66 results match your criteria Artificial DNA PNA & XNA[Journal]


General Recognition of U-G, U-A, and C-G Pairs by Double-Stranded RNA-Binding PNAs Incorporated with an Artificial Nucleobase.

Biochemistry 2019 Mar 1;58(10):1319-1331. Epub 2019 Mar 1.

Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.

Chemically modified peptide nucleic acids (PNAs) show great promise in the recognition of RNA duplexes by major-groove PNA·RNA-RNA triplex formation. Triplex formation is favored for RNA duplexes with a purine tract within one of the RNA duplex strands, and is severely destabilized if the purine tract is interrupted by pyrimidine residues. Here, we report the synthesis of a PNA monomer incorporated with an artificial nucleobase S, followed by the binding studies of a series of S-modified PNAs. Read More

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http://dx.doi.org/10.1021/acs.biochem.8b01313DOI Listing
March 2019
1 Read
3.015 Impact Factor

Single layer colloid centrifugation technique improves motility, viability and chromatin integrity of ram spermatozoa after thawing.

Cryobiology 2019 Feb 4;86:77-83. Epub 2018 Dec 4.

Clinic for Reproduction and Large Animals, University of Ljubljana, Vet Faculty, Ljubljana, Slovenia.

The cell membrane of ram spermatozoa is more sensitive to the freezing process than in other species due to its composition. As a result, the quality and viability of frozen thawed ram spermatozoa are often poor, which together with the specific structure of the ewe's cervix are the main reasons for lower fertility in ewes after intracervical insemination. In the present study we investigated the effects of semen centrifugation through a single layer of a species-specific colloid (Androcoll-O) on post-thaw quality of ram spermatozoa. Read More

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http://dx.doi.org/10.1016/j.cryobiol.2018.12.001DOI Listing
February 2019
4 Reads

Oligonucleotide Determination via Peptide Nucleic Acid Macromolecular Imprinting in an Electropolymerized CG-Rich Artificial Oligomer Analogue.

ACS Appl Mater Interfaces 2018 Aug 9;10(33):27562-27569. Epub 2018 Aug 9.

Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland.

We devised and fabricated a chemosensor for determination of the genetically relevant 5'-GCGGCGGC-3' (G = guanine; C = cytosine) oligonucleotide. For that, we simultaneously electrosynthesized and electrode-immobilized a sequence-defined octakis(2,2'-bithien-5-yl) DNA hybridizing probe using both a "macromolecular imprinting in polymer strategy" and a sequence-programmable peptide nucleic acid (PNA) template. With electrochemical impedance spectroscopy (EIS) and surface plasmon resonance (SPR) transductions under stagnant-solution and flow injection analysis (FIA) conditions, respectively, we determined the above oligonucleotide with 200-pM EIS limit of detection. Read More

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http://dx.doi.org/10.1021/acsami.8b09296DOI Listing
August 2018
3 Reads

Single-Molecule, Real-Time Dissecting of Peptide Nucleic Acid-DNA Duplexes with a Protein Nanopore Tweezer.

Anal Chem 2018 06 6;90(12):7682-7690. Epub 2018 Jun 6.

Department of Physics , Alexandru I. Cuza University , Iasi 700506 , Romania.

Peptide nucleic acids (PNAs) are artificial, oligonucleotides analogues, where the sugar-phosphate backbone has been substituted with a peptide-like N-(2-aminoethyl)glycine backbone. Because of their inherent benefits, such as increased stability and enhanced binding affinity toward DNA or RNA substrates, PNAs are intensively studied and considered beneficial for the fields of materials and nanotechnology science. Herein, we designed cationic polypeptide-functionalized, 10-mer PNAs, and demonstrated the feasible detection of hybridization with short, complementary DNA substrates, following analytes interaction with the vestibule entry of an α-hemolysin (α-HL) nanopore. Read More

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http://dx.doi.org/10.1021/acs.analchem.8b01568DOI Listing

Variation in post-thaw sperm quality of white-tailed deer bucks (Odocoileus virginianus) during rut.

Anim Reprod Sci 2018 May 19. Epub 2018 May 19.

Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, 61802, United States. Electronic address:

White-tailed deer farming is a growing industry in the United States, with breeding operations contributing significantly to the industry's economic impact. Artificial insemination with frozen semen allows for selection and dissemination of valuable genetics, yet surprisingly little is known regarding the best time throughout rut to perform semen cryopreservation. The objective of this study was to compare semen quality following cryopreservation of white-tailed deer bucks collected early in the breeding season (September, n = 6), at peak rut (December, n = 8), and late season (March, n = 7). Read More

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http://dx.doi.org/10.1016/j.anireprosci.2018.05.014DOI Listing
May 2018
1.510 Impact Factor

A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

Biochim Biophys Acta Gene Regul Mech 2018 Feb 31;1861(2):158-166. Epub 2018 Jan 31.

