Synthesis
and Properties of Phosphonic Acid Containing Cyanine and Squaraine Dyes
for Use as Fluorescent Labels Reddington, Mark V. Bioconjugate Chem
2007, 18(6), 2178-2190.
Methylotrophic
Methanogens in the Water Column of an Upwelling Zone with a Strong
Oxygen Gradient off Central Chile. Levipan, H.A.; Quiñones, R.A.;
Johansson, H.E.; Urrutia, H. Microbes and Environments 2007,
22(3), 268-278.
Solid
Phase Synthesis of Dual Labeled Peptides: Development of Cell Permeable
Calpain Specific Substrates. Polster, B.M.; Arze, R.; Lyttle, M.H.;
Nicholls, D.G.; Hudson, D. Int. J. Pep. Res. Therapeut. 2007,
in press.
Development
of a Red-Shifted Fluorescence-Based Assay for SARS-Coronavirus 3CL
Protease: Identification of a Novel Class of Anti-SARS Agents from
the Tropical Marine Sponge Axinella corrugata. Hamill,
P.; Hudson, D.; Kao, R.Y.; Chow, P.; Raj, M.; Xu, H.; Richer, M.J.;
Jean, F. Biol. Chem., 2006, 387, 1063-1074.
Choosing
Reporter-Quencher Pairs for Efficient Quenching Through Formation
of Intramolecular Dimers. Johansson, M.K. In Methods in
Molecular Biology, v. 335; V.V. Didenko, Ed; Humana Press: Totowa, NJ,
2006; pp 17-29.
Time
Gating Improves Sensitivity in Energy Transfer Assays with Terbium
Chelate/Dark Quencher Oligonucleotide Probes. Johansson, M.K.;
Cook, R.M.; Xu, J.; Raymond, K.N. J. Am. Chem. Soc. 2004,
126(50), 16451-16455.
Intramolecular
Dimers: A New Design Strategy for Fluorescence-Quenched
Probes. Johansson, M.K.; Cook, R.M. Chem.--Eur. J.
2003, 9, 3466-3471. (This paper was also the
subject of this issue's cover
art; see sidebar.)
Photoluminescence
and Electrochemiluminescence of a Ru(II)(bpy)3-Quencher
Dual-Labeled Oligonucleotide Probe. Wilson, R.; Johansson,
M.K. Chem. Commun. 2003, 2710-2711.
Intramolecular
Dimers: A New Strategy to Fluorescence Quenching in Dual-Labeled
Oligonucleotide Probes. Johansson, M.K.; Fidder, H.;
Dick, D.; Cook, R.M. J. Am. Chem. Soc. 2002,
124, 6950-6956.
Evaluation
of New Linkers and Synthetic Methods for Internal Modified
Oligonucleotides. Walton, T.A. ; Lyttle, M.H.; Dick,
D.J.; Cook, R.M. Bioconjugate Chem. 2002,
13, 1155-1158.
New
Reagents and Methods for the Synthesis of Internal and 3'-Labeled
DNA. Lyttle, M.H.; Walton, T.A.; Dick, D.J.; Carter,
T.G.; Beckman, J.H.; Cook, R.M. Bioconjugate Chem.
2002, 13, 1146-1154.
Fmoc
Chemistry Compatible Methods for Thio-Ligation Assembly
Of Proteins. Biancalana, S.; Hudson, D.; Songster, M.F.;
Thompson, S.A. In Peptides: The Wave of the Future;
Lebl, M.; Houghten, R.A., Eds.; American Peptide Society:
San Diego, 2001; pp 117-118.
New
Quencher Derivatives for Fluorescent Quenching Peptide Assays.
Walton, T.A.; Dick, D.J.; Hudson, D.; Johansson, M.K.; Lyttle,
M.H.; Songster, M.F.; Cook, R.M. In Peptides: The Wave
of the Future; Lebl, M.; Houghten, R.A., Eds.; American
Peptide Society: San Diego, 2001; pp 54-55.
Improved
Synthetic Procedures for 4,7,2',7'-Tetrachloro- and 4',5'-Dichloro-2',7'-dimethoxy-5(and
6)-carboxyfluoresceins. Lyttle, M.H.; Carter, T.G.;
Cook, R.M. Org. Process Res. Dev. 2001, 5,
45-49.
A
Tetramethyl Rhodamine (Tamra) Phosphoramidite Facilitates
Solid-Phase-Supported Synthesis of 5'-Tamra DNA. Lyttle,
M.H.; Carter, T.G.; Dick, D.J.; Cook, R.M. J. Org. Chem.
2000, 65, 9033-9038.
Fmoc
Chemistry Compatible Thio-ligation Assembly of Proteins.
Biancalana, S.; Hudson, D.; Songster, M.F.; Thompson, S.A.
Lett. Pept. Sci. 2000, 7, 291-297.
Orthogonal
Methods for the Synthesis of Multiply Labeled Peptide Probes
and Substrates. Songster, M.F.; Biancalana, S.; Cook, R.M.;
Dick, D.J.; Hudson, D. In Peptides for the New Millennium;
Fields, G.B.; Tam, J.P.; Barany, G., Eds.; Kluwer: Dordrecht,
The Netherlands, 2000; pp 111-112.
