We describe a simple, quantitative assay for any amplifiable DNA sequence that uses a video camera to monitor multiple polymerase chain reactions (PCRs) simultaneously over the course of thermocycling. The video camera detects the accumulation of double-stranded DNA (dsDNA) in each PCR using the increase in the fluorescence of ethidium bromide (EtBr) that results from its binding duplex DNA. The kinetics of fluorescence accumulation during thermocycling are directly related to the starting number of DNA copies. The fewer cycles necessary to produce a detectable fluorescence, the greater the number of target sequences. Results obtained with this approach indicate that a kinetic approach to PCR analysis can quantitate DNA sensitively, selectively and over a large dynamic range. This approach also provides a means of determining the effect of different reaction conditions on the efficacy of the amplification and so can provide insight into fundamental PCR processes.

We have used intramolecular cross-linking, MS, and sequence threading to rapidly identify the fold of a model protein, bovine basic fibroblast growth factor (FGF)-2. Its tertiary structure was probed with a lysine-specific cross-linking agent, bis(sulfosuccinimidyl) suberate (BS 3 ). Sites of cross-linking were determined by tryptic peptide mapping by using time-of-flight MS. Eighteen unique intramolecular lysine (Lys-Lys) cross-links were identified. The assignments for eight cross-linked peptides were confirmed by using post source decay MS. The interatomic distance constraints were all consistent with the tertiary structure of FGF-2. These relatively few constraints, in conjunction with threading, correctly identified FGF-2 as a member of the ␤-trefoil fold family. To further demonstrate utility, we used the top-scoring homolog, IL-1␤, to build an FGF-2 homology model with a backbone error of 4.8 Å (rms deviation). This method is fast, is general, uses small amounts of material, and is amenable to automation. In recent years, the number of novel proteins identified by genomic (1, 2) and proteomic projects has dramatically increased, with a concomitant need for more rapid determination of their tertiary structures.Visualization of the three-dimensional structures of proteins has traditionally been realized by x-ray crystallography and NMR. These techniques produce high resolution atomic data but require relatively large amounts (10 to 100 mg) of pure analyte in a particular solution or crystalline state. Even if these conditions are met, it can take months or even years to generate a molecular structure by following these methodologies.To develop an alternative approach to structure determination that could keep pace with the rate of novel protein identification, we have re-examined cross-linking technology in the light of newer analytical protocols for the separation and identification of complex peptide mixtures. Previous investigators have shown that cross-linking experiments can provide low resolution interatomic distance information (3). In theory, given enough distance information, it is possible to solve the tertiary structure of a macromolecule (4, 5).The challenge we faced in trying to generate such information in a short time using cross-linking technology was to devise a rapid method for identifying cross-linked residues. MS affords high throughput but has rarely been used for the identification of cross-links. One study has been published where disuccinimidyl ester cross-linking, Edman sequencing, and MS were used to validate a model of human erythropoietin (6). Recent advances in MS (7, 8) gave us the means whereby we could determine the masses and sequences of large peptides with high accuracy and sensitivity (9, 10). These improvements make it feasible to analyze complex peptide mixtures from proteolytically digested, cross-linked proteins (11) very quickly. Specifically, we describe the use of chemical cross-linking and time-of-flight (TOF) MS to identify Lys-Lys cross-links. We also show how t...

We have enhanced the polymerase chain reaction (PCR) such that specific DNA sequences can be detected without opening the reaction tube. This enhancement requires the addition of ethidium bromide (EtBr) to a PCR. Since the fluorescence of EtBr increases in the presence of double-stranded (ds) DNA an increase in fluorescence in such a PCR indicates a positive amplification, which can be easily monitored externally. In fact, amplification can be continuously monitored in order to follow its progress. The ability to simultaneously amplify specific DNA sequences and detect the product of the amplification both simplifies and improves PCR and may facilitate its automation and more widespread use in the clinic or in other situations requiring high sample throughput.

Fourier transform infrared difference spectroscopy has been used to obtain the vibrational modes. in the chro-*mophore and apoprotein 'that change in intensity or position between light-adapted bacteriorhodopsin and the K and M-intermediates in its photocycle and between dark-adapted and lightadapted bacteriorhodopsin. Our infrared' measurements provide independent verification of resonance Raman results that in lightadapted bacteriorhodopsin the protein-chromophore linkage is a protonated Schiff base and in the M state the Schiff base is un-,protonated. Although we cannot unambiguously identify the Schiff base stretching frequency in the K state, the most'likely interpretation of deuterium shifts of the chromophore hydrogen out-ofplane vibrations is that the Schiff base in K is protonated. The intensity of the hydrogen out-of-plane vibrations in the K state compared with the intensities of.those in light-adapted and'darkadapted bacteriorhodopsin shows that the conformation of the chromophore in K is considerably distorted. In addition, we find evidence that the conformation of the protein changes during the photocycle.Bacteriorhodopsin (bR) is the light-energy transducing protein found in the purple membrane (PM) of the extreme halophile Halobacterium halobium (1-4). The chromophore in bacteriorhodopsin is a single molecule of retinal, covalently bound to the £-amino group of a lysine (Lys-216) via a Schiffbase linkage (Fig 1). Upon absorption of light, the light-adapted form of bR (bR ) undergoes a photocycle, bRLA +--* K --L --M -O 0 bRLA, during which protons are pumped from the inside of the cell to the extracellular medium. The resulting proton gradient is used by the cell to generate chemical energy in the form ofATP and drive other energy-requiring processes. In the dark, bRLA thermally converts to the dark-adapted form of bR (bRDA).The mechanism of this light driven proton pump has been studied by using visible and ultraviolet, resonance Raman (5), and infrared (IR) (6-8) spectroscopies and chemical extraction techniques. These investigations strongly suggest that during the photocycle changes occur in both the isomeric state of the chromophore and the state ofprotonation of the Schiff'base. In particular, chemical extraction experiments have provided evidence that the chromophore in bRLA is in an all-trans configuration, that in the L and M states it is in a 13-cis configuration, and that in bRDA the chromophore exists in two isomeric forms, all-trans and 13-cis, in a ratio of approximately 1: 1 (9-11).Evidence for the conformation of the chromophore in situ comes primarily from comparisons between the resonance Raman vibrational spectra in both 'H20 and 2H20 of native bR, bR in which analogs ofretinal have been incorporated, and retinal 'Schiff bases. Analysis of the results from such work is dif-CH3 CH3