Department of Biology, Stanford University, Stanford, CA 94305-5020, United States. Electronic address:

The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. Read More

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http://dx.doi.org/10.1016/j.bbagrm.2017.12.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820110PMC
February 2018
1 Read

Acetyl-L-carnitine: An effective antioxidant against cryo-damage on human spermatozoa with asthenospermia.

J Huazhong Univ Sci Technolog Med Sci 2017 Dec 21;37(6):915-921. Epub 2017 Dec 21.

Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, 430060, China.

A variety of natural and artificial cryoprotectant extenders have been explored to enhance sperm recovery following cryopreservation-thawing process. The current investigation is aimed at evaluating the effect of acetyl-L-carnitine on human spermatozoa and reactive species oxygen (ROS) level after freezing-thawing process. The spermatozoa were collected from 35 male patients diagnosed as having asthenospermia. Read More

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http://dx.doi.org/10.1007/s11596-017-1827-4DOI Listing
December 2017
6 Reads

DNA G-Wire Formation Using an Artificial Peptide is Controlled by Protease Activity.

Molecules 2017 Nov 16;22(11). Epub 2017 Nov 16.

Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.

The development of a switching system for guanine nanowire (G-wire) formation by external signals is important for nanobiotechnological applications. Here, we demonstrate a DNA nanostructural switch (G-wire <--> particles) using a designed peptide and a protease. The peptide consists of a PNA sequence for inducing DNA to form DNA-PNA hybrid G-quadruplex structures, and a protease substrate sequence acting as a switching module that is dependent on the activity of a particular protease. Read More

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http://dx.doi.org/10.3390/molecules22111991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6150327PMC
November 2017
2 Reads

Applications of PNA-Based Artificial Restriction DNA Cutters.

Molecules 2017 Sep 21;22(10). Epub 2017 Sep 21.

World Premier International (WPI) Research Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan.

More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In this article, recent progress of these man-made tools have been reviewed. Read More

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http://dx.doi.org/10.3390/molecules22101586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151779PMC
September 2017
6 Reads

Monolithic Peptide-Nucleic Acid Hybrid Functioning as an Artificial Microperoxidase.

Bioconjug Chem 2017 08 25;28(8):2031-2034. Epub 2017 Jul 25.

Department of Applied Chemistry, Faculty of Engineering, Kyushu University , 744 Motooka, Nishi-ku, Fukuoka, Japan.

A new peptide nucleic acid (PNA) with an installed peroxidase function has been developed. Fmoc solid phase peptide synthesis prepared a PNA hybrid (VQKCAQCHTVE-(CHO)CH-[PNA(T)]-G) that renders the microperoxidase backbone, followed by reconstitution with hemin. The resulting holocompound catalyzed the oxidation of 3,3',5,5'-tetramthylbenzidine by HO to 50% that of natural microperoxidase-11, whereas the apo-form and hemin gave no responses. Read More

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http://dx.doi.org/10.1021/acs.bioconjchem.7b00216DOI Listing
August 2017
7 Reads

Programmed Transfer of Sequence Information into a Molecularly Imprinted Polymer for Hexakis(2,2'-bithien-5-yl) DNA Analogue Formation toward Single-Nucleotide-Polymorphism Detection.

ACS Appl Mater Interfaces 2017 Feb 23;9(4):3948-3958. Epub 2017 Jan 23.

Institute of Physical Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland.

A new strategy of simple, inexpensive, rapid, and label-free single-nucleotide-polymorphism (SNP) detection using robust chemosensors with piezomicrogravimetric, surface plasmon resonance, or capacitive impedimetry (CI) signal transduction is reported. Using these chemosensors, selective detection of a genetically relevant oligonucleotide under FIA conditions within 2 min is accomplished. An invulnerable-to-nonspecific interaction molecularly imprinted polymer (MIP) with electrochemically synthesized probes of hexameric 2,2'-bithien-5-yl DNA analogues discriminating single purine-nucleobase mismatch at room temperature was used. Read More

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http://dx.doi.org/10.1021/acsami.6b14340DOI Listing
February 2017
5 Reads

Is it possible to study the kinetic parameters of interaction between PNA and parallel and antiparallel DNA by stopped-flow fluorescence?

