| Int.
J. Mol. Sci. (ISSN 1422-0067, CODEN: IJMCFK) |
Special Issue: "Nucleic Acid
Derivatives in
Emerging Technologies" The
special issue belongs to the section "Biochemistry,
Molecular
Biology and Biophysics"
|
 |
[Editors] [Call for Papers] [Published Papers] [Announced Papers][Leading Review Papers] [List of Keywords]
Deadline for manuscript submission: 31 March 2008
Guest Editor
Prof. Dr. Lajos Kovacs
E-Mail: kovacs@ovrisc.mdche.u-szeged.hu
Editorial Advisor
Prof. Dr. Richard I. Gumport
Department of Biochemistry, 419 Roger Adams Lab B-4, 600 S Mathews Ave, Urbana, IL 61801, USA
E-Mail: gumport@uiuc.edu; Link: http://www.life.uiuc.edu/biochem/f_gumport.html
Keywords: Nucleic Acid Enzymology, Protein-DNA Interactions
Prof. Dr. Lajos Kovacs
E-Mail: kovacs@ovrisc.mdche.u-szeged.hu
Editorial Advisor
Prof. Dr. Richard I. Gumport
Department of Biochemistry, 419 Roger Adams Lab B-4, 600 S Mathews Ave, Urbana, IL 61801, USA
E-Mail: gumport@uiuc.edu; Link: http://www.life.uiuc.edu/biochem/f_gumport.html
Keywords: Nucleic Acid Enzymology, Protein-DNA Interactions
Call for Papers:
Announced Papers:
Review articles: Before writing their manuscripts, potential authors of review articles should forward the title and a short abstract to the Guest Editor. The Guest Editor will then provide feedback on the suitability of the topic upon consultation with other editors and/or members of the Editorial Board. Authors are encouraged to write reviews that provide a critical appraisal of areas of Nucleic Acid Derivatives in Emerging Technologies.
Manuscript ID: IJMS-20-07
Type: Review
Title: Partial words for DNA strings
Author: Dipankar Mazumdar
Department of Mathematics, Visva-Bharati, Santiniketan 731235, West Bengal, India; E-mail: itsmedip@rediffmail.com; dmazumda@science.uva.nl
Abstract:
In this review we have tried to show that partial words are useful
tools in modeling DNA behaviour. Berstel and Boasson have introduced
the concept of partial words. Mazumdar has introduced the fuzzy partial
words. Blanchet-Sadri has contributed many results regarding the
periodicity of partial words. Later Leupold has used partial words in
DNA coding. The various results regarding partial words are scattered
in Computer science, DNA computing, Bioinformatics and of course
combinatorics literature. In this review we have gathered the results
and inferred the outlook towards the application to DNA sequence
analysis.
Manuscript ID: IJMS-20-05
Type: Review
Title: Delivery Carriers for Nucleic Acid Derivatives
Author: Avi Domb
Affiliations: Department of Medicinal Chemistry & Natural Products, School of Pharmacy - Faculty of Medicine, The Hebrew University, Jerusalem, Israel; Tel: 972-50-6272355; e-mail: avid@ekmd.huji.ac.il
Abstract:
Nucleic
acid delivery has many applications in basic science,
biotechnology,agriculture, and medicine. Gene therapy, an approach for
treatment or prevention of diseases associated with defective gene
expression, involves the insertion of a therapeutic gene into cells,
followed by expression and production of the required proteins. This
approach enables replacement of damaged genes or expression inhibition
of undesired genes. Alternatively, short DNA or RNA segment that can
deactivate specific genes have found application in treating certain
diseases such as cancer and monogenetic disorders. This review will
focus on non-viral plasmid DNA and short chain DNA and RNA carrier with
applications in treating of various diseases. Cationic polymers and
lipids
Manuscript ID: IJMS-20-06
Type: Review
Title: Recent Updates in DNA Incorporated Carbon Nanotubes and Metal Nanoparticles for Electrochemical Sensors and Biosensors - A Review
Authors: Umasankar Yogeswaran, Soundappan Thiagarajan and Shen-Ming Chen *
Affiliations: Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, No.1, Section 3, Chung-Hsiao East Road , Taipei 106, Taiwan (ROC); E-mail: smchen78@ms15.hinet.net
Abstract:
Recently,
the electrochemical sensors and biosensors possess more advantageous
over the other sensors because; in these, the electrodes can sense the
materials which are present within the host without doing any damage to
the host system. The active sensing materials used in these type of
sensors maybe of any kind which ever acts as a catalyst for sensing a
particular analyte or a set of analytes. Among these various kinds,
deoxyribonucleic acid (DNA), carbon nanotubes (CNTs), metal
nanoparticles have received considerable attraction in recent years.
