Special Issue: Nucleic Acid Derivatives in Emerging Technologies

This 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]
Link to Special Issue on Nucleic Acids of Molecules

Editors

  

Guest Editor
Prof. Dr. Lajos Kovacs
Department of Medicinal Chemistry, Universtiy of Szeged
Dom ter 8, H-6720 Szeged, Hungary
E-Mail: [email protected]

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
E-Mail: [email protected]
http://www.life.uiuc.edu/biochem/f_gumport.html
Keywords: Nucleic Acid Enzymology, Protein-DNA Interactions
 
Call for Papers
 
Link to Special Issue on Nucleic Acids of Molecules
 
Published Papers
 
Open Access
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: [email protected], [email protected]
2 Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China; E-mails: [email protected], [email protected], [email protected] , [email protected]
* Authors to whom correspondance should be addressed: E-mails: [email protected], [email protected]
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)
 
Open Access
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: [email protected]
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)
 
Open Access
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: [email protected]
2 Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P. R. China; E-mail: [email protected] (for Shiping Song); [email protected] (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: [email protected]
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)
 
Open Access
Jia Sheng and Zhen Huang *
Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
* Author to whom correspondence should be addressed: E-mail: [email protected]
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)
 
Open Access
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: [email protected] (Nicoletta Potenza); [email protected] (Vincenzo Salvatore); [email protected] (Aniello Russo)
2 Department of Environmental Sciences, Second University of Naples, Via Vivaldi 43, I-81100 Caserta, Italy; E-mail: [email protected] (Loredana Moggio); [email protected] (Giovanna Milano); [email protected] (Anna Messere)
* Author to whom correspondance should be addressed; E-Mail: [email protected]
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)
  
Open Access  
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: [email protected]; 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)

Open Access
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: [email protected]
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)
 
Open Access
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: [email protected]
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)
 
Open Access
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: [email protected]
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)
 
Open Access
 Rudy J. Castellani 1,*, Akihiko Nunomura 2, Raj K. Rolston 3, Paula I. Moreira 4, Atsushi Takeda 5, George Perry 3,6 and Mark A. Smith 3,*
1 Department of Pathology, University of Maryland, Baltimore, Maryland, USA
2 Department of Neuropsychiatry, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Yamanashi, Japan
3 Department of Pathology, Case Western Reserve University, Cleveland, Ohio, USA
4 Center for Neuroscience and Cell Biology of Coimbra, University of Coimbra, Coimbra, Portugal
5 Department of Neurology, Tohoku University School of Medicine, Sendai, Japan
6 College of Sciences, University of Texas at San Antonio, San Antonio, Texas, USA
E-Mails: [email protected] (R. J. C.); [email protected] (A. N.); [email protected] (R. K. R.); [email protected] (P. I. M.); [email protected] (A. T.); [email protected] (G. P.); [email protected] (M. A. S.)
* Authors to whom correspondence should be addressed; E-mail: [email protected]; Tel.: +1-410-328-5422 (R.J.C.) and E-mail: [email protected]; Tel.: +1-216-368-3670 (M.A.S.)
Received: 25 April 2008; in revised form: 15 May 2008 / Accepted: 16 May 2008 / Published: 20 May 2008
Review: Sublethal RNA Oxidation as a Mechanism for Neurodegenerative Disease
Int. J. Mol. Sci. 2008, 9, 789-806 (PDF format, 292K); DOI: 10.3390/ijms9050789

Open Access
Zhen Liu, Alhousseynou Sall and Decheng Yang *
Department of Pathology and Laboratory Medicine, University of British Columbia, The Heart and Lung Institute, St. Paul’s Hospital, Vancouver, Canada
* Author to whom correspondence should be addressed; The James Hogg iCapture Center, University of British Columbia, St. Paul's Hospital, 1081 Burrard Street, Vancouver V6Z 1Y6, B.C., Canada; Tel.: (604)-682-2344 Ext 62872; Fax: (604)-806-9274; E-mail: [email protected]
Received: 7 April 2008; in revised form: 16 May 2008 / Accepted: 27 May 2008 / Published: 13 June 2008
Review: MicroRNA: an Emerging Therapeutic Target and Intervention Tool
Int. J. Mol. Sci. 2008, 9, 978-999 (PDF format, 281K); DOI: 10.3390/ijms9060978
 