J Photochem Photobiol B 2016 Oct 6;163:296-302. Epub 2016 Aug 6.

Molecular Biotechnology and Health Sciences Department, University of Torino, Via Quarello 15, 10135 Torino, Italy.

Peptide nucleic acids (PNAs) are among the most interesting and versatile artificial structural mimics of nucleic acids and exhibit peculiar and important properties (i.e. high chemical stability, and a high resistance to cellular enzymes and nucleases). Read More

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http://dx.doi.org/10.1016/j.jphotobiol.2016.08.007DOI Listing
October 2016

Novel Methodology for Rapid Detection of KRAS Mutation Using PNA-LNA Mediated Loop-Mediated Isothermal Amplification.

PLoS One 2016 21;11(3):e0151654. Epub 2016 Mar 21.

Department of Human Pathology, Wakayama Medical University, Wakayama, Japan.

Detecting point mutation of human cancer cells quickly and accurately is gaining in importance for pathological diagnosis and choice of therapeutic approach. In the present study, we present novel methodology, peptide nucleic acid-locked nucleic acid mediated loop-mediated isothermal amplification (PNA-LNA mediated LAMP), for rapid detection of KRAS mutation using advantages of both artificial DNA and LAMP. PNA-LNA mediated LAMP reactions occurred under isothermal temperature conditions of with 4 primary primers set for the target regions on the KRAS gene, clamping PNA probe that was complimentary to the wild type sequence and LNA primers complementary to the mutated sequences. Read More

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151654PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801409PMC
August 2016
11 Reads

Chemical modifications of artificial restriction DNA cutter (ARCUT) to promote its in vivo and in vitro applications.

Authors:
Makoto Komiyama

Artif DNA PNA XNA 2014 Dec;5(3):e1112457

a Life Science Center of Tsukuba Advanced Research Alliance; University of Tsukuba ; Tsukuba , Ibaraki , Japan.

Recently, completely chemistry-based tools for site-selective scission of DNA (ARCUT) have been prepared by combining 2 strands of pseudo-complementary PNA (pcPNA: site-selective activator) and a Ce(IV)-EDTA complex (molecular scissors). Its site-specificity is sufficient to cut the whole human genome at one predetermined site. In this first-generation ARCUT, however, there still remain several problems to be solved for wider applications. Read More

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http://dx.doi.org/10.1080/1949095X.2015.1112457DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5329899PMC
December 2014
5 Reads

Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques.

Bioconjug Chem 2015 Dec 12;26(12):2514-9. Epub 2015 Nov 12.

Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany.

A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. Read More

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http://dx.doi.org/10.1021/acs.bioconjchem.5b00534DOI Listing
December 2015
1 Read

Evaluation of dual-color fluorescence in situ hybridization with peptide nucleic acid probes for the detection of Mycobacterium tuberculosis and non-tuberculous mycobacteria in clinical specimens.

Ann Lab Med 2015 Sep;35(5):500-5

Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, Korea.

Background: Peptide nucleic acid (PNA) probes are artificial DNA analogues with a hydrophobic nature that can penetrate the mycobacterial cell wall. We evaluated a FISH method for simultaneous detection and identification of Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM) in clinical respiratory specimens using differentially labeled PNA probes.

Methods: PNA probes targeting the mycobacterial 16S ribosomal RNA were synthesized. Read More

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http://dx.doi.org/10.3343/alm.2015.35.5.500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510502PMC
September 2015
2 Reads

Sequence-specific RNA cleavage by PNA conjugates of the metal-free artificial ribonuclease tris(2-aminobenzimidazole).

Beilstein J Org Chem 2015 16;11:493-8. Epub 2015 Apr 16.

Institute for Organic Chemistry and Chemical Biology, Goethe Universität Frankfurt, Max-von-Laue-Straße 7, D-60438 Frankfurt am Main, Germany.

Tris(2-aminobenzimidazole) conjugates with antisense oligonucleotides are effective site-specific RNA cleavers. Their mechanism of action is independent of metal ions. Here we investigate conjugates with peptide nucleic acids (PNA). Read More

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http://dx.doi.org/10.3762/bjoc.11.55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4419560PMC
May 2015
1 Read

Imidazolo-dC metal-mediated base pairs: purine nucleosides capture two Ag(+) ions and form a duplex with the stability of a covalent DNA cross-link.

Chemistry 2014 Dec 21;20(49):16248-57. Epub 2014 Oct 21.

Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstraße 11, 48149 Münster (Germany), Fax: (+49) 251-53406857; Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastraße 7, 49069 Osnabrück (Germany).