Obviously, DNA is one of the class of natural polymer, its interactions
with CNTs and metal nanoparticles lead a way for the application of new
type of composite and hybrid materials in sensors. Similarly, CNTs and
metal nanoparticles are the promising new materials for biosensors
applications, which have the advantages in characteristics such as low
weight of extraordinary and multifunctional properties. In this
article, the advantages of the DNA incorporated CNTs and metal
nanoparticle hybrid materials towards electrochemical sensors and
biosensors have been presented in detail with some key results from the
literature.
Keywords:
DNA, carbon nanotubes, metal nanoparticles,
electrochemical sensors and biosensors. Manuscript ID: IJMS-20-09
Type: Review
Title: Uracil in DNA: Physiological Occurrence and Applications
Authors: Beata G. Vertessy
Affiliations: Howard Hughes Scholar, Institute of Enzymology, Hungarian Academy of Sciences, Karolina 29, H-1113, Budapest, Hungary; E-mail: vertessy@enzim.hu
Abstract:
There
are two ways that may lead to appearance of uracil in DNA under
physiological circumstances. First, frequent and spontaneous
deamination of cytosine leads to formation of uracil with a
frequency of around several hundred evenyts/day in mammalian genomes.
This alteration changes the base-pairing character and will lead to a
point mutation (replacement of a C:G base pair with an A:U base pair)
in the next replication cycle. Second, uracil may get incorporated to
replace thymine if the cellular ratio of the respective building blocks
dUTP/dTTP is elevated. Thymine-replacing uracils are not mutagenic per
se but may lead to recognition perturbances. Repair of uracil-DNA is
initiated by uracil-DNA glycosylases. In addition to the mistake
character of uracil in DNA, recent data indicate that this base may
have specific signal transduction role as well in diversification of
immunoglobulin genes and in initiating cell death during metamorphosis.
Specific recognition of uracil-DNA has found applications in genetic
engineering and also in cancerchemotherapy. The present review covers
recent developments and provides an outlook in this field.
Manuscript ID: IJMS-20-14
Type: Review
Title:Peptide-based strategy for ex-vivo and in vivo delivery of nucleic acids and derivatives
Authors: L. Crombez and Gilles Divita
Affiliations: CRBM - CNRS -FRE-2593, Molecular Biophysics & Therapeutics, 1919 route de Mende, 34293 Montpellier cedex 5, FRANCE; Tel: + 33 (0)4 67 61 33 92; Fax: 33 (0)4 67 52 15 59; E-mail : gilles.divita@crbm.cnrs.fr
Abstract: The major obstacle to clinical development of most of the nucleic acid-based strategies, including short interfering RNAs, is their poor cellular uptake and bioavailability. Although, several viral and non-viral strategies have been proposed to improve nucleic acids delivery their applications in vivo remain a major challenge. Several new technologies have been designed to improve cellular uptake of therapeutic molecules, including cell-penetrating peptides (CPPs), which represent a new and innovative concept to bypass the problem of bioavailability of drugs. Two CPP-strategies have been described so far, the first one requires chemical linkage between the drug and the carrier for cellular drug internalization and the second is based on the formation of stable complexes with drugs depending on their chemical nature. We have developed a new strategy, based on a short amphipathic peptides, MPG/PEP, that are able to form stable nanoparticles with nucleic acids and can efficiently deliver siRNA in a fully biologically active form into a variety of cell lines and in vivo. This short review will discuss the mechanism and the potency of the non-covalent peptide-based strategy for nucleic acid and derivative delivery both in vitro and in vivo.
Manuscript ID: IJMS-20-15
Type: Review
Title: Nucleic Acid Derived Indices in Marine Ecology
Authors: Maria Alexandra Chícharo
Affiliations: CCMAR/University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; E-mail: mchichar@ualg.pt; URL: http://w3.ualg.pt/~mchichar/
Abstract: Some of most used indices in marine ecology are nucleic acids derived indices. They can be divided in three target levels: 1) at organism level indices, such as RNA/DNA ratios, DNA/dry weight RNA/protein, 2) at population level as starvation incidence, and 3) community level such as exergy indices. The nucleic acids derived indices have been applied with success as indicators of nutritional condition, well been and growth in aquatic invertebrates and fishes. They are also useful as stress indicators of anthropogenic impacts in marine population and communities, such as dredge fisheries or eutrophication. The paper will also include a general characterization of most used nucleic acid derived indices in marine ecology, a description of the methodology and also advantages and limitations of them.
