Integrated DNA Technologies

IDT Publications

A bibliography of research papers published by IDT scientists. Click on the reference and you will be redirected to the PubMed abstract. If available, you will be able to obtain a PDF download of the paper through the Pubmed site.

piRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets. 2008 Devor EJ, Huang L, Samollow PB. Mamm Genome. 19: 581-6

Small RNA regulation of ovule development in the cotton plant, G. hirsutum L. 2008 Abdurakhmonov IY, Devor EJ, Buriev ZT, Huang L, Makamov A, Shermatov SE, Bozorov T, Kushanov FN, Mavlonov GT, Abdukarimov A. BMC Plant Biol. 8: 93

Chemical modification patterns compatible with high potency dicer-substrate small interfering RNAs. 2008 Collingwood MA, Rose SD, Huang L, Hillier C, Amarzguioui M, Wiiger MT, Soifer HS, Rossi JJ, Behlke MA. Oligonucleotides 18: 187-200

Assessing the sensitivity of commercially available fluorophores to the intracellular environment. 2008 Chen AK, Cheng Z, Behlke MA, Tsourkas A. Anal Chem. 80: 7437-44

Regulation of Bacteria-Induced Intercellular Adhesion Molecule-1 by CCAAT/Enhancer Binding Proteins. 2008 Manzel LJ, Chin CL, Behlke MA, Look DC. Am J Respir Cell Mol Biol. Aug 14: ahead of print

Howard KA, Paludan SR, Behlke MA, Besenbacher F, Deleuran B, Kjems J. 2008 Chitosan/siRNA Nanoparticle-mediated TNF-alpha Knockdown in Peritoneal Macrophages for Anti-inflammatory Treatment in a Murine Arthritis Model. Mol Ther Sep 30: ahead of print

Soifer HS, Sano M, Sakurai K, Chomchan P, Saetrom P, Sherman MA, Collingwood MA, Behlke MA, Rossi JJ. 2008 A role for the Dicer helicase domain in the processing of thermodynamically unstable hairpin RNAs. Nucleic Acids Res. 36: 6511-22

Behlke MA 2008 Chemical Modification of siRNAs for In Vivo Use. Oligonucleotides 18: 305-20

Chen AK, Behlke MA, Tsourkas A. 2008 Efficient cytosolic delivery of molecular beacon conjugates and flow cytometric analysis of target RNA. Nucleic Acids Res. 12: 69

Doré-Savard L, Roussy G, Dansereau MA, Collingwood MA, Lennox KA, Rose SD, Beaudet N, Behlke MA, Sarret P. 2008 Central delivery of Dicer-substrate siRNA: a direct application for pain research. Mol Ther. 7: 1331-9

Owczarzy R, Tataurov AV, Wu Y, Manthey JA, McQuisten KA, Almabrazi HG, Pedersen KF, Lin Y, Garretson J, McEntaggart NO, Sailor CA, Dawson RB, Peek AS. 2008 IDT SciTools: a suite for analysis and design of nucleic acid oligomers. Nucleic Acids Res. 36: 163-9

Tataurov AV, You Y, Owczarzy R. 2008 Predicting ultraviolet spectrum of single stranded and double stranded deoxyribonucleic acids. Biophys Chem. 3: 66-70

Hildebrand MS, Newton SS, Gubbels SP, Sheffield AM, Kochhar A, de Silva MG, Dahl HH, Rose SD, Behlke MA, Smith RJ. 2008 Advances in molecular and cellular therapies for hearing loss. Mol Ther. 2: 224-36

Gantier, M.P., Tong, S., Behlke, M.A., Xu, D., Phipps, S., Foster, P.S., and Williams, B.R.G. 2008 TLR7 Is Involved in Sequence-Specific Sensing of Single-Stranded RNAs in Human Macrophages. J Immunol. 4: 2117-24

Owczarzy R, Moreira BG, You Y, Behlke MA, Walder JA. 2008 Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. Biochemistry. 19: 5336-53

Zamanian-Daryoush M, Marques JT, Gantier MP, Behlke MA, John M, Rayman P, Finke J, Williams BR.. 2008 Determinants of cytokine induction by small interfering RNA in human peripheral blood mononuclear cells. J Interferon Cytokine Res. 4: 221-23

Devor EJ, Samollow PB. 2008 In vitro and in silico annotation of conserved and nonconserved microRNAs in the genome of the marsupial Monodelphis domestica. J Hered. 1: 66-72

Brown DW, Gunning KB, Henry DM, Awdeh ZL, Brinker JP, Tzipori S, Herrmann JE 2008 A DNA oligonucleotide microarray for detecting human astrovirus serotypes. J Virol Methods 147: 86-92

Chen AK, Behlke MA, Tsourkas A 2007 Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells. Nucleic Acids Res. 35: 105

Melton PE, Briceno I, Gomez A, Devor EJ, Bernal JE, Crawford MH. 2007 Biological relationship between Central and South American Chibchan speaking populations: evidence from mtDNA. American Journal of Physical Anthropology 133: 753-770

Peek AS, Behlke MA. 2007 Design of active small interfering RNAs. Current Opinion in Molecular Therapeutics 9: 110-118

McQuisten KA, Peek AS. 2007 Identification of sequence motifs significantly associated with antisense activity. BMC Bioinformatics 8: 184

Peek AS. 2007 Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features. BMC Bioinformatics 8: 182

Amarzguioui M, Lundberg P, Cantin E, Hagstrom J, Behlke MA, Rossi JJ. 2006 Rational design and in vitro and in vivo delivery of Dicer substrate siRNA. Nature Protocols 1: 508-517

Robbins MA, Li M, Leung I, Li H, Boyer DV, Song Y, Behlke MA, Rossi JJ. 2006 Stable expression of shRNAs in human CD34(+) progenitor cells can avoid induction of interferon responses to siRNAs in vitro. Nat Biotechnol. 5: 566-71

Marques JT, Devosse T, Wang D, Zamanian-Daryoush M, Serbinowski P, Hartmann R, Fujita T, Behlke MA, Williams BR. 2006 A structural basis for discriminating between self and nonself double-stranded RNAs in mammalian cells. Nat Biotechnol. 5: 559-65.