8-Phenylimidazolo-dC ((ph) ImidC, 2) forms metal-mediated DNA base pairs by entrapping two silver ions. To this end, the fluorescent "purine" 2'-deoxyribonucleoside 2 has been synthesised and converted into the phosphoramidite 6. Owing to the ease of nucleobase deprotonation, the new Ag(+) -mediated base pair containing a "purine" skeleton is much stronger than that derived from the pyrrolo- [3,4-d]pyrimidine system ((ph) PyrdC, 1). Read More

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http://dx.doi.org/10.1002/chem.201404422DOI Listing
December 2014
8 Reads

PNA binding to the non-template DNA strand interferes with transcription, suggesting a blockage mechanism mediated by R-loop formation.

Mol Carcinog 2015 Nov 30;54(11):1508-12. Epub 2014 Aug 30.

Department of Biology, Stanford University, Stanford, California.

Peptide Nucleic Acids (PNAs) are artificial DNA mimics with superior nucleic acid binding capabilities. T7 RNA polymerase (T7 RNAP) transcription upon encountering PNA bound to the non-template DNA strand was studied in vitro. A characteristic pattern of blockage signals was observed, extending downstream from the PNA binding site, similar to that produced by G-rich homopurine-homopyrimidine (hPu-hPy) sequences and likely caused by R-loop formation. Read More

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http://dx.doi.org/10.1002/mc.22209DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4345152PMC
November 2015
3 Reads

Enhanced splice correction by 3', 5'-serinol and 2'-(ω-O-methylserinol) guarded OMe-RNA/DNA mixmers in cells.

Artif DNA PNA XNA 2013 Jul-Dec;4(3):77-83. Epub 2013 Dec 2.

Organic Chemistry Division; CSIR-National Chemical Laboratory; Pune, India.

Development of artificial nucleic acids for therapeutic applications warrants that the oligomers be endowed with high specificity, enzymatic stability and with no/reduced off-target effects. The balance between strength of the duplex with target RNA and enzyme stability is therefore the key factor for the designed modification. The chiral serinol derivative combines the attributes of amino- and methoxy- substitution when at 2'- position and at 3'- and 5'- ends, effectively balancing the duplex stability and resistance to hydrolytic enzymes. Read More

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http://dx.doi.org/10.4161/adna.27279DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3962517PMC
November 2014
8 Reads

Site-selective scission of human genome using PNA-based artificial restriction DNA cutter.

Methods Mol Biol 2014 ;1050:111-20

Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.

Site-selective scission of genomes is quite important for future biotechnology. However, naturally occurring restriction enzymes cut these huge DNAs at too many sites and cannot be used for this purpose. Recently, we have developed a completely chemistry-based artificial restriction DNA cutter (ARCUT) by combining a pair of pseudo-complementary PNA (pcPNA) strands (sequence recognition moiety) and Ce(IV)/EDTA complex (molecular scissors). Read More

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http://dx.doi.org/10.1007/978-1-62703-553-8_9DOI Listing
July 2014
4 Reads

Highly stable duplex formation by artificial nucleic acids acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) with acyclic scaffolds.

Chemistry 2013 Oct 23;19(42):14151-8. Epub 2013 Aug 23.

Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).

The stabilities of duplexes formed by strands of novel artificial nucleic acids composed of acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) building blocks were compared with duplexes formed by the acyclic glycol nucleic acid (GNA), peptide nucleic acid (PNA), and native DNA and RNA. All acyclic nucleic acid homoduplexes examined in this study had significantly higher thermal stability than DNA and RNA duplexes. Melting temperatures of homoduplexes were in the order of aTNA>PNA≈GNA≥SNA≫RNA>DNA. Read More

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http://doi.wiley.com/10.1002/chem.201301578
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http://dx.doi.org/10.1002/chem.201301578DOI Listing
October 2013
7 Reads

Multitasking water-soluble synthetic G-quartets: from preferential RNA-quadruplex interaction to biocatalytic activity.

Chemistry 2013 Sep 6;19(38):12739-47. Epub 2013 Aug 6.

Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR6302, 9, Avenue Alain Savary, 21000 Dijon (France), Fax: (+33) 380-396-117.

Natural G-quartets, a cyclic and coplanar array of four guanine residues held together through a Watson-Crick/Hoogsteen hydrogen-bond network, have received recently much attention due to their involvement in G-quadruplex DNA, an alternative higher-order DNA structure strongly suspected to play important roles in key cellular events. Besides this, synthetic G-quartets (SQ), which artificially mimic native G-quartets, have also been widely studied for their involvement in nanotechnological applications (i.e. Read More

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http://dx.doi.org/10.1002/chem.201300791DOI Listing
September 2013
1 Read

Digitizing humanity.

