inflammatory diseases and procoagulant conditions. DNA released upon the death of neutrophils at injury sites binds CatG. Moreover, short DNA fragments are more inhibitory than genomic DNA. Defibrotide, a single stranded polydeoxyribonucleotide with antithrombotic effect is also a potent CatG inhibitor. Given the above experimental evidences we employed a selection protocol to assess whether DNA inhibition of CatG may be ascribed to specific sequences present in defibrotide DNA. A Selex protocol was applied to identify the single-stranded DNA sequences exhibiting the highest affinity for CatG, the diversity of a combinatorial pool of oligodeoxyribonucleotides being a good representation of the complexity found in defibrotide. Biophysical and biochemical studies confirmed that the selected sequences bind tightly to the target enzyme and also efficiently inhibit its catalytic activity. Sequence analysis carried out to unveil a motif responsible for CatG recognition showed a recurrence of alternating TG repeats in the selected CatG binders, adopting an extended conformation that grants maximal interaction with the highly charged protein surface. This unprecedented finding is validated by our results showing high affinity and inhibition of CatG by specific DNA sequences of variable length designed to maximally reduce pairing/folding interactions.
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Received: 2 April 2008; in revised form: 11 June 2008 / Accepted: 12 June 2008 / Published: 8 July 2008
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Abstract: This work describes the immobilization of purine and pyrimidine bases and immobilization/hybridization of synthetic oligonucleotides on graphite electrodes modified with poly(4-methoxyphenethylamine) produced in acid medium. The immobilization of adenine, guanine, cytosine and thymine on these modified electrodes was efficient, producing characteristic peaks. Another relevant observation is that, according to the literature, pyrimidine bases, cytosine and thymine are more difficult to detect. However, when immobilized onto the poly(4-methoxyphenethylamine), a significant increase in the magnitude of the current was obtained. The observation of the hybridization between the poly(GA) probe and its complementary, poly(CT) target, was possible by monitoring the guanosine and adenosine peaks or through methylene blue indicator, using differential pulse voltammetry. Hybridization results in a decrease of the peak current of guanosine and adenosine or the signal of methylene blue accumulated on the modified electrode surface. The hybridization with the complementary target was also investigated by electrochemical impedance spectroscopy. The results showed a significant modification in the Nyquist plot, after addition of the complementary target, with increase of the charge transference resistance.
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Received: 7 April 2008; in revised form: 6 June 2008 / Accepted: 14 July 2008 / Published: 14 July 2008
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Abstract: The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is vital for the proper functioning of RNAs. Consequently, RNA structure and dynamics necessarily determine their biological function. In the post-genomic era, it is clear that RNAs comprise a larger proportion (>50%) of the transcribed genome compared to proteins (≤ 2%). Yet the determination of the 3D structures of RNAs lags considerably behind those of proteins and to date there are even fewer investigations of dynamics in RNAs compared to proteins. Site specific incorporation of various structural and dynamic probes into nucleic acids would likely transform RNA structural biology. Therefore, various methods for introducing probes for structural, functional, and biotechnological applications are critically assessed here. These probes include stable isotopes such as 2H, 13C, 15N, and 19F. Incorporation of these probes using improved RNA ligation strategies promises to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as nuclear magnetic resonance (NMR) spectroscopy, X-ray crystallography and Raman spectroscopy. Finally, some of the structural and dynamic problems that can be addressed using these technological advances are outlined.
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Received: 31 March 2008; in revised form: 4 June 2008 / Accepted: 14 July 2008 / Published: 16 July 2008
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Abstract: Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cellpenetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10-30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisenseoligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls.
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Received: 2 April 2008; in revised form: 6 August 2008 / Accepted: 7 August 2008 / Published: 20 August 2008
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Abstract: Some of most used indicators in marine ecology are nucleic acid-derived indices. They can be divided by target levels in three groups: 1) at the organism level as ecophysiologic indicators, indicators such as RNA:DNA ratios, DNA:dry weight and RNA:protein, 2) at the population level, indicators such as growth rate, starvation incidence or fisheries impact indicators, and 3) at the community level, indicators such as trophic interactions, exergy indices and prey identification. The nucleic acids derived indices, especially RNA:DNA ratio, have been applied with success as indicators of nutritional condition, well been and growth in marine organisms. They are also useful as indicators of natural or anthropogenic impacts in marine population and communities, such as upwelling or dredge fisheries, respectively. They can help in understanding important issues of marine ecology such as trophic interactions in marine environment, fish and invertebrate recruitment failure and biodiversity changes, without laborious work of counting, measuring and identification of small marine organisms. Besides the objective of integrate nucleic acid derived indices across levels of organization, the paper will also include a general characterization of most used nucleic acid derived indices in marine ecology and also advantages and limitations of them. We can conclude that using indicators, such RNA:DNA ratios and other nucleic acids derived indices concomitantly with organism and ecosystems measures of responses to climate change (distribution, abundance, activity, metabolic rate, survival) will allow for the development of more rigorous and realistic predictions of the effects of anthropogenic climate change on marine systems.
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Received: 18 April 2008 / Accepted: 29 August 2008 / Published: 1 September 2008
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Abstract: Development of antivirals has focused primarily on vaccines and on treatments for specific viral agents. Although effective, these approaches may be limited in situations where the etiologic agent is unknown or when the target virus has undergone mutation, recombination or reassortment. Augmentation of the innate immune response may be an effective alternative for disease amelioration. Nonspecific, broad-spectrum immune responses can be induced by double-stranded (ds)RNAs such as poly (ICLC), or oligonucleotides (ODNs) containing unmethylated deocycytidyl-deoxyguanosinyl (CpG) motifs. These may offer protection against various bacterial and viral pathogens regardless of their genetic makeup, zoonotic origin or drug resistance.
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Received: 2 April 2008; in revised form: 24 September 2008 / Accepted: 6 October 2008 / Published: 20 October 2008
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Abstract: Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection of a nucleic acid region and as such, DNA molecules have typically been used to probe for the sequences of interest. However, since the turn of the century, an increasing number of laboratories have started to move on to the more robust DNA mimics methods, most notably peptide and locked nucleic acids (PNA and LNA). In this review, we will cover the state-of-the-art of the different DNA mimics in regard to their application as efficient markers for the presence of individual microbial cells, and consider their potential advantages and pitfalls. Available PNA probes are then reassessed in terms of sensitivity and specificity using rRNA databases. In addition, we also attempt to predict the applicability of DNA mimics in well-known techniques attempting to detect in situ low number of copies of specific nucleic acid sequences such as catalyzed reporter deposition (CARD) and recognition of individual genes (RING) FISH.
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Last update: 21 February 2011
