Surface charges play a key role in determining the structure and function of proteins, DNA, and larger biomolecular structures. Here we report on the measurement of the electrostatic surface potential of individual DNA and avidin molecules with nanometer resolution using Kelvin probe force microscopy. We also show, for the first time, the surface potential of buffer salts shielding individual DNA molecules, which would not be possible with conventional ensemble techniques.

We describe nanoscale protein pores modified with a single hyperbranched dendrimer molecule inside the channel lumen. Sulfhydryl-reactive polyamido amine (PAMAM) dendrimers of generations 2, 3 and 5 were synthesized, chemically characterized, and reacted with engineered cysteine residues in the transmembrane pore alpha-hemolysin. Successful coupling was monitored using an electrophoretic mobility shift assay. The results indicate that G2 and G3 but not G5 dendrimers permeated through the 2.9 nm cis entrance to couple inside the pore. The defined molecular weight cutoff for the passage of hyperbranched PAMAM polymers is in contrast to the less restricted accessibility of flexible linear poly(ethylene glycol) polymers of comparable hydrodynamic volume. Their higher compactness makes sulfhydryl-reactive PAMAM dendrimers promising research reagents to probe the structure of porous membrane proteins with wide internal diameters. The conductance properties of PAMAM-modified proteins pores were characterized with single-channel current recordings. A G3 dendrimer molecule in the channel lumen reduced the ionic current by 45%, indicating that the hyperbranched and positively charged polymer blocked the passage of ions through the pore. In line with expectations, a smaller and less dense G2 dendrimer led to a less pronounced current reduction of 25%. Comparisons to recordings of PEG-modified pores revealed striking dissimilarities, suggesting that differences in the structural dynamics of flexible linear polymers vs compact dendrimers can be observed at the single-molecule level. Current recordings also revealed that dendrimers functioned as ion-selectivity filters and molecular sieves for the controlled passage of molecules. The alteration of pore properties with charged and hyperbranched dendrimers is a new approach and might be extended to inorganic nanopores with applications in sensing and separation technology.

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Analyzing DNA or RNA strands at the single-molecule level is an important research area which has delivered new insights for basic science. [1][2][3] Single-molecule DNA detection can also have a positive impact on biosensing and molecular diagnosis [4, 5] by offering reduced reagent consumption and the ability to examine minimal sample volumes without PCR amplification.[6] Several fluorescence-based methods have been developed to sequence-specifically detect individual nucleic acid strands and to identify mutations. These methods are capable of uncovering variations in the copy numbers of mRNA strands, [7][8][9][10] relatively large genetic alterations such as DNA deletions of at least 2 kb, [11][12][13][14] or small sequence changes up to five bases long. [15][16][17] Herein, we present a new approach to derive sequence information from DNA strands several hundred bases long. Within the method, base-specific fluorescence labeling is combined with brightness measurements to infer the number of trinucleotide repeats in highly repetitive DNA strands at the single-molecule level. The approach fills a methodological gap left by existing technologies and illustrates that measuring the fluorescence brightness of individual DNA molecules is a valid strategy to obtain sequence-specific information.Existing fluorescence-based approaches derive different types of genetic data from specific modes of fluorescence information. For example, copy numbers of cDNA or RNA [7][8][9][10] as well as single-point mutations [18] can be ascertained by the presence and/or localization of fluorescent signals from sequence-specific probes. Furthermore, large gene rearrangements, such as deletions, insertions or gene repetitions, are determined by measuring the spatial distance between two fluorescence probes bound to elongated DNA strands. [11][12][13][14] Sequencing methods, on the other hand, are used for the analysis of short base stretches by tracking the temporal order of fluorescence signals stemming from the release [15] or incorporation of several fluorescence-labeled nucleotides. [16,17] Fluorescence brightness measurements have also been used to size the length of DNA restriction fragments to determine point mutations at restriction cleavage sites. [19] But there are few other single-molecule approaches which apply fluorescence brightness measurements to infer more extensive sequence information from DNA strands.In order to address this shortage we developed an approach which determines the number of times a specific base occurs within a gene region using brightness information. The strategy is based on 1) the tagging of a specific base with fluorescence dyes followed by 2) the measurement of the accumulated brightness of the labeled strands via single-molecule fluorescence microscopy. To demonstrate its biological application potential, the approach is tested using huntingtin sequences with CAG trinucleotide repeats. Huntington's disease and at least eight other inherited neurodegenerative diseases share CAG triplet repeat exp...

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