V V Demidov

Summary

Affiliation: Boston University
Country: USA

Publications

  1. pmc Specific versus nonspecific binding of cationic PNAs to duplex DNA
    Ayome Abibi
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Biophys J 86:3070-8. 2004
  2. pmc Fast complementation of split fluorescent protein triggered by DNA hybridization
    Vadim V Demidov
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 103:2052-6. 2006
  3. ncbi request reprint Rolling-circle amplification in DNA diagnostics: the power of simplicity
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Expert Rev Mol Diagn 2:542-8. 2002
  4. ncbi request reprint PNA and LNA throw light on DNA
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Trends Biotechnol 21:4-7. 2003
  5. ncbi request reprint Profluorescent protein fragments for fast bimolecular fluorescence complementation in vitro
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    Nat Protoc 1:714-9. 2006
  6. pmc Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:5953-8. 2002
  7. ncbi request reprint PD-loop technology: PNA openers at work
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Expert Rev Mol Diagn 1:343-51. 2001
  8. ncbi request reprint Earrings and padlocks for the double helix: topological labeling of duplex DNA
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Trends Biotechnol 21:148-51. 2003
  9. ncbi request reprint An artificial primosome: design, function, and applications
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Chembiochem 2:133-9. 2001
  10. ncbi request reprint Heavy isotopes to avert ageing?
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington St, Boston, MA 02215, USA
    Trends Biotechnol 25:371-5. 2007