Manuscript ID: IJMS-20-16
Type: Review
Title: Nucleic Acid Derived Indices in Marine Ecology
Authors: N. F. Azevedo 1,2, C. Almeida 1,2, C. W. Keevil 2 and M. J. Vieira 1,*
Affiliations: 1 1IBB - Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal 2 2Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom; * Author to whom correspondence should be addressed; E-Mail: mjv@deb.uminho.pt
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 probes are then assessed in terms of theoretical sensitivity and specificity. In addition, a list of what remains to be done to further impose this method as a gold-standard for the whole-cell detection of microorganisms in different settings is presented.
Manuscript ID: IJMS-20-17
Type: Review
Title: Key RNA labeling technologies to tackle sizeable problems in structural biology
Authors: Kwaku T. Dayie
Affiliations: Lerner Research Institute, Department of Molecular Genetics and Center for Structural Biology, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195
Abstract: The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is key for the proper functioning of RNAs. Consequently, it has become axiomatic that 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 (NA) promises to revolutionarize NA structural biology in this postgenomic era. We, therefore, critically assess here various methods for introducing probes into NA for structural, functional, and biotechnological applications. The probes surveyed include non-radioactive stable isotopes (2H, 13C, 15N, 19F, 77Se) and photo-stable fluorophores. Incorporation of these probes using improved RNA ligation strategies promise to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as NMR spectroscopy, X-ray crystallography, Fluorescence and Raman spectroscopy. Finally, we outline some of the structural and dynamic problems that could be amenable to these technological advances.
Keywords: dynamics, FRET, isotopic labeling, ligation, Mass Spectrometry, NMR, Raman, RNA dynamics and folding and structure, X-ray crystallography.
Manuscript ID: IJMS-20-19
Type: Full Research Paper
Title: Designs and efficacies of broad-spectrum and virus-specific approaches using nucleic acid-based agents against influenza A viruses
Authors: Jonathan Wong
Affiliations: Molecular Biology Group, Biotechnology Section, Defence R&D Canada – Suffield, Box 4000 Main Station, Medicine Hat, Alberta, Canada T1A 8K6
Abstract: The global increases in the number of influenza A virus isolates resistant to amantadine and tamiflu undermine our ability to defend against potential influenza pandemics. There are compelling reasons to fast track research and development of novel antiviral agents which can protect against drug-resistant and potentially pandemic strains of deadly influenza viruses. Nucleic acid-based drugs represent a promising class of antiviral agents that could play a role in the prevention and treatment of influenza virus infections. Antisense oligonucleotides designed to inhibit the expressions of key virus proteins (nucleoprotein, heamagglutinin and polymerase) have been designed and are found to be therapeutically effective against influenza A viruses in both tissue culture and animal studies. Gene-silencing approaches such as antisense and small interfering RNA are highly sequence specific and their efficacies can be compromised by antigenic shifts and drifts in virus genes. Alternatively, nucleic acids such as ds RNA and oligonucleotides containing unmethylated CpG motifs can be designed to elicit antiviral immunity via the toll-like receptor (TLR-3 and -9, respectively) activation pathways. Efficacy studies in mice have shown that ds RNA such as poly ICLC can provide effective and broad-spectrum protection against lethal challenges against various strains of influenza A virus, including seasonal and avian H5N1. Similarly, CpG-containing oligonucleotides (15-22-mers) have been shown to be effectively against influenza A viruses. The versatility and potency of nucleic acid-based drugs make them potential drug candidates which could be used in conjunction with existing antiviral drugs to combat seasonal or pandemic influenza virus infections.
Type: Review
Title: Recent developments in peptide-based cellular delivery of nucleic acids
Authors: Sandra Veldhoen, Sandra D. Laufer and Tobias Restle
Affiliations: Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Institute of Molecular Medicine, Ratzeburger Allee 160, 23538 Lübeck, Germany
Type: Review
Title: MicroRNA: A Potential Therapeutic Target and Intervention Tool
Authors: Zhen Liu, Alhousseynou Sall and Decheng Yang
Affiliations: Department of Pathology and Laboratory Medicine, The James Hogg iCapture Center, University of British Columbia, Vancouver, Canada
Abstract: MicroRNAs (miRNAs) are a class of 20 to 24-nt non-coding RNAs that post-transcriptionally regulate target mRNA by imperfect base-pairing with the 3’-untranslated region (3UTR) or other targets to inhibit translation or RNA stability. To date, more than 460 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs.