Artif DNA PNA XNA 2013 Apr-Jun;4(2):37-8

The application of ex vivo synthetic DNA as a high capacity information storage medium is well documented. Herein, we consider the potential for synthetic DNA to be incorporated as part of the human genome; providing a definitive, accessible, in vivo database of patient history. Read More

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771996PMC
March 2014
1 Read

PNA-NLS conjugates as single-molecular activators of target sites in double-stranded DNA for site-selective scission.

Org Biomol Chem 2013 Aug;11(32):5233-8

Life Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8577, Japan.

Artificial DNA cutters have been developed by us in our previous studies by combining two strands of pseudo-complementary peptide nucleic acid (pcPNA) with Ce(IV)-EDTA-promoted hydrolysis. The pcPNAs have two modified nucleobases (2,6-diaminopurine and 2-thiouracil) instead of conventional A and T, and can invade double-stranded DNA to activate the target site for the scission. This system has been applied to site-selective scissions of plasmid, λ-phage, E. Read More

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http://dx.doi.org/10.1039/c3ob40947cDOI Listing
August 2013
11 Reads

New calix[4]arene derivatives as ionophores in polymeric membrane electrodes for Ag(I): comparative selectivity studies and detection of DNA hybridization.

Talanta 2013 Feb 27;105:1-7. Epub 2012 Nov 27.

Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.

Four calix[4]arene derivatives containing various donor atoms and different topology (L1-L4) have been synthesized and used as neutral ionophores to fabricate silver ion selective electrodes (Ag-ISEs) which were characterized in terms of their potentiometric selectivities and complex formation constants. The ionophore L2 having two nitrogen and two sulfur donors showed stronger interactions with Ag(+) and the highest selectivity coefficient towards Ag(+). The best membrane electrode was prepared from L2 and used to fabricate silver ion selective microelectrodes (Ag-ISμEs) which could detect silver ions in 1000 μL samples with detection limit around 1 μM using sodium ion microelectrodes as a pseudo reference electrode. Read More

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http://dx.doi.org/10.1016/j.talanta.2012.11.046DOI Listing
February 2013
5 Reads

PNA-peptide assembly in a 3D DNA nanocage at room temperature.

J Am Chem Soc 2013 May 12;135(18):6985-93. Epub 2013 Apr 12.

Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, Arizona 85287, United States.

Proteins and peptides fold into dynamic structures that access a broad functional landscape; however, designing artificial polypeptide systems is still a great challenge. Conversely, DNA engineering is now routinely used to build a wide variety of 2D and 3D nanostructures from hybridization based rules, and their functional diversity can be significantly expanded through site specific incorporation of the appropriate guest molecules. Here we demonstrate a new approach to rationally design 3D nucleic acid-amino acid complexes using peptide nucleic acid (PNA) to assemble peptides inside a 3D DNA nanocage. Read More

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http://dx.doi.org/10.1021/ja400762cDOI Listing
May 2013
8 Reads

Templating effect in DNA proximity ligation enables use of non-bioorthogonal chemistry in biological fluids.

Artif DNA PNA XNA 2012 Jul 1;3(3):123-8. Epub 2012 Jul 1.

Department of Chemistry, Center for Cell and Genome Science, University of Utah, Salt Lake City, UT USA.

Here we describe the first example of selective reductive amination in biological fluids using split aptamer proximity ligation (StAPL). Utilizing the cocaine split aptamer, we demonstrate small-molecule-dependent ligation that is dose-dependent over a wide range of target concentrations in buffer, human blood serum and artificial urine medium. We explore the substrate binding preferences of the split aptamer and find that the cinchona alkaloids quinine and quinidine bind to the aptamer with higher affinity than cocaine. Read More

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http://dx.doi.org/10.4161/adna.23842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581511PMC

Triplex-forming peptide nucleic acids induce heritable elevations in gamma-globin expression in hematopoietic progenitor cells.

Mol Ther 2013 Mar 22;21(3):580-7. Epub 2013 Jan 22.

Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA.

Potentiating homologous recombination using triplex-forming peptide nucleic acids (PNAs) can be used to mediate targeted sequence editing by donor DNAs and thereby induce functional gene expression to supplant non-functional counterparts. Mutations that disrupt the normal function of the β-globin subunit cause hemoglobinopathies such as sickle cell disease and β-thalassemias. However, expression of the functional γ-globin subunit in adults, a benign condition called hereditary persistence of fetal hemoglobin (HPFH), can ameliorate the severity of these disorders, but this expression is normally silenced. Read More

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http://dx.doi.org/10.1038/mt.2012.262DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3589157PMC
March 2013
14 Reads

Assessment of different functional parameters of frozen-thawed buffalo spermatozoa by using cytofluorimetric determinations.

