The Chromatin Structure of Well-Spread Demembranated Human Sperm Nuclei Revealed by Atomic Force Microscopy

The fundamental structure formed when genomic DNA is packaged by protamine in the human sperm nucleus still remains essentially unresolved. It is known that the binding of protamine, a small arginine-rich protein, to DNA generates a large dense, hydrophobic complex making the sperm chromatin structure difficult to study microscopically. To visualize the internal nuclear structures, isolated human sperm nuclei were swollen extensively in saline buffer using only a reducing agent. The nuclei were swollen during deposition onto coverglass and then imaged in the atomic force microscope (AFM). The two main results obtained from imaging individual well-spread nuclei indicate that native human sperm chromatin is: (1) particulate, consisting primarily of large nodular structures averaging 98 nm in diameter, and (2) also composed of smaller, nucleosome-like particles observed to form linear chains near the nuclear periphery. These two types of chromatin particles imaged by AFM are remarkably similar to other AFM measurements made on native and reconstituted sperm and somatic chromatin

Scanning Tunneling Microscope Images of Adenine and Thymine at Atomic Resolution

The scanning tunneling microscope has been used to obtain images of DNA that reveal its major and minor grooves and the direction of helical coiling, but sufficient resolution has not yet been achieved to identify its bases. To determine if this technology is capable of identifying individual DNA bases, we have examined the molecular arrangements of adenine and thymine attached to the basal plane of highly oriented pyrolytic graphite. Both molecules form highly organized lattices following deposition on heated graphite. Lattice dimensions, structural periodicities, and the epitaxy of adenine and thymine molecules with respect to the basal plane of graphite have been determined. Images of these molecules at atomic resolution reveal that the aromatic regions are strongly detected in both molecules while the various side-groups are not well-resolved. These studies provide the first evidence that tunneling microscopy can be used to discriminate between purines and pyrimidines

Analysis of Synthetic DNAs and DNA-Protamine Complexes with the Scanning Tunneling Microscope

Three duplex DNAs 22, 47, and 100 base-pairs in length have been imaged with the scanning tunneling microscope (STM) after deposition on highly oriented pyrolytic graphite (HOPG). Images of the 47 base-pair (bp) molecules are resolved sufficiently to identify the two phosphodiester strands, the direction of helical coiling (this molecule contains three turns of left-handed helix), and single-stranded ends. Length measurements indicate that all three DNA sequences have adopted an A-like conformation. DNA-protamine complexes were also prepared and imaged under similar conditions. Length measurements of the complexes demonstrate that the binding of bull protamine 1 to the 47-mer stabilizes the DNA in a B conformation and prevents the B to A transition that has been shown to occur as the DNA molecules dehydrate on the surface. Measurements of the diameter of the complex (3 nm) were also obtained and were found to be only slightly larger than the DNA molecule. This observation is consistent with the binding of the protamine molecule inside one of the grooves

Monitoring Dynamic Protein Expression in Single Living E. Coli. Bacterial Cells by Laser Tweezers Raman Spectroscopy

Laser tweezers Raman spectroscopy (LTRS) is a novel, nondestructive, and label-free method that can be used to quantitatively measure changes in cellular activity in single living cells. Here, we demonstrate its use to monitor changes in a population of E. coli cells that occur during overexpression of a protein, the extracellular domain of myelin oligodendrocyte glycoprotein (MOG(1-120)) