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  • End Invasion of Peptide Nucleic Acids (PNAs) with Mixed-Base Composition into Linear DNA Duplexes 

    Smolina, Irina V.; Demidov, Vadim V.; Soldatenkov, Viatcheslav A.; Chasovskikh, Sergey G.; Frank-Kamenetskii, Maxim D. (Oxford University Press, 2005-10-04)
    Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers ...
  • Tuning and Controlling Gene Expression Noise in Synthetic Gene Networks 

    Murphy, Kevin F.; Adams, Rhys M.; Wang, Xiao; Balázsi, Gábor; Collins, James J. (Oxford University Press, 2010-03-08)
    Synthetic gene networks can be used to control gene expression and cellular phenotypes in a variety of applications. In many instances, however, such networks can behave unreliably due to gene expression noise. Accordingly, ...
  • Labeling of Unique Sequences in Double-Stranded DNA at Sites of Vicinal Nicks Generated by Nicking Endonucleases 

    Kuhn, Heiko; Frank-Kamenetskii, Maxim D. (Oxford University Press, 2008-4)
    We describe a new approach for labeling of unique sequences within dsDNA under nondenaturing conditions. The method is based on the site-specific formation of vicinal nicks, which are created by nicking endonucleases ...
  • Base-Stacking and Base-Pairing Contributions into Thermal Stability of the DNA Double Helix 

    Yakovchuk, Peter; Protozanova, Ekaterina; Frank-Kamenetskii, Maxim D. (Oxford University Press, 2006-01-31)
    Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure ...
  • Gyrase Inhibitors Induce an Oxidative Damage Cellular Death Pathway in Escherichia Coli 

    Dwyer, Daniel J.; Kohanski, Michael A.; Hayete, Boris; Collins, James J. (2007-03-13)
    Modulation of bacterial chromosomal supercoiling is a function of DNA gyrase-catalyzed strand breakage and rejoining. This reaction is exploited by both antibiotic and proteic gyrase inhibitors, which trap the gyrase ...
  • Biological Context Networks: A Mosaic View of the Interactome 

    Rachlin, John; Cohen, Dikla Dotan; Cantor, Charles; Kasif, Simon (2006-11-28)
    Network models are a fundamental tool for the visualization and analysis of molecular interactions occurring in biological systems. While broadly illuminating the molecular machinery of the cell, graphical representations ...
  • MuPlex: Multi-Objective Multiplex PCR Assay Design 

    Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon (Oxford University Press, 2005-06-27)
    We have developed a web-enabled system called MuPlex that aids researchers in the design of multiplex PCR assays. Multiplex PCR is a key technology for an endless list of applications, including detecting infectious ...
  • Simultaneous Quantitative and Allele-Specific Expression Analysis with Real Competitive PCR 

    Ding, Chunming; Maier, Esther; Roscher, Adelbert A; Braun, Andreas; Cantor, Charles R (BioMed Central, 2004-5-5)
    BACKGROUND. For a diploid organism such as human, the two alleles of a particular gene can be expressed at different levels due to X chromosome inactivation, gene imprinting, different local promoter activity, or mRNA ...
  • Computational Tradeoffs in Multiplex PCR Assay Design for SNP Genotyping 

    Rachlin, John; Ding, Chunming; Cantor, Charles; Kasif, Simon (BioMed Central, 2005-7-25)
    BACKGROUND: Multiplex PCR is a key technology for detecting infectious microorganisms, whole-genome sequencing, forensic analysis, and for enabling flexible yet low-cost genotyping. However, the design of a multiplex PCR ...