Reprod Domest Anim 2013 Apr 27;48(2):317-24. Epub 2012 Jul 27.

Institute of Sciences of Food Production, ISPA, National Research Council, Bari, Italy.

Flow cytometry is a useful tool that provides an accurate, objective and rapid evaluation of semen quality. The use of this technique could significantly improve the quality of buffalo semen samples used in artificial insemination. This study was carried out to evaluate, by flow cytometry, frozen-thawed buffalo spermatozoa quality parameters such as sperm viability by SYBR-14/propidium iodide staining; mitochondrial function by JC-1 potentiometric probe; sperm chromatin stability (SCSA) by acridine orange; and acrosome reaction (AR) by FITC-PNA staining. Read More

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http://dx.doi.org/10.1111/j.1439-0531.2012.02152.xDOI Listing

Artificial DNA and surface plasmon resonance.

Artif DNA PNA XNA 2012 Apr-Jun;3(2):45-52. Epub 2012 Apr 1.

Dipartimento di Scienze Chimiche, Università di Catania, Catania, Italy.

The combined use of surface plasmon resonance (SPR) and modified or mimic oligonucleotides have expanded diagnostic capabilities of SPR-based biosensors and have allowed detailed studies of molecular recognition processes. This review summarizes the most significant advances made in this area over the past 15 years.   Functional and conformationally restricted DNA analogs (e. Read More

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http://www.tandfonline.com/doi/abs/10.4161/adna.21383
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http://dx.doi.org/10.4161/adna.21383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3429530PMC
April 2013
1 Read

Estimation of binding constants of peptide nucleic acid and secondary-structured DNA by affinity capillary electrophoresis.

Anal Chem 2012 Jun 5;84(12):5204-9. Epub 2012 Jun 5.

Bioengineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.

An affinity capillary electrophoresis method was developed to determine a binding constant between a peptide nucleic acid (PNA) and a hairpin-structured DNA. A diblock copolymer composed of PNA and polyethylene glycol (PEG) was synthesized as a novel affinity probe. The base sequence of the probe's PNA segment was complementary to a hairpin-structured region of a 60-base single-stranded DNA (ssDNA). Read More

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http://dx.doi.org/10.1021/ac301025mDOI Listing

Impedimetric detection of single-stranded PCR products derived from methicillin resistant Staphylococcus aureus (MRSA) isolates.

Biosens Bioelectron 2012 Apr 9;34(1):178-84. Epub 2012 Feb 9.

Division of Pathway Medicine, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, Scotland, UK.

Using electrochemical impedance spectroscopy (EIS) the sensitive and specific detection of the antibiotic resistance gene mecA has been demonstrated. The gene sequence was obtained from clinical Staphylococcus aureus isolates. Initially a mecA specific probe was selected from hybridisation tests with a 3' and 5' version of a previously published probe sequence. Read More

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http://linkinghub.elsevier.com/retrieve/pii/S095656631200058
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http://dx.doi.org/10.1016/j.bios.2012.01.040DOI Listing
April 2012
9 Reads

Artificial DNA structures.

Authors:
Peter E Nielsen

Artif DNA PNA XNA 2011 Apr;2(2):39

Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen, Denmark.

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http://dx.doi.org/10.4161/adna.2.2.17085DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166487PMC
April 2011
1 Read

Site-selective DNA hydrolysis induced by a metal-free peptide nucleic acid-cyclen conjugate.

Chem Commun (Camb) 2011 Oct 7;47(39):11059-61. Epub 2011 Sep 7.

Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu, 610064, PR China.

A metal-free artificial restriction DNA cutter which is composed of cyclen and classical peptide nucleic acid (PNA) was synthesized. Analysis of DNA cleavage products indicates the site-selective hydrolysis. Read More

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http://dx.doi.org/10.1039/c1cc14185fDOI Listing
October 2011
3 Reads

Natural - synthetic - artificial!

Authors:
Peter E Nielsen

Artif DNA PNA XNA 2010 Jul;1(1):58-59

Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen, Denmark.

The terms "natural," "synthetic" and "artificial" are discussed in relation to synthetic and artificial chromosomes and genomes, synthetic and artificial cells and artificial life. Read More

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http://dx.doi.org/10.4161/adna.1.1.12934DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109441PMC
July 2010
2 Reads

Introducing Artificial DNA: PNA & XNA.