Besides their essential physiological role in mammalian development and tissue identity, their significance in human disease is just beginning to be disclosed. Accumulating evidence has linked the deregulated expression patterns of miRNAs to a variety of diseases, such as cancer, cardiovascular diseases and viral infections. Studies in human cancer indicate different individual miRNAs can act as either classical tumor suppressor or oncogenes, revealing the potential of phenotype recovery through miRNA intervention. Differentially regulation of cardiac specific miRNAs, e.g. the primarily miR-1 and miR-133, has also shown to be correlated with cardiac hypertrophy and other heart diseases. Some viruses not only encode their own miRNA targeting viral and cellular genes for regulating latency and avoiding host immune response, but also may take the advantage to exploit cellular miRNA machinery for its own replication, thereby possibly contributing to their tissue tropism, one of the striking example is the liver enriched miR-22 bind to 5’UTR of HCV and promotes its replication.
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, adding to the routinely used nucleic acid-based gene-silencing molecules such as siRNAs. In this regard, different types of modified antisense oligonucleotides, including 2’-OMe, 2’-MOE and LNA that are complementary to mRNA targets, have shown certain success of inhibiting specific endogenous miRNAs both in vitro and in vivo. Alternatively, synthetic mRNAs that contain the binding sites of miRNA can work as “decoy” or “miRNA sponge” to inhibit the function of specific miRNA. On the other hand, to overexpress specific miRNAs, various miRNA expression vectors and double-stranded miRNA mimetics have been experimentally validated. miRNA expression vectors with a pol II promoter have shown the promise of tissue-specific and inducible expression. Endogenous precursor miRNAs have also been used as scaffolds for the expression of RNA interference, which exhibited the advantage on specificity and efficacy over common short hairpin RNA. Artificial miRNAs can also be designed for specific target sets or with modulated specificity. In this article we will review the recent progress on this emerging technology as a powerful tool for gene regulation studies and as a rationale strategy for development of therapeutics. In addition, the limitations and challenges on the potential application of these miR-based interventions will also be discussed.
Type: Review
Title: Enhanced allelic discrimination ability of a Locked Nucleic Acid attached at the 3'-end of oligonucleotide
Authors: Yuichi Michikawa, Tomo Suga, Yoshimi Ohtsuka, Mayumi Iwakawa, Takashi Imai
Affiliation: RadGenomics Project, Research Center for Charged Particle Therapy National Institute of Radiological Sciences, Japan
E-mail: y_michi@nirs.go.jp
Manuscript ID: IJMS-20-14
Type: Review
Title:Peptide-based strategy for ex-vivo and in vivo delivery of nucleic acids and derivatives
Authors: L. Crombez and Gilles Divita
Affiliations: CRBM - CNRS -FRE-2593, Molecular Biophysics & Therapeutics, 1919 route de Mende, 34293 Montpellier cedex 5, FRANCE; Tel: + 33 (0)4 67 61 33 92; Fax: 33 (0)4 67 52 15 59; E-mail : gilles.divita@crbm.cnrs.fr
Abstract: The major obstacle to clinical development of most of the nucleic acid-based strategies, including short interfering RNAs, is their poor cellular uptake and bioavailability. Although, several viral and non-viral strategies have been proposed to improve nucleic acids delivery their applications in vivo remain a major challenge. Several new technologies have been designed to improve cellular uptake of therapeutic molecules, including cell-penetrating peptides (CPPs), which represent a new and innovative concept to bypass the problem of bioavailability of drugs. Two CPP-strategies have been described so far, the first one requires chemical linkage between the drug and the carrier for cellular drug internalization and the second is based on the formation of stable complexes with drugs depending on their chemical nature. We have developed a new strategy, based on a short amphipathic peptides, MPG/PEP, that are able to form stable nanoparticles with nucleic acids and can efficiently deliver siRNA in a fully biologically active form into a variety of cell lines and in vivo. This short review will discuss the mechanism and the potency of the non-covalent peptide-based strategy for nucleic acid and derivative delivery both in vitro and in vivo.