You Y, Moreira BG, Behlke MA, Owczarzy R 2006 Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res. 8: 60.

Lennox KA, Sabel JL, Johnson MJ, Moreira BG, Fletcher CA, Rose SD, Behlke MA, Laikhter AL, Walder JA, Dagle JM. 2006 Characterization of Modified Antisense Oligonucleotides in Xenopus laevis Embryos. Oligonucleotides 16: 26-42.

Devor EJ. 2006 Primate MicroRNAs miR-220 and miR-492 Lie within Processed Pseudogenes. J Hered. 97: 186-90.

Zlojutro M, Rubicz R, Devor EJ, Spitsyn VA, Makarov SV, Wilson K, Crawford MH. 2006 Genetic structure of the Aleuts and Circumpolar populations based on mitochondrial DNA sequences: a synthesis. Am J Phys Anthropol. 129: 446-64.

Behlke MA. 2006 Progress towards in Vivo Use of siRNAs. Mol Ther. 13: 644-70.

Ramaswamy M, L Shi, SM Varga, S Barik, MA Behlke, and DC Look 2006 Respiratory syncytial virus nonstructural protein 2 specifically inhibits type I interferon signal transduction. Virology 344: 328-339.

Owczarzy R. 2005 Melting temperatures of nucleic acids: Discrepancies in analysis. Biophys Chem. 117: 207-215.

Eberhard S, Jain M, Im CS, Pollock S, Shrager J, Lin Y, Peek AS, Grossman AR 2005 Generation of an oligonucleotide array for analysis of gene expression in Chlamydomonas reinhardtii. Curr Genet. : 1-19.

Rose, SD, Kim, DH, Amarzguioui, M, Heidel, JD, Collingwood, MA, Davis, ME, Rossi, JJ, and Behlke, MA 2005 Functional polarity is introduced by Dicer processing of short substrate RNAs. Nucleic Acids Res. 33: 4140-56.

Soifer HS, A Zaragoza, M Peyvan, MA Behlke, and JJ Rossi 2005 A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon. Nucleic Acids Res. 33: 846-56.

Kim DH, MA Behlke, SD Rose, M-S Chang S Choi, and JJ Rossi 2005 Synthetic dsRNA dicer-substrates enhance RNAi potency and efficacy. Nature Biotechnology 23: 222-226

Moreira BG, Y You, MA Behlke, and R Owczarzy 2005 Effects of fluorescent dyes, quenchers, and dangling ends on DNA duplex stability. Biochem Biophys Res Comm 327: 473-484

Devor EJ, and K Moffat-Wilson 2004 An ancient RNase HI splice junction mutant preserved in a 19-million-year old genetic fossil in ape genomes. Journal of Heredity 95: 257-261

Hail ME, B Elliott, and A Anderson 2004 High-throughput analysis of oligonucleotides using automated electrospray ionization mass spectrometry. American Biotechnology Laboratory 22: 12-14

Montanelli L, JJJ van Durme, G Smits, M Bonomi, P Rodien, EJ Devor, K Moffat-Wilson, L Pardo, G Vassart, and S Costagliola 2004 Modulation of ligand selectivity associated with activation of the transmembrane region of the human follitropin receptor. Molecular Endocrinology 18: 2061-2073

Owczarzy R, Y You, B Moreira, JA Manthey, L Huang, MA Behlke, and JA Walder 2004 Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures. Biochemistry 43: 3537-3554

Devor EJ, and K Moffat-Wilson 2003 Molecular and temporal characteristics of human retropseuodgenes. Human Biology 75: 661-672

Owczarzy R, I Dunietz, MA Behlke, IM Klotz, and JA Walder 2003 Thermodynamic treatment of oligonucleotide duplex-simplex equilibria. Proceedings of the National Academy of Science USA 100: 14840-14845

Tsourkas A, MA Behlke, SD Rose, and G Bao 2003 Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Research 31: 1319-1330

Tsourkis A, MA Behlke, Y Xu, and G Bao 2003 Spectroscopic features of dual fluorescence/luminescence energy-transfer molecular beacons. Analytical Chemistry 75: 3697-3703

Tsourkas A, MA Behlke, and G Bao 2002 Structure-function relationships of shared stem and conventional molecular beacons. Nucleic Acids Research 30: 4208-4215

Tsourkis A, MA Behlke, and G Bao 2002 Hybridization of 2’-O-methyl and 2’-deoxy molecular beacons to RNA and DNA targets. Nucleic Acids Research 30: 5168-5174

Zhang L, Peek AS, Dunams D, Gaut BS 2002 Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis). Genetics 162: 851-860

Devor EJ 2001 Use of molecular beacons to verify that the serine hydroxymethyltransferase pseudogene SHMT-ps1 is unique to the order Primates. GenomeBiology 2: 0006.1-0006.5

Devor EJ 2001 Molecular archeology of an SP100 splice variant revisted: dating the retrotranscription and Alu insertion events. GenomeBiology 2: 0040.1-0040.6

Park C, BR Keleman, TA Klink, R Sweeney, MA Behlke, SR Eubanks, and RT Raines 2001 Fast, facile, hypersensitive assays for ribonucleolytic activity. Methods in Enzymology 341: 81-94