Authors:
Peter E Nielsen

Artif DNA PNA XNA 2010 Jul;1(1)

Department of Cellular and Molecular Medicine; Faculty of Health Sciences; The Panum Institute; University of Copenhagen; Copenhagen, Denmark.

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http://dx.doi.org/10.4161/adna.1.1.12932DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109443PMC

Small RNAs hit a new target: Modulation of gene expression by targeting the non-coding sequences downstream from a gene.

Authors:
Vadim V Demidov

Artif DNA PNA XNA 2010 Oct;1(2):64-65

Global Prior Art, Inc.; Boston, MA USA.

The University of Texas researchers have recently discovered that small synthetic RNAs (sRNAs) that are complementary to sequences located 3'-outside of genes can efficiently modulate gene expression. These new findings significantly expand the transcription-regulatory potential of sRNAs, and they also may provide useful leads for other artificial nucleobase oligomers to target sequences beyond the 3' termini of mRNA. Read More

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http://dx.doi.org/10.4161/adna.1.2.13945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3116577PMC
October 2010

Artificial restriction DNA cutters to promote homologous recombination in human cells.

Curr Gene Ther 2011 Feb;11(1):38-45

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo, Japan.

Homologous recombination is almost the only way to modify the genome in a predetermined fashion, despite its quite low frequency in mammalian cells. It has been already reported that the frequency of this biological process can be notably increased by inducing a double strand break (DSB) at target site. This article presents completely chemistry-based artificial restriction DNA cutter (ARCUT) for the promotion of homologous recombination in human cells. Read More

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February 2011
2 Reads

Sperm chromatin structural integrity in normospermic boars is not related to semen storage and fertility after routine AI.

Theriogenology 2011 Jan 18;75(2):337-45. Epub 2010 Oct 18.

Unit for Reproductive Medicine of Clinics/Clinic for Pigs and Small Ruminants, University of Veterinary Medicine Hannover Foundation, Bünteweg 15, D-30559 Hannover, Germany.

Standard semen parameters are limited in their capacity to distinguish subfertile boars and to assess storage influences on liquid preserved boar semen. The evaluation of sperm chromatin structural integrity could have potential as a diagnostic tool in AI practice. This study assessed whether the determination of sperm DNA integrity adds a useful diagnostic tool for selection of boar ejaculates in routine AI procedure and assessment of storage effects in diluted semen. Read More

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http://dx.doi.org/10.1016/j.theriogenology.2010.09.004DOI Listing
January 2011
2 Reads

Gene targeting and expression modulation by peptide nucleic acids (PNA).

Authors:
Peter E Nielsen

Curr Pharm Des 2010 ;16(28):3118-23

Department of Cellular and Molecular Medicine, Faculty of Health Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, DK-2200, Copenhagen N, Denmark.

Peptide nucleic acids (PNA) are artificial structural mimics of nucleic acids capable of sequence specific hybridization to both RNA and DNA. Thus they have obvious potential as gene targeting agents for drug discovery approaches. An overview with emphasis on recent progress on RNA "interference" (antisense), targeting of duplex DNA and gene targeted repair and transcription interference using PNA, as well as on PNA delivery and potential PNA anti-infectives is given. Read More

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PNAzymes that are artificial RNA restriction enzymes.

J Am Chem Soc 2010 Jul;132(26):8984-90

Department of Biosciences and Nutrition, Karolinska Institutet, Novum, S-14183, Huddinge, Sweden.

DNA-cleaving restriction enzymes are well-known tools in biomedical and biotechnological research. There are, however, no corresponding enzymes known for RNA cleavage. There has been an ongoing development of artificial ribonucleases, including some attempts at sequence selectivity. Read More

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http://dx.doi.org/10.1021/ja1008739DOI Listing
July 2010
1 Read

A highly effective and long-lasting inhibition of miRNAs with PNA-based antisense oligonucleotides.

Mol Cells 2009 Oct 30;28(4):341-5. Epub 2009 Sep 30.

Panagene Inc., Daejeon, 305-345, Korea.

MiRNAs are non-coding RNAs that play a role in the regulation of major processes. The inhibition of miRNAs using antisense oligonucleotides (ASOs) is a unique and effective technique for the characterization and subsequent therapeutic targeting of miRNA function. Recent advances in ASO chemistry have been used to increase both the resistance to nucleases and the target affinity and specificity of these ASOs. Read More

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http://dx.doi.org/10.1007/s10059-009-0134-8DOI Listing
October 2009
4 Reads

Origin of high fidelity in target-sequence recognition by PNA-Ce(IV)/EDTA combinations as site-selective DNA cutters.