Manuscript ID: IJMS-20-15
Type: Review
Title: Nucleic Acid Derived Indices in Marine Ecology
Authors: Maria Alexandra Chícharo
Affiliations: CCMAR/University of Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; E-mail: mchichar@ualg.pt; URL: http://w3.ualg.pt/~mchichar/
Abstract: Some of most used indices in marine ecology are nucleic acids derived indices. They can be divided in three target levels: 1) at organism level indices, such as RNA/DNA ratios, DNA/dry weight RNA/protein, 2) at population level as starvation incidence, and 3) community level such as exergy indices. The nucleic acids derived indices have been applied with success as indicators of nutritional condition, well been and growth in aquatic invertebrates and fishes. They are also useful as stress indicators of anthropogenic impacts in marine population and communities, such as dredge fisheries or eutrophication. The paper will also include a general characterization of most used nucleic acid derived indices in marine ecology, a description of the methodology and also advantages and limitations of them.
Manuscript ID: IJMS-20-16
Type: Review
Title: Nucleic Acid Derived Indices in Marine Ecology
Authors: N. F. Azevedo 1,2, C. Almeida 1,2, C. W. Keevil 2 and M. J. Vieira 1,*
Affiliations: 1 1IBB - Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar 4710-057, Braga, Portugal 2 2Environmental Healthcare Unit, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, United Kingdom; * Author to whom correspondence should be addressed; E-Mail: mjv@deb.uminho.pt
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 probes are then assessed in terms of theoretical sensitivity and specificity. In addition, a list of what remains to be done to further impose this method as a gold-standard for the whole-cell detection of microorganisms in different settings is presented.
Manuscript ID: IJMS-20-17
Type: Review
Title: Key RNA labeling technologies to tackle sizeable problems in structural biology
Authors: Kwaku T. Dayie
Affiliations: Lerner Research Institute, Department of Molecular Genetics and Center for Structural Biology, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH, 44195
Abstract: The ability to adopt complex three-dimensional (3D) structures that can rapidly interconvert between multiple functional states (folding and dynamics) is key for the proper functioning of RNAs. Consequently, it has become axiomatic that 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 (NA) promises to revolutionarize NA structural biology in this postgenomic era. We, therefore, critically assess here various methods for introducing probes into NA for structural, functional, and biotechnological applications. The probes surveyed include non-radioactive stable isotopes (2H, 13C, 15N, 19F, 77Se) and photo-stable fluorophores. Incorporation of these probes using improved RNA ligation strategies promise to change the landscape of structural biology of supramacromolecules probed by biophysical tools such as NMR spectroscopy, X-ray crystallography, Fluorescence and Raman spectroscopy. Finally, we outline some of the structural and dynamic problems that could be amenable to these technological advances.
Keywords: dynamics, FRET, isotopic labeling, ligation, Mass Spectrometry, NMR, Raman, RNA dynamics and folding and structure, X-ray crystallography.
Manuscript ID: IJMS-20-19
Type: Full Research Paper
Title: Designs and efficacies of broad-spectrum and virus-specific approaches using nucleic acid-based agents against influenza A viruses
Authors: Jonathan Wong
Affiliations: Molecular Biology Group, Biotechnology Section, Defence R&D Canada – Suffield, Box 4000 Main Station, Medicine Hat, Alberta, Canada T1A 8K6
Abstract: The global increases in the number of influenza A virus isolates resistant to amantadine and tamiflu undermine our ability to defend against potential influenza pandemics. There are compelling reasons to fast track research and development of novel antiviral agents which can protect against drug-resistant and potentially pandemic strains of deadly influenza viruses. Nucleic acid-based drugs represent a promising class of antiviral agents that could play a role in the prevention and treatment of influenza virus infections. Antisense oligonucleotides designed to inhibit the expressions of key virus proteins (nucleoprotein, heamagglutinin and polymerase) have been designed and are found to be therapeutically effective against influenza A viruses in both tissue culture and animal studies. Gene-silencing approaches such as antisense and small interfering RNA are highly sequence specific and their efficacies can be compromised by antigenic shifts and drifts in virus genes. Alternatively, nucleic acids such as ds RNA and oligonucleotides containing unmethylated CpG motifs can be designed to elicit antiviral immunity via the toll-like receptor (TLR-3 and -9, respectively) activation pathways. Efficacy studies in mice have shown that ds RNA such as poly ICLC can provide effective and broad-spectrum protection against lethal challenges against various strains of influenza A virus, including seasonal and avian H5N1. Similarly, CpG-containing oligonucleotides (15-22-mers) have been shown to be effectively against influenza A viruses. The versatility and potency of nucleic acid-based drugs make them potential drug candidates which could be used in conjunction with existing antiviral drugs to combat seasonal or pandemic influenza virus infections.