Collaborators

Detail Information

Publications40

  1. pmc Specific versus nonspecific binding of cationic PNAs to duplex DNA
    Ayome Abibi
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Biophys J 86:3070-8. 2004
    ..This understanding is important for design of and manipulation with the DNA-binding polycationic ligands in general and PNA-based drugs in particular...
  2. pmc Fast complementation of split fluorescent protein triggered by DNA hybridization
    Vadim V Demidov
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 103:2052-6. 2006
    ..The ability of our EGFP system to respond quickly to DNA hybridization should be useful for detecting the kinetics of many other types of pairwise interactions both in vitro and in living cells...
  3. ncbi request reprint Rolling-circle amplification in DNA diagnostics: the power of simplicity
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Expert Rev Mol Diagn 2:542-8. 2002
    ..Underlying mechanisms, current controversies and principal advantages of rolling-circle amplification are also considered. Possible future directions for the further advancement of this diagnostic methodology are outlined...
  4. ncbi request reprint PNA and LNA throw light on DNA
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Trends Biotechnol 21:4-7. 2003
    ..However, the recent additions to the field - locked nucleic acids (LNAs) and peptide nucleic acids (PNAs) - significantly increase the potential of profluorescent probes and provide a robust impulse for their new uses...
  5. ncbi request reprint Profluorescent protein fragments for fast bimolecular fluorescence complementation in vitro
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    Nat Protoc 1:714-9. 2006
    ..The isolation of profluorescent protein fragments from recombinant E. coli cells requires approximately 3 d, and their conjugation to oligonucleotides requires 1-4 h...
  6. pmc Kinetics and mechanism of the DNA double helix invasion by pseudocomplementary peptide nucleic acids
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 99:5953-8. 2002
    ..A simplified kinetic model for pcPNAs helix invasion is proposed that interprets all unusual features of pcPNAs binding to dsDNA. Our findings have important implications for rational use of pcPNAs...
  7. ncbi request reprint PD-loop technology: PNA openers at work
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Expert Rev Mol Diagn 1:343-51. 2001
    ..Advantages of these new PNA-based assays over existing techniques for sequence-specific detection and manipulation of DNA duplexes are discussed. Future prospects for the further development of PD-loop technology are highlighted...
  8. ncbi request reprint Earrings and padlocks for the double helix: topological labeling of duplex DNA
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Trends Biotechnol 21:148-51. 2003
    ..The latest development in this direction takes advantage of oligonucleotide uptake by supercoiled DNA and is an important step forward...
  9. ncbi request reprint An artificial primosome: design, function, and applications
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Chembiochem 2:133-9. 2001
    ..This approach opens the way to direct isothermal reading of the DNA sequence against a background of unrelated DNA, thereby eliminating the need for purification of the target DNA...
  10. ncbi request reprint Heavy isotopes to avert ageing?
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington St, Boston, MA 02215, USA
    Trends Biotechnol 25:371-5. 2007
    ....
  11. ncbi request reprint 65th birthday of Edwin M. Southern, molecular biology and biotechnology mastermind
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Fl 2nd, Boston, MA 02215, USA
    Drug Discov Today 8:666-7. 2003
  12. ncbi request reprint Two sides of the coin: affinity and specificity of nucleic acid interactions
    Vadim V Demidov
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Trends Biochem Sci 29:62-71. 2004
    ....
  13. ncbi request reprint Peptide nucleic acid-assisted topological labeling of duplex dna
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    Methods 23:123-31. 2001
    ....
  14. ncbi request reprint Sequence-specific targeting of duplex DNA by peptide nucleic acids via triplex strand invasion
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    Methods 23:108-22. 2001
    ..The experimental and theoretical data presented make it possible to select those solution parameters and cpyPNA constructions that are most favorable for sequence specificity without compromising the affinity of dsDNA targeting...
  15. ncbi request reprint PNA openers as a tool for direct quantification of specific targets in duplex DNA
    N E Broude
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, MA 02215, USA
    J Biomol Struct Dyn 17:237-44. 1999
    ..The developed robust methodology is highly discriminative to single mutations, thus being of practical use for DNA analysis...
  16. pmc Rolling-circle amplification under topological constraints
    Heiko Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 30:574-80. 2002
    ..Our finding may have practical implications in the area of DNA diagnostics...
  17. pmc Kinetic analysis of specificity of duplex DNA targeting by homopyrimidine peptide nucleic acids
    V V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Massachusetts 02215, USA
    Biophys J 72:2763-9. 1997
    ..Differential dissociation of hpyPNA/dsDNA complexes is shown to enhance the selectivity of DNA targeting by PNA...
  18. ncbi request reprint PNA beacons for duplex DNA
    H Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, MA 02215, USA
    Antisense Nucleic Acid Drug Dev 11:265-70. 2001
    ..This feature of PNA beacons and our innovative hybridization strategy may find applications in emerging fluorescent DNA diagnostics...