Open Access
Barbara Gatto 1,*, Elena Vianini 1, Lorena Lucatello 1, Claudia Sissi 1, Danilo Moltrasio 2, Rodolfo Pescador 2, Roberto Porta 2 and Manlio Palumbo 1
1 Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
2 Gentium S.p.A., Piazza XX Settembre 2, 22079 Villa Guardia, Italy
* Author to whom correspondence should be addressed; E-mail: [email protected]
Received: 5 May 2008; in revised form: 6 June 2008 / Accepted: 10 June 2008 / Published: 20 June 2008
Article: Effective DNA Inhibitors of Cathepsin G by In Vitro Selection
Int. J. Mol. Sci. 2008, 9, 1008-1023 (PDF format, 293K); DOI: 10.3390/ijms9061008
 
Open Access
Francielle B. Silva 1, Sabrina N. Vieira 1, Luiz R. Goulart Filho 2, Julien F. C. Boodts 1, Ana G. Brito-Madurro 1 and João M. Madurro 1,*
1 Institute of Chemistry, Federal University of Uberlândia, Uberlândia, 38400-902, Brazil
2 Institute of Genetics and Biochemistry, Federal Univ. of Uberlândia, Uberlândia, 38400-902, Brazil
E-Mails: [email protected] (F. S.); [email protected] (S. V.); [email protected] (L. R.), [email protected] (J. B.); [email protected] (A. B-M.); [email protected] (J. M.)
* Author to whom correspondence should be addressed; Tel.: +55-(34)-3239-4442
Received: 2 April 2008; in revised form: 11 June 2008 / Accepted: 12 June 2008 / Published: 8 July 2008
Article: Electrochemical Investigation of Oligonucleotide-DNA Hybridization on Poly(4-Methoxyphenethylamine)
Int. J. Mol. Sci. 2008, 9, 1173-1187 (PDF format, 965K); DOI: 10.3390/ijms9071173
 
Open Access
Kwaku T. Dayie
Lerner Research Institute, Department of Molecular Genetics and Center for Structural Biology, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA
Tel.: +1-216-445-0637; Fax: +1-216-444-0512; Email: [email protected]; URL: http://www.lerner.ccf.org/molecbio/dayie/
Received: 7 April 2008: in revised form: 6 June 2008 / Accepted: 14 July 2008 / Published: 14 July 2008
Review: Key Labeling Technologies to Tackle Sizeable Problems in RNA Structural Biology
Int. J. Mol. Sci. 2008, 9, 1214-1240 (PDF format, 624K); DOI: 10.3390/ijms9071214
 
Open Access
Sandra Veldhoen 1,*, Sandra D. Laufer 2 and Tobias Restle 2
1 Department of Metabolomics, ISAS - Institute for Analytical Sciences, Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
2 Institut für Molekulare Medizin, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
* Author to whom correspondence should be addressed; E-mail: [email protected]
Received: 31 March 2008; in revised form: 4 June 2008 / Accepted: 14 July 2008 / Published: 16 July 2008
Review: Recent Developments in Peptide-Based Nucleic Acid Delivery
Int. J. Mol. Sci. 2008, 9, 1276-1320 (PDF format, 1347K); DOI: 10.3390/ijms9071276