Type: Review
Title: Recent developments in peptide-based cellular delivery of nucleic acids
Authors: Sandra Veldhoen, Sandra D. Laufer and Tobias Restle
Affiliations: Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Institute of Molecular Medicine, Ratzeburger Allee 160, 23538 Lübeck, Germany
Type: Review
Title: MicroRNA: A Potential Therapeutic Target and Intervention Tool
Authors: Zhen Liu, Alhousseynou Sall and Decheng Yang
Affiliations: Department of Pathology and Laboratory Medicine, The James Hogg iCapture Center, University of British Columbia, Vancouver, Canada
Abstract: MicroRNAs (miRNAs) are a class of 20 to 24-nt non-coding RNAs that post-transcriptionally regulate target mRNA by imperfect base-pairing with the 3’-untranslated region (3UTR) or other targets to inhibit translation or RNA stability. To date, more than 460 human miRNAs have been experimentally identified, and estimated to regulate more than one third of cellular messenger RNAs.
Besides their essential physiological role in mammalian development and tissue identity, their significance in human disease is just beginning to be disclosed. Accumulating evidence has linked the deregulated expression patterns of miRNAs to a variety of diseases, such as cancer, cardiovascular diseases and viral infections. Studies in human cancer indicate different individual miRNAs can act as either classical tumor suppressor or oncogenes, revealing the potential of phenotype recovery through miRNA intervention. Differentially regulation of cardiac specific miRNAs, e.g. the primarily miR-1 and miR-133, has also shown to be correlated with cardiac hypertrophy and other heart diseases. Some viruses not only encode their own miRNA targeting viral and cellular genes for regulating latency and avoiding host immune response, but also may take the advantage to exploit cellular miRNA machinery for its own replication, thereby possibly contributing to their tissue tropism, one of the striking example is the liver enriched miR-22 bind to 5’UTR of HCV and promotes its replication.
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, adding to the routinely used nucleic acid-based gene-silencing molecules such as siRNAs. In this regard, different types of modified antisense oligonucleotides, including 2’-OMe, 2’-MOE and LNA that are complementary to mRNA targets, have shown certain success of inhibiting specific endogenous miRNAs both in vitro and in vivo. Alternatively, synthetic mRNAs that contain the binding sites of miRNA can work as “decoy” or “miRNA sponge” to inhibit the function of specific miRNA. On the other hand, to overexpress specific miRNAs, various miRNA expression vectors and double-stranded miRNA mimetics have been experimentally validated. miRNA expression vectors with a pol II promoter have shown the promise of tissue-specific and inducible expression. Endogenous precursor miRNAs have also been used as scaffolds for the expression of RNA interference, which exhibited the advantage on specificity and efficacy over common short hairpin RNA. Artificial miRNAs can also be designed for specific target sets or with modulated specificity. In this article we will review the recent progress on this emerging technology as a powerful tool for gene regulation studies and as a rationale strategy for development of therapeutics. In addition, the limitations and challenges on the potential application of these miR-based interventions will also be discussed.
Type: Review
Title: Enhanced allelic discrimination ability of a Locked Nucleic Acid attached at the 3'-end of oligonucleotide
Authors: Yuichi Michikawa, Tomo Suga, Yoshimi Ohtsuka, Mayumi Iwakawa, Takashi Imai
Affiliation: RadGenomics Project, Research Center for Charged Particle Therapy National Institute of Radiological Sciences, Japan
E-mail: y_michi@nirs.go.jp
Published Papers:
Zhiqiang Liang 1,2, Juan Zhang 2, Lihua Wang 2,*, Shiping Song 2 , Chunhai Fan 2 and Genxi Li 1,*
1 Department of Biochemistry, Nanjing University, Jiangsu 210093, China; E-mails: genxili@nju.edu.cn, suyuanyuan@sinap.ac.cn