  19. ncbi request reprint Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets
    Heiko Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    J Am Chem Soc 124:1097-103. 2002
    ....
  20. ncbi request reprint Pausing of DNA polymerases on duplex DNA templates due to ligand binding in vitro
    Irina V Smolina
    Department of Biomedical Engineering, Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    J Mol Biol 326:1113-25. 2003
    ....
  21. ncbi request reprint High-purity preparation of a large DNA dumbbell
    H Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, MA 02215, USA
    Antisense Nucleic Acid Drug Dev 11:149-53. 2001
    ..Considering the promising therapeutic potential of DNA dumbbells, the developed biosynthetic approach could be used for high-purity preparation of longer, covalently closed DNA decoys...
  22. pmc Tailoring the activity of restriction endonuclease PleI by PNA-induced DNA looping
    Ekaterina Protozanova
    Center for Advanced Biotechnology, Boston University, MA 02115, USA
    EMBO Rep 3:956-61. 2002
    ..Our findings imply a general approach for the fine-tuning of proteins bound to DNA sites well separated along the DNA chain...
  23. ncbi request reprint Real-time monitoring of branched rolling-circle DNA amplification with peptide nucleic acid beacon
    Irina V Smolina
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Anal Biochem 335:326-9. 2004
  24. pmc End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes
    Irina V Smolina
    Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:e146. 2005
    ..We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection...
  25. ncbi request reprint Artificial site-specific DNA-nicking system based on common restriction enzyme assisted by PNA openers
    Heiko Kuhn
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    Biochemistry 42:4985-92. 2003
    ..This new RCA format demonstrates the practical potential of the novel biomolecular tool we propose for DNA technology and DNA diagnostics...
  26. ncbi request reprint Sequence-universal recognition of duplex DNA by oligonucleotides via pseudocomplementarity and helix invasion
    Irina V Smolina
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Chem Biol 10:591-5. 2003
    ..Using this basically general approach, we selectively tagged a unique mixed-base site on the target dsDNA fragment with streptavidin and/or multiply labeled this site with fluorophores via the primer-extension reaction...
  27. pmc Pseudocomplementary PNAs as selective modifiers of protein activity on duplex DNA: the case of type IIs restriction enzymes
    Ekaterina Protozanova
    Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 31:3929-35. 2003
    ..Our results have general implications for effective pcPNA interference with the performance of DNA-processing proteins, thus being important for prospective applications of pcPNAs...
  28. ncbi request reprint Tough nuts to crack: encouraging progress in peptide nucleic acid hybridization to structured DNA/RNA targets
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA, USA
    Drug Discov Today 8:390. 2003
  29. ncbi request reprint High-density fluorescently labeled rolling-circle amplicons for DNA diagnostics
    Irina V Smolina
    Center for Advanced Biotechnology, Boston University, MA 02215, USA
    Anal Biochem 347:152-5. 2005
  30. ncbi request reprint Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay
    Heiko Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Electrophoresis 23:2384-7. 2002
    ..Therefore, EMSA monitoring of differential mobility change caused by nicks within various DNA sequences could be useful for studying the differential base stacking and nearest-neighbor energetics...
  31. pmc Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids
    Heiko Kuhn
    Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, MA 02215, USA
    Proc Natl Acad Sci U S A 101:7548-53. 2004
    ..We conclude that pcPNAs are promising tools for inducing bends in DNA at virtually any chosen site...
  32. ncbi request reprint PNA openers and their applications
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA, USA
    Methods Mol Biol 208:119-30. 2002
  33. ncbi request reprint Targeting linear duplex DNA with mixed-base peptide nucleic acid oligomers facilitated by bisPNA openers
    Igor G Panyutin
    Department of Nuclear Medicine, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
    Anal Biochem 362:145-7. 2007
  34. ncbi request reprint Golden jubilee of the DNA double helix
    Vadim V Demidov
    Trends Biotechnol 21:139-40. 2003
  35. ncbi request reprint DNA diagnostics in the fifty-year retrospect
    Vadim V Demidov
    Expert Rev Mol Diagn 3:121-4. 2003
  36. ncbi request reprint New kids on the block: emerging PNA-based DNA diagnostics
    Vadim V Demidov
    Expert Rev Mol Diagn 2:199-201. 2002
  37. pmc Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms
    Feng Ding
    Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    RNA 14:1164-73. 2008
    ..Our method allows rapid conformational sampling of RNA folding, with computational time increasing linearly with RNA length. We envision this approach as a promising tool for RNA structural and functional analyses...
  38. ncbi request reprint 10 years of rolling the minicircles: RCA assays in DNA diagnostics
    Vadim V Demidov
    Expert Rev Mol Diagn 5:477-8. 2005
  39. ncbi request reprint Sequence-specific DNA strand cleavage by 111In-labeled peptide nucleic acids
    Yujian He
    Department of Nuclear Medicine, Warren G Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892 1180, USA
    Eur J Nucl Med Mol Imaging 31:837-45. 2004
    ..Accordingly, we believe that PNA oligomers are promising radionuclide delivery tools for future antisense/antigene radiotherapy trials...
  40. ncbi request reprint PNA comes of age: from infancy to maturity
    Vadim V Demidov
    Drug Discov Today 7:153-5. 2002