J Am Chem Soc 2009 Feb;131(7):2657-62

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.

Double-duplex invasion of pseudocomplementary peptide nucleic acid (pcPNA) is one of the most important strategies for recognizing a specific site in double-stranded DNA (Proc. Natl. Acad. Read More

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http://dx.doi.org/10.1021/ja808290eDOI Listing
February 2009
3 Reads

PNA-PEG modified silicon platforms as functional bio-interfaces for applications in DNA microarrays and biosensors.

Biomacromolecules 2009 Mar;10(3):489-96

Walter Schottky Institute, Technische Universität München, Garching, Germany.

The synthesis and characterization of two types of silicon-based biofunctional interfaces are reported; each interface bonds a dense layer of poly(ethylene glycol) (PEG(n)) and peptide nucleic acid (PNA) probes. Phosphonate self-assembled monolayers were derivatized with PNA using a maleimido-terminated PEG(45). Similarly, siloxane monolayers were functionalized with PNA using a maleimido-terminated PEG(45) spacer and were subsequently modified with a shorter methoxy-terminated PEG(12) ("back-filling"). Read More

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http://dx.doi.org/10.1021/bm801406wDOI Listing
March 2009
3 Reads

Development of artificial restriction DNA cutter composed of Ce(Iv)/EDTA and PNA.

Nucleosides Nucleotides Nucleic Acids 2007 ;26(10-12):1265-8

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Muguro-ku, Tokyo, Japan.

An artificial restriction enzyme, which we developed recently by combining Ce(IV)/EDTA and peptide nucleic acids, was used for PCR-free construction of a fusion protein. The fusion protein was successfully expressed in mammalian cells. This artificial DNA cutter can be also applied to site-selective scission of huge DNAs. Read More

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http://dx.doi.org/10.1080/15257770701528321DOI Listing

Site-selective hydrolysis of huge DNA by artificial restriction DNA cutter.

Nucleic Acids Symp Ser (Oxf) 2006 (50):265-6

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.

Genomic DNAs of lambda phage (48.5 kbp) and E. coli (4. Read More

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http://dx.doi.org/10.1093/nass/nrl132DOI Listing
August 2007
1 Read

Highly active artificial restriction enzyme composed of Ce(IV)/EDTA and PNA bearing phosphate group--relationship between the promotion by phosphate and the structure of invasion complex.

Nucleic Acids Symp Ser (Oxf) 2006 (50):255-6

Research center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.

Recently, we developed artificial restriction DNA cutter (ARCUT) composed of pseudo-complementary peptide nucleic acid (pcPNA) and Ce(IV)/EDTA complex (EDTA = ethylenediamine-N,N,N',N'-tetraacetate). Here we promoted the site-selective hydrolysis by attaching phosphate groups to the pcPNAs. The promotion by the phosphates increased with decreasing length of the gap-like site. Read More

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http://academic.oup.com/nass/article/50/1/255/1341834/Highly
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http://dx.doi.org/10.1093/nass/nrl127DOI Listing
August 2007
3 Reads

Manipulation of double-stranded DNA by artificial restriction enzyme composed of Ce(IV)/EDTA and PNA.

Nucleic Acids Symp Ser (Oxf) 2004 (48):279-80

Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan.

Through the invasion of pseudo-complementary PNA (pePNA) to double-stranded DNA, gap-like structures were formed at predetermined sites in both strands of PBR322 plasmid DNA. These gap-like sites were selectively hydrolyzed by Ce(IV)/EDTA complex, and two designed fragments were obtained. Furthermore, the scission fragment by this artificial restriction enzyme was successfully ligated with foreign DNA. Read More

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http://dx.doi.org/10.1093/nass/48.1.279DOI Listing
July 2007
2 Reads

Peptide nucleic acid conjugates: synthesis, properties and applications.

Curr Top Med Chem 2005 ;5(12):1119-31

Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA.

Artificial control of gene expression has great potential in the treatment of many human diseases, and peptide nucleic acids (PNAs) offer several potential advantages for silencing gene expression in mammalian cells. The pseudopeptide backbone of the PNA makes it resistant to enzymatic degradation, and PNAs bind complementary DNA and RNA with high affinity and specificity. PNAs are potentially leading agents for antigene and antisense therapeutics, but the application of PNAs in the in vivo setting is hampered by their poor intracellular delivery. Read More

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January 2006
2 Reads