Zhang DY, Liu B. (2003) Detection of target nucleic acids and proteins by amplification of circularizable probes. Expert Review of Molecular Diagnostics. 3(2), 237–248
Zhang W, Cohenford M, Lentrichia B, Isenberg HD, Simson E, Li H, Yi J, Zhang DY. (2002) Detection of Chlamydia trachomatis by Isothermal ramification Amplification Method: a Feasibility Study. Journal of Clinical Microbiology, 40 (1): 128-132. (view PDF of full article)
Zhang DY, Zhang W, Cohenford M, Lentricia B, Li H, Yi J. (2001) Detection of Chlamydia trachomatis by Isothermal Ramilfication Amplification Method Clinical Chemistry, 47 (11): 2078. (view PDF of abstract (#4) in Clinical Chemistry)
Zhang DY, Zhang W, Li X, Konomi Y. (2001) Detection of rare DNA targets by isothermal ramification amplification. Gene, 274(1-2):209-216. (view PubMed abstract)
Zhang DY, Brandwein M, Hsuih T, Li H. (2001) Ramification amplification (RAM): A novel isothermal DNA amplification method. Molecular Diagnosis, 6:141-150. (view PubMed abstract)
Zhang DY, Brandwein M, Hsuih T, Li H. (1998) Amplification of target-specific, ligation-dependent circular probe. Gene, 211: 277-285. (view PubMed abstract)
(For Technical Narratives, please see Technical Descriptions)
RCA
Smolina IV, Cherny DI, Nietupsk RMi, Beals T,
Smith JH, Lane DJ, Broude NE, Demidov VV. (2005) High-density fluorescently labeled rolling-circle amplicons for
DNA diagnostics. Analytical Biochemistry 347:152–155. Read Full Article (PDF)
Smolina IV, Demidov VV, Cantor CR, Broude NE. (2004) Real-time monitoring of branched rolling-circle DNA amplification
with peptide nucleic acid beacon. Analytical Biochemistry 335:326–329. Read Full Article (PDF)
DNA Hybridization
Demidov VV, Dokholyan NV, Witte-Hoffmann C, Chalasani P, Yiu HW, Ding F, Yu Y, Cantor CR, Broude NE. (2006) Fast complementation of split fluorescent protein
triggered by DNA hybridization. PNAS 103(7):2052–2056. Read Full Article (PDF)
Single Cell PCR
Pierce KE, Rice JE, Sanchez JA, Brenner C, Wangh LJ. (2000) Real-time PCR using molecular beacons for accurate detection of the Y chromosome in single human blastomeres. Molec Human Reproduction, 6(12):1155-1164. (view PubMed abstract)
Molecular Beacons
Bonnet G, Tyagi S, Libchaber A, Kramer FR. (1999) Thermodynamic basis of the enhanced specificity of molecular beacons. Proc Natl Acad Sci USA 96: 6171-6176. (view PubMed abstract)
Ehricht R, Kirner T, Ellinger T, Foerster P, McCaskill JS. (1997) Monitoring the amplification of CATCH, a 3SR based cooperatively coupled isothermal amplification system, by fluorimetric methods. Nucleic Acids Res, 25:4697-4699. (view PubMed abstract)
Gao W, Tyagi S, Kramer FR, Goldman E. (1997) Messenger RNA release from ribosomes during 5'-translational blockage byconsecutive low-usage arginine but not leucine codons in Escherichia coli. Mol Microbiol, 25:707-716. (view PubMed abstract)
Giesendorf BA, Vet JA, Tyagi S, Mensink EJ, Trijbels FJ, Blom HJ. (1998) Molecular beacons: a new approach for semiautomated mutation analysis. Clin Chem; 44:482-486. (view PubMed abstract)
Kostrikis LG, Huang Y, Moore JP, Wolinsky SM, Zhang L, Guo Y, Deutsch L, Phair J, Neumann AU, Ho DD. (1998) A chemokine receptor CCR2 allele delays HIV-1 disease progression and is associated with a CCR5 promoter mutation. Nat Med, 4:350-353. (view PubMed abstract)