A
Phosphate Bound Universal Linker for DNA Synthesis. Lyttle,
M.H.; Dick, D.J.; Hudson, D.; Cook, R.M. Nucleosides
Nucleotides 1999, 18, 1809-1824.
Matrix
Assisted Synthetic Transformations: A Mosaic of Diverse
Contributions. II. The Pattern Is Completed. Hudson,
D. J. Comb. Chem. 1999, 1, 403-457.
Matrix
Assisted Synthetic Transformations: A Mosaic of Diverse
Contributions. I. The Pattern Emerges. Hudson, D. J.
Comb. Chem. 1999, 1, 333-360.
An
Investigation of the Role of Environment, Spacer Arm and
Site Isolation Effects in PEG-Polystyrene Graft Copolymers.
Hudson, D.; Cook, R.M.; Lyttle, M.H.; Adams, J.H.; Songster,
M.F.; White, P. In Peptides: 1998; Bajusz, S.; Judecz,
F., Eds.; Akadémiai Kiadó: Budapest, Hungary,
1999; pp 40-41.
A
Reinvestigation of the Preparation, Properties, and Applications
of Aminomethyl and 4-Methylbenzhydrylamine Polystyrene Resins.
Adams, J.H.; Cook, R.M.; Hudson, D.; Jammalamadaka, V.;
Lyttle, M.H.; Songster, M.F. J. Org. Chem. 1998,
63, 3706-3716.
Improved
Supports and Methods for Solid Phase Mediated Transformations.
Adams, J.H.; Cook, R.M.; Hudson, D.; Jammalamadaka, V.;
Lyttle, M.H.; Songster, M.F. In Innovation and Perspectives
in Solid Phase Synthesis and Combinatorial Libraries: 1998;
Epton, R., Ed.; Mayflower Scientific: Kingswinford, England,
1998; pp 23-30.
Versatile
Linker Chemistry for Synthesis of 3'-Modified DNA. Lyttle,
M.H.; Adams, H.; Hudson, D.; Cook, R.M. Bioconjugate
Chem. 1997, 8, 193-198.
A
New Universal Linker for Solid Phase DNA Synthesis.
Lyttle, M.H.; Hudson, D.; Cook, R.M. Nucleic Acids Res.
1996, 24, 2793-2798.
Chemically
Modified Polyolefin Particles for Biomolecule Synthesis,
Analysis and Display. Cook, R.M.; Hudson, D. In Peptides:
Chemistry, Structure and Biology; Kaumaya, P.T.P.; Hodges,
R.S., Eds.; Mayflower Scientific: Kingswinford, England,
1996; pp 39-41.
The
Synthesis and Separation of Peptides, DNA and Hybrid Molecules.
Cook, R.M.; Hudson, D. In Innovation and Perspectives
in Solid Phase Synthesis and Combinatorial Libraries: 1996;
Epton, R., Ed.; Mayflower Scientific: Kingswinford, England,
1996; pp 19-26.
The
Preparation and Synthetic Application of Heterobifunctional
Biocompatible Spacer Arms. Cook, R.M.; Adams, J.H.; Hudson,
D. Tetrahedron Lett. 1994, 35, 6777-6780.
top
Xanthene Dyes. Reddington, M.; Lyttle, M. U.S. Patent
7 344 701, 2008.
Fluorescence Energy Transfer Probes with Stabilized Conformations.
Cook, R.M.; U.S. Patent 7 160 996, 2007.
Dark Quenchers for Donor-Acceptor Energy Transfer. Cook, R.M.;
Lyttle, M.; Dick, D. U.S. Patent 7 109 312, 2006.
Water Soluble Fluorescent Compounds. Reddington, M.;
U.S. Patent Application, 2006.
Dark Quenchers for Donor-Acceptor Energy Transfer. Cook, R.M.;
Lyttle, M.; Dick, D. U.S. Patent Application, 2006.
Dark Quenchers for Donor-Acceptor Energy Transfer. Cook, R.M.;
Lyttle, M.; Dick, D. U.S. Patent 7 019 129, 2006.
Inducible Fluorescence Assay. Cook, R.M.; Armstrong, E.S.;
Johansson, H.E. U.S. Patent Application, 2005.
Cyanine Dyes. Carter, T.; Reddington, M. U.S. Patent Application,
2005.
Column for Solid Phase Processing. Cook, R.M.; Dill, R.
U.S. Patent 6 761 855, 2004.
Multi-Channel Reagent Dispensing Apparatus. Cook, R.M.; Dill, R.;
Baltzley, A. U.S. Patent 6 696 298, 2004.
Luminescent Metal Ion Complexes. Cook, R.M.; Lyttle, M.;
Johansson, M.K. U.S. Patent Application, 2003.
Method for Production of Acylthio Derivatives. Hudson, D.;
Thompson, S. U.S. Patent 6 277 957, 2001.
Linker
for Immobilization, Modification and Subsequent Release
of Oligomers with a Terminal Hydroxyl Group. Lyttle, M.H.
U.S. Patent 5 688 940, 1997.
