Single-molecule detection of specific nucleic acid sequences in unamplified genomic DNA.
AuthorsCastro A, Williams JG
JournalAnal Chem
PubMed ID9322430
'A new technique is described for the rapid detection of specific nucleic acid sequences in unamplified DNA samples. The method consists of using two nucleic acid probes complementary to different sites on a target DNA sequence. The two probes are each labeled with different fluorescent dyes. When mixed with a ... More
Wavelength-shifting molecular beacons.
AuthorsTyagi S, Marras SA, Kramer FR
JournalNat Biotechnol
PubMed ID11062440
'We describe wavelength-shifting molecular beacons, which are nucleic acid hybridization probes that fluoresce in a variety of different colors, yet are excited by a common monochromatic light source. The twin functions of absorption of energy from the excitation light and emission of that energy in the form of fluorescent light ... More
Determination of optimal rhodamine fluorophore for in vivo optical imaging.
AuthorsLongmire MR, Ogawa M, Hama Y, Kosaka N, Regino CA, Choyke PL, Kobayashi H,
JournalBioconjug Chem
PubMed ID18610943
'Optical imaging has the potential to improve the efficacy of surgical and endoscopic approaches to cancer treatment; however, the optimal type of fluorescent probe has not yet been established. It is well-known that rhodamine-core-derived fluorophores offer a combination of desirable properties such as good photostability, high extinction coefficient, and high ... More
H-type dimer formation of fluorophores: a mechanism for activatable, in vivo optical molecular imaging.
AuthorsOgawa M, Kosaka N, Choyke PL, Kobayashi H,
JournalACS Chem Biol
PubMed ID19480464
'In vivo molecular imaging with target-specific activatable '
Kinetics of conformational fluctuations in DNA hairpin-loops.
AuthorsBonnet G, Krichevsky O, Libchaber A
JournalProc Natl Acad Sci U S A
PubMed ID9671724
'The kinetics of DNA hairpin-loop fluctuations has been investigated by using a combination of fluorescence energy transfer and fluorescence correlation spectroscopy. We measure the chemical rates and the activation energies associated with the opening and the closing of the hairpin for different sizes and sequences of the loop and for ... More
Energy transfer primers with 5- or 6-carboxyrhodamine-6G as acceptor chromophores.
AuthorsHung SC, Ju J, Mathies RA, Glazer AN
JournalAnal Biochem
PubMed ID8660606
'Energy-transfer (ET) fluorescent primers for DNA sequencing and multiplex genetic analysis (Ju, J., Ruan, C., Fuller, C. W., Glazer, A. N., and Mathies, R. A. (1995) Proc. Natl. Acad. Sci. USA 92, 4347-4351) are named according to the convention D-N-A, where D is the donor, N is the number of ... More
Custom fluorescent-nucleotide synthesis as an alternative method for nucleic acid labeling.
AuthorsHenegariu O, Bray-Ward P, Ward DC
JournalNat Biotechnol
PubMed ID10700155
The variety of potentially useful dyes or haptenes available for fluorescent nucleic acid hybridization assays is far greater than what can be obtained from commercial sources. Since this diversity could be useful in many laboratory applications, we have developed a simple and inexpensive procedure for preparing nonpurified labeled nucleotides, for ... More
Single-molecule detection and identification of multiple species by multiparameter fluorescence detection.
AuthorsWidengren J, Kudryavtsev V, Antonik M, Berger S, Gerken M, Seidel CA
JournalAnal Chem
PubMed ID16536444
Two general strategies are introduced to identify and quantify single molecules in dilute solutions by employing a spectroscopic method for data registration and specific burst analysis, denoted multiparameter fluorescence detection (MFD). MFD uses pulsed excitation and time-correlated single-photon counting to simultaneously monitor the evolution of the eight-dimensional fluorescence information (fundamental ... More
DNA analysis by fluorescence quenching detection.
AuthorsXiao M, Kwok PY
JournalGenome Res
PubMed ID12727909
The analysis of human genetic variations such as single nucleotide polymorphisms (SNPs) has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching as the detection. The template-directed dye-terminator incorporation with fluorescence quenching detection ... More
Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy.
AuthorsTalaga DS, Lau WL, Roder H, Tang J, Jia Y, DeGrado WF, Hochstrasser RM
JournalProc Natl Acad Sci U S A
PubMed ID11087856
We report single-molecule measurements on the folding and unfolding conformational equilibrium distributions and dynamics of a disulfide crosslinked version of the two-stranded coiled coil from GCN4. The peptide has a fluorescent donor and acceptor at the N termini of its two chains and a Cys disulfide near its C terminus. ... More
Optimization of spectroscopic and electrophoretic properties of energy transfer primers.
AuthorsHung SC, Mathies RA, Glazer AN
JournalAnal Biochem
PubMed ID9324944
We have synthesized and characterized the spectroscopic properties of 56 energy transfer (ET) fluorescent dye-labeled primers differing in (i) the spacing between the donor and acceptor, (ii) the nature of the spacer (either oligonucleotide or polydideoxyribose phosphate), (iii) the primer sequence (M13 (-40), M13 (-21), M13 reverse, SP6, T3, and ... More