Open Access
Maria Alexandra Chícharo * and Luis Chícharo
Centre of Marine Sciences, CCMAR, University of Algarve. Campus de Gambelas, 8005-139 Faro, Portugal. E-Mail: [email protected] (L. C.)
* Author to whom correspondence should be addressed; E-Mail: [email protected] (M. C.)
Received: 2 April 2008; in revised form: 6 August 2008 / Accepted: 7 August 2008 / Published: 20 August 2008
Review: RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology
Int. J. Mol. Sci. 2008, 9, 1453-1471 (PDF format, 264K); DOI: 10.3390/ijms9081453

Open Access
Mary E. Christopher* and Jonathan P. Wong
Defence Research & Development Canada – Suffield, Box 4000, Station Main, Medicine Hat, AB, Canada T1A 8K6. E-Mail: [email protected] (J. W.)
* Author to whom correspondence should be addressed; E-Mail: [email protected]
Received: 18 April 2008; in revised form: 21 August 2008 / Accepted: 29 August 2008 / Published: 1 September 2008
Review: Broad-Spectrum Drugs Against Viral Agents
Int. J. Mol. Sci. 2008, 9, 1561-1594 (PDF format, 235K); DOI: 10.3390/ijms9091561

Leading Review Papers

  1. Winssinger, N.; Harris, J. L. Microarray-based functional protein profiling using peptide nucleic acid-encoded libraries. Expert Rev. Proteom. 2005, 2, 937-947.
  2. Gothelf, K. V.; LaBean, T. H. DNA-programmed assembly of nanostructures. Org. Biomol. Chem. 2005, 3, 4023-4037.
  3. Bertram, J. MATra - Magnet assisted transfection: Combining nanotechnology and magnetic forces to improve intracellular delivery of nucleic acids. Curr. Pharmaceut. Biotechnol. 2006, 7, 277-285.
  4. Van Aerschot, A. Oligonucleotides as antivirals: Dream or realistic perspective? Antiviral Res. 2006, 71, 307-316.
  5. Herdewijn, P. The interplay between antiviral activity, oligonucleotide hybridisation and nucleic acids incorporation studies. Antiviral Res. 2006, 71, 317-321.
  6. Sel, S.; Henke, W.; Dietrich, A.; Herz, U.; Renz, H. Treatment of allergic asthma by targeting transcription factors using nucleic-acid based technologies. Curr. Pharm. Design 2006, 12, 3293-3304.
  7. Binder, W. H.; Kluger, C. Azide/alkyne-"click" reactions: Applications in material science and organic synthesis. Curr. Org. Chem. 2006, 10, 1791-1815.
  8. Babkina, S. S.; Budnikov, G. K. Electrochemical biosensors based on nucleic acids and their use in bioaffinity assays for determining DNA and its effectors. J. Anal. Chem. 2006, 61, 728-739.
  9. Karkare, S.; Bhatnagar, D. Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino. Appl. Microbiol. Biotechnol. 2006, 71, 575-586.
  10. Len, C.; Postel, D. Synthesis of 2',3'-didehydro-2',3'-dideoxynucleosides via nucleoside route. Curr. Org. Synth. 2006, 3, 261-281.
  11. Briones, C.; Martin-Gago, J. A. Nucleic acids and their analogs as nanomaterials for biosensor development. Curr. Nanosci. 2006, 2, 257-273.
  12. Navani, N. K.; Li, Y. F. Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol. 2006, 10, 272-281.
  13. Christopher, M. E.; Wong, J. P. Recent developments in delivery of nucleic acid-based antiviral agents. Curr. Pharm. Design 2006, 12, 1995-2006.
  14. Shakeel, S.; Karim, S.; Ali, A. Peptide nucleic acid (PNA) - a review. J. Chem. Technol. Biotechnol. 2006, 81, 892-899.
  15. Graham, D.; Enright, A. Cycloadditions as a method for oligonucleotide conjugation. Curr. Org. Synth. 2006, 3, 9-17.
  16. Loy, A.; Bodrossy, L. Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin. Chim. Acta 2006, 363, 106-119.
Keywords
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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