Oxidized
Polyethylene of Polypropylene Particulate Supports. Hudson,
D.; Cook, R.M. U.S. Patent 5 679 539, 1997.
top
Genotyping
with BHQplus™ - Fortified Probes Achieve Powerful
Discrimination (PDF 1.8 MB) Sowers, B.A.; Messenger, V.E.;
Cook, R.M. Presented at qPCR Symposium USA, Palo Alto,
California, October 2007.
Intricacies
of PCR Multiplexing As Revealed Through a Pathogen Detection
Assay (PDF 1.7 MB) Messenger, V.E.; Sowers, B.A.; Cook, R.M.
Presented at qPCR 2007 Event: 3rd International qPCR Symposium &
Industrial Exhibition & Application Workshop, Freising-Weihenstephan,
Germany.
RealTimeDesign™
- Free Web-based Software For TaqMan® and Amplifluor®
Design (PDF 1.4 MB) Sowers, B.A.; Songster, M.F.; Smith,
K.E.; Snyder, D.L.; Cook, R.M. Presented at 20th Anniversary
San Diego Conference DNA Probe Technology, San Diego, CA,
March 2006.
RealTimeDesign™
Software - An Advanced Web-based Program for Real-time PCR
Sequence Design (PDF 1.4 MB) Sowers, B.A.; Songster, M.F.;
Snyder, D.L.; Smith, K.E.; Cook, R.M. Presented at 2nd International
qPCR Event, Freising-Weihenstephan, Germany, September, 2005.
Pulsar-Z:
A New Cell-Permeable Dye for Cell Cycle Analysis Using Flow
Cytometry and Laser Scanning Cytometry at 488 nM (PDF 494 KB)
Tighe, S.W.; Johansson, M.K.; Resnikoff, J; Cook, R.M. Presented
Montpellier, France, May, 2005.
Optimization
of Probe Performance in Real-Time PCR through an Understanding
of Synthesis Impurities. (PDF - 4.1 MB) Sowers, B.A.;
Peterson, E.J.; Grant, R.E.; Lin, W.Y.; Dick, D.J.; Cook, R.M.
Presented at Quantitative PCR, San Diego, CA, March, 2005.
CAL
Fluor® Dyes: Multiplexing Reporters for Real-Time PCR
Instruments and Probe Designs (PDF - 1.3 MB) Sowers, B.A.;
Reddington, M.; Lyttle, M.; Johansson, M.K.; Cook, R. Presented
at Quantitative PCR, San Diego, CA, March 2004.
BHQs
Efficiently Quench a Wide Variety of Fluorophores Including
IR Dyes, Lanthanides and Ru Complexes. Johansson, M.K.;
Lyttle, M.; Carter, T.; Dick, D.; Cook, R. Presented at
CHI's Profiling PCR and Beyond, Washington, D.C., June,
2002.
Development
and Evaluation of Passive Reference Candidate Compounds
for Normalization of Signal in Real-Time PCR. Potter,
C.; Johansson, M.K.; Dick, D.; Cook, R. Presented at ABRF
2002: Biomolecular Technologies: Tools for Discovery in
Proteomics and Genomics, Austin, TX, March, 2002; poster
P13-S.
Development
of Ru(bpy)3 CPG for Solid-Phase
Synthesis of 3'-Labeled Oligonucleotides. Johansson,
M.K.; Lyttle, M.H.; Cook, R.M. Presented at TIGR's 13th
International Genome Sequencing and Analysis Conference,
San Diego, CA, October, 2001; poster P080.
Fmoc
Chemistry Compatible Methods for Thio-Ligation Assembly
Of Proteins. Biancalana, S.; Hudson, D.; Songster, M.F.;
Thompson, S.A. Presented at the 17th American Peptide Symposium,
San Diego, CA, June, 2001; poster P157.
New
Quencher Derivatives for Fluorescent Quenching Peptide Assays.
Walton, T.A.; Dick, D.J.; Hudson, D.; Johansson, M.K.; Lyttle,
M.H.; Songster, M.F.; Cook, R.M. Presented at the 17th American
Peptide Symposium, San Diego, CA, June, 2001; poster P158.
Alternatives
to FRET: Design of Fluorescence-Quenched Oligonucleotide
Probes with Extremely High Signal/Noise Ratios. Johansson,
M.K.; Cook, R.M.; Dick, D.; Lyttle, M. Presented at TIGR's
12th International Genome Sequencing and Analysis Conference,
Miami, FL, September, 2000; poster P080.
New
PEG-PS Resins for Solid-Phase Organic Synthesis. Adams,
H.A.; Hudson, D.; Steinauer, R.; White, P. Presented at
CHI's 4th Annual High-Throughput Organic Synthesis Symposium,
San Diego, CA, February, 1999; poster 1.
Improved
Synthesis Procedures for Aminomethyl- and MBHA-Functionalized
Polystyrene Resins. Lyttle, M.H.; Hudson, D.; Adams, H.A.;
Jammalamadaka, V.; Songster, M.F.; Cook, R.M. Presented
at the 2nd Lake Tahoe Symposia on Molecular Diversity, Lake
Tahoe, CA, January, 1998.
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