2 Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; E-mails: suyuanyuan@sinap.ac.cn, wanglihua@sinap.ac.cn, songshiping@sinap.ac.cn , fchh@sinap.ac.cn
* Authors to whom correspondance should be addressed: E-mails: genxili@nju.edu.cn, wanglihua@sinap.ac.cn
Received: 18 April 2007; in Revised Form: 11 May 2007 / Accepted: 15 May 2007 / Published: 13 June 2007
Full Research Paper: Effects of Ultracentrifugation on Synthesis of Gold Nanoparticles and their Application in DNA Self-assembly and Biodetection
Int. J. Mol. Sci. 2007, 8, 526-532 (PDF format, 654 K)
Jun Huang 1, Qing-Dong Huang 1, Ji Zhang 1, Li-Hong Zhou 1, Qiang-Lin Li 1, Kun Li 1, Ning Jiang 2, Hong-Hui Lin 2,*, Jiang Wu 1,* and Xiao-Qi Yu 1, 3,*
1 Department of Chemistry, Key Laboratory of Green Chemistry and Technology (Ministry of Education), Sichuan University, Chengdu, 610064, P. R. China
2 Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, Sichuan, 610064, P. R. China
3 State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P. R .China
* Authors to whom correspondance should be addressed: Fax: +86 28 85415886; E-mail: xqyu@tfol.com
Received: 6 March 2007; in Revised Form: 6 June 2007 / Accepted: 14 June 2007 / Published: 9 July 2007
Full Research Paper: Dinuclear Zinc (II) Complexes of Macrocyclic Polyamine Ligands Containing an Imidazolium Bridge: Synthesis, Characterization, and Their Interaction with Plasmid DNA
Int. J. Mol. Sci. 2007, 8, 606-617 (PDF format, 164 K)
Zhiqiang Liang 1,2, Ruojun Lao 2, Jing Wang 1,2, Yongbiao Liu 3, Lihua Wang 2, Qing Huang 2, Shiping Song 2,*, Genxi Li 1,* and Chunhai Fan 2
1 Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China; E-mail: genxili@nju.edu.cn
2 Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China; E-mail: spsong@sinap.ac.cn (for Shiping Song); fchh@sinap.ac.cn (for Chunhai Fan)
3 The People’s Hospital of Jiangsu Province, Nanjing 210029, P. R. China
* Author to whom correspondance should be addressed; Tel: +86 21 59554607; Fax: +86 21 59556902; E-mail: spsong@sinap.ac.cn
Received: 31 May 2007 /in Revised Form: 29 June 2007/ Accepted: 13 July 2007/ Published: 23 July 2007
Full Research Paper: Solubilization of Single-walled Carbon Nanotubes with Single-stranded DNA Generated from Asymmetric PCR
Int. J. Mol. Sci. 2007, 8, 705-713 (PDF format, 395 K)
Jia Sheng and Zhen Huang *
Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
* Author to whom correspondence should be addressed: E-mail: huang@gsu.edu
Received: 3 December 2007 / Accepted: 25 February 2008 / Published: 12 March 2008
Review: Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography
Int. J. Mol. Sci. 2008, 9, 258-271 (PDF format, 304K)
Nicoletta Potenza 1, Loredana Moggio 2, Giovanna Milano 2, Vincenzo Salvatore 1, Benedetto Di Blasio 2, Aniello Russo 1 and Anna Messere 2,*
1 Department of Life Sciences, Second University of Naples, Via Vivaldi 43, I-81100 Caserta, Italy; Email: nicoletta.potenza@unina2.it (Nicoletta Potenza); vincenzo.salvatore@unina2.it (Vincenzo Salvatore); aniello.russo@unina2.it (Aniello Russo)
2 Department of Environmental Sciences, Second University of Naples, Via Vivaldi 43, I-81100 Caserta, Italy; E-mail: loredana.moggio@unina2.it (Loredana Moggio); giovanna.milano@unina2.it (Giovanna Milano); anna.messera@unina2.it (Anna Messere)
* Author to whom correspondance should be addressed; E-Mail: anna.messere@unina2.it
Received: 13 December 2007; in revised form: 29 February 2008 / Accepted: 29 February 2008 / Published: 12 March 2008
Full Research Paper: RNA Interference in Mammalia Cells by RNA-3’-PNA Chimeras
Int. J. Mol. Sci. 2008, 9, 299-315 (PDF format, 277K)
Da-Peng Zhang, Wei-Li Wu, Hai-Yan Long, Yun-Chun Liu, Zhou-Sheng Yang *
College of Chemistry and Materials Science, Anhui Key Laboratory of Chemo-Biosensing, Anhui Normal University, Wuhu 241000, P.R. China
*Author to whom correspondence should be addressed; E-mail: yzhoushe@mail.ahnu.edu.cn; Tel.: +86-553-3869303
Received: 3 December 2007; in revised form: 15 February 2008 / Accepted: 29 February 2008 / Published: 12 March 2008
Full Research Paper: Voltammetric Behavior of o-Nitrophenol and Damage to DNA
Int. J. Mol. Sci. 2008, 9, 316-326 (PDF format, 361K)
Laura Bonifacio 1, Frank C. Church 2 and Michael B. Jarstfer 1,*
1 Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
2 Departments of Pathology and Laboratory Medicine, Pharmacology and Medicine, Carolina Cardiovascular Biology Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
* Author to whom correspondence should be addressed; School of Pharmacy, Division of Medicinal Chemistry and Natural Products, CB # 7360, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7360, USA. Tel.: 919-966-6422; Fax: 919-966-0204; E-mail: jarstfer@unc.edu
Received: 23 January 2008; in revised form: 17 March 2007 / Accepted: 18 March 2008 / Published: 24 March 2008
Full Research Paper: Effect of Locked-Nucleic Acid on a Biologically Active G-Quadruplex. A Structure-Activity Relationship of the Thrombin Aptamer
Int. J. Mol. Sci. 2008, 9, 422-433 (PDF format, 271K)
Kathryn Schallhorn 1,2, Micky Kim 1 and Pu Chun Ke 1,*
1 Laboratory of Single-Molecule Biophysics and Polymer Physics, Clemson University, Clemson, SC 29634-0978, USA
2 Carl Zeiss MicroImaging, Inc. One Zeiss Drive, Thornwood, NY 10594, USA
* Author to whom correspondence should be addressed. Fax: 864-656-0558; E-mail: pcke11@clemson.edu
Received: 21 December 2007; in revised form: 22 April 2008 / Accepted: 23 April 2008 / Published: 25 April 2008
Communication: A Single-Molecule Study on the Structural Damage of Ultraviolet Radiated DNA
Int. J. Mol. Sci. 2008, 9, 662-667 (PDF format, 540K)
Ke-Tai Guo, Gerhard Ziemer, Angela Paul, Hans P. Wendel *
Department of Thoracic, Cardiac and Vascular surgery, University Hospital Tuebingen, Tuebingen, Germany, Calwerstr.7/1, D72076 Tuebingen, Germany
* Author to whom correspondence should be addressed; E-mail: hp.wendel@uni-tuebingen.de
Review: CELL-SELEX: a Technology Comes of Age - Novel Perspectives of Aptamer-Based Therapeutics
Received: 18 December 2007; in revised form: 3 April 2008; Accepted: 10 April 2008 / Published: 25 April 2008
Int. J. Mol. Sci. 2008, 9, 668-678 (PDF format, 261K)
- Winssinger, N.; Harris, J. L. Microarray-based functional protein profiling using peptide nucleic acid-encoded libraries. Expert Rev. Proteom. 2005, 2, 937-947.
allergy; amide-bond formation;
antigene; antisense; antiviral activity; aptamer; asthma; avidin;
beacons; bioconjugation; biosensor; biotin; branched oligonucleotides;
capillary gel-electrophoresis; carbon-paste electrodes; cationic
liposomes; cellular uptake; cleaving DNAzyme; click chemistry;
colloidal gold nanoparticles; colorimetric detection; combinatorial
chemistry; copper(i)-catalyzed azide-alkyne; crossover molecules;
cycloadditions; density oligonucleotide arrays; Diels-Alder
bioconjugation; directed synthesis; disposable DNA; DNA microarrays;
DNA synthesis; DNA triple-helix; DNA-directed immobilization;
double-stranded DNA; double-stranded RNA; drug-delivery;
electrochemical detection; electrochemical stripping detection;
fluorescent oligonucleotides; gene delivery; gold electrode; gold
surfaces; HCMV; HIV; HSV; human telomerase;
human-immunodeficiency-virus; hybridization; immobilization;
intracellular delivery ; in-vitro selection; light-up probes; LNA;
locked nucleic-acids; magnet assisted transfection; magnetic gene
transfection; magnetic nanoparticles ; mass-spectrometry; microarray;
molecular recognition; morpholino analogues; nanoparticles; NF-kappa-b;
nucleic-acid based technology; nucleobases; nucleosides; nucleotides;
oligonucleotide dendrimers; oligonucleotide synthesis; on-column
conjugation; peptide nucleic acid; phosphorothioate
oligodeoxynucleotides; ph-sensitive liposomes; plasmid-DNA; PNA; PNA
molecular beacons; reversible polymers; RNA interference; RNA
liposomes; RNA synthesis; self-assembled monolayers (SAM);
self-assembly; sensor; short interfering RNA; shRNA; single-nucleotide
polymorphisms; siRNA; site-specific modification; small interfering
RNA; SNP ; streptavidin; surface-plasmon resonance; switching signaling
aptamers; synthesis; templated organic synthesis; transcription factor;
viral vectors; voltammetry; walled carbon nanotubes
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Updated on 24 April 2008