Kostrikis LG, Tyagi S, Mhlanga MM, Ho DD, Kramer FR. (1998) Spectral genotyping of human alleles. Science, 279:1228-1229. (no PubMed abstract available)
Leone G, van Schijndel H, van Gemen B, Kramer FR, Schoen CD. (1998) Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Res, 26:2150-2155. (view PubMed abstract)
Lewin SR, Vesanen M, Kostrikis L, Hurley A, Duran M, Zhang L, Ho DD, Markowitz M.(1999) Use of real-time PCR and molecular beacons to detect virus replication in human immunodeficiency virus type 1 infected individuals on prolonged effective antiretroviral therapy. J VIROL 73: (7) 6099-6103. (view PubMed abstract)
Li JJ, Fang X, Schuster SM, Tan W. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization probes. J Am Chem Soc, 121:2921-2922. (no PubMed abstract available)
Manganelli R, Dubnau E, Tyagi S, Kramer FR, Smith I. (1999) Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis. Mol Microbiol, 31:715-724. (view PubMed abstract)
Marras SAE, Kramer FR, and Tyagi S. (1999) Multiplex detection of single -nucleotide variations using molecular beacons. Genetic Analysis, 14:151-156. (view PubMed abstract)
Matsuo T. (1998) In situ visualization of mRNA for basic fibroblast growth factor in living cells. Biochimica et Biophysica Acta, 1379, 178-184. (view PubMed abstract)
Ortiz E, Estrada G, Lizardi PM. (1998) PNA molecular beacons for rapid detection of PCR amplicons. Mol Cell Probes, 12:219-226. (view PubMed abstract)
Piatek AS, Tyagi S, Pol AC, Telenti A, Miller LP, Kramer FR, Alland D. (1998) Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat Biotechnol, 16:359-363. (view PubMed abstract)
Rhee JT, Piatek AS, Small PM, Harris LM, Chaparro SV, Kramer FR, Alland D. (1999) Molecular epidemiologic evaluation of transmissibility and virulence of Mycobacterium tuberculosis. J Clin Microbiol 37: (6) 1764-1770. (view PubMed abstract)
Schofield P, Pell AN, Krause DO. (1997) Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria. Appl Environ Microbiol, 63:1143-1147. (view PubMed abstract)
Sokol DL, Zhang X, Lu P, Gewirtz AM. (1998) Real time detection of DNA:RNA hybridization in living cells. Proc Natl Acad Sci U S A 95:11538-11543. (view PubMed abstract)
Tyagi S, Bratu DP, Kramer FR. (1998) Multicolor molecular beacons for allele discrimination. Nat Biotechnol, 16:49-53. (view PubMed abstract)
Tyagi S, Kramer FR. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 14:303-308. (view PubMed abstract)
Vet JA, Majithia AR, Marras SA, Tyagi S, Dube S, Poiesz BJ, Kramer FR. (1999) Multiplex detection of four pathogenic retroviruses using molecular beacons. Proc Natl Acad Sci USA. 96: 6394-6399. (view PubMed abstract)
Vogelstein B, Kinzler KW. (1999) Digital PCR. Proc Natl Acad Sci USA. 96: 9236-9241. (view PubMed abstract)
Zhang L, Lewin SR, Markowitz M, Lin HH, Skulsky E, Karanicolas R, He Y, Jin X, Tuttleton S, Vesanen M, Spiegel H, Kost R, van Lunzen J, Stellbrink HJ, Wolinsky S, Borkowsky W, Palumbo P, Kostrikis LG, Ho DD. (1999) Measuring recent thymic emigrants in blood of normal and HIV-1-infected individuals before and after effective therapy. J Exp Med 190: (5) 725-732. (view PubMed abstract)
