Single-particle fluorescence intensity fluctuations of carbon nanodots.

Fluorescent carbon nanodots (CNDs) were synthesized in oxidized and reduced forms and were analyzed at the single-particle level. Images of single CNDs at different excitation energies revealed significant heterogeneity in the lower energy trap sites between particles. We observed that a high percentage of reduced CND particles transitioned between multiple fluorescence intensity levels indicative of multichromophoric systems. Despite this behavior, individual CNDs exhibit single-step photobleaching and transient blinking to the background level suggesting single-molecule behavior.

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.

We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics.

Transition between two regimes describing internal fluctuation of DNA in a nanochannel.

We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA.

Single molecule linear analysis of DNA in nano-channel labeled with sequence specific fluorescent probes.

An array of nano-channels was fabricated from silicon based semiconductor materials to stretch long, native dsDNA. Here we present a labeling scheme in which it is possible to identify the location of specific sequences along the stretched DNA molecules. The scheme proceeds by first using the strand displacement activity of the Vent (exo-) polymerase to generate single strand flaps on nicked dsDNA. These single strand flaps are hybridized with sequence specific fluorophore-labeled probes. Subsequent imaging of the DNA molecules inside a nano-channel array device allows for quantitative identification of the location of probes. The highly efficient DNA hybridization on the ss-DNA flaps is an excellent method to identify the sequence motifs of dsDNA as it gives us unique ability to control the length of the probe sequence and thus the frequency of hybridization sites on the DNA. We have also shown that this technique can be extended to a multi color labeling scheme by using different dye labeled probes or by combining with a DNA- polymerase-mediated incorporation of fluorophore-labeled nucleotides on nicking sites. Thus this labeling chemistry in conjunction with the nano-channel platform can be a powerful tool to solve complex structural variations in DNA which is of importance for both research and clinical diagnostics of genetic diseases.

FCS study of the thermodynamics of membrane protein insertion into the lipid bilayer chaperoned by fluorinated surfactants.

Experimental determination of the free energy (DeltaG) stabilizing the structure of membrane proteins (MPs) in their native environment has been hampered by the aggregation and precipitation of MPs outside the lipid bilayer. We recently demonstrated that the latter process can be prevented by the use of fluorinated surfactants, FTACs, that act as chaperones for MP insertion without partitioning in the membrane themselves. Here we combine the advantages of the chaperone-like ability of FTACs with the sensitivity of fluorescence correlation spectroscopy measurements to determine DeltaG of bilayer insertion of model MPs. First, we calibrate our approach by examining the effects of chaperoned insertion on DeltaG of transmembrane insertion of Annexin B12. We find that a shorter-chained surfactant, FTAC-C6, for which the working concentration range of 0.05-0.2 mM falls below CMC = 0.33 mM, has a mild effect on an apparent DeltaG. In contrast, additions of a longer-chained FTAC-C8 (CMC = 0.03 mM) result in a steep and nonlinear concentration dependence of DeltaG. We then apply the same methodology to the pH-triggered insertion of diphtheria toxin T-domain, which is known to be affected by nonproductive aggregation in solution. We find that the correction of the DeltaG value needed to compensate for unchaperoned insertion of the T-domain exceeds 3 kcal/mole. A relatively shallow and linear dependence of the DeltaG for Annexin B12 and T-domain insertion on FTAC-C6 concentration is encouraging for future applications of this surfactant in thermodynamic studies of the stability of other MPs.

Electron transfer reactions of redox cofactors in spinach photosystem I reaction center protein in lipid films on electrodes.

Thin film voltammetry was used to obtain direct, reversible, electron transfer between electrodes and spinach Photosystem I reaction center (PS I) in lipid films for the first time. This reaction center (RC) protein retains its native conformation in the films, and AFM showed that film structure rearranges during the first several minutes of rehydration of the film. Two well-defined chemically reversible reduction-oxidation peaks were observed for native PS I in the dimyristoylphosphatidylcholine films, and were assigned to phylloquinone, A(1) (E(m) = -0.54 V) and iron-sulfur clusters, F(A)/F(B) (E(m) = -0.19 V) by comparisons with PS I samples selectively depleted of these cofactors. Observed E(m) values may be influenced by protein-lipid interactions and electrode double-layer effects. Voltammetry was consistent with simple kinetically limited electron transfers, and analysis of reduction-oxidation peak separations gave electrochemical rate constants of 7.2 s(-)(1) for A(1) and 65 s(-)(1) for F(A)/F(B). A catalytic process was observed in which electrons were injected from PS I in films to ferredoxin in solution, mimicking in vivo electron shuttle from the terminal F(A)/F(B) cofactors to soluble ferredoxin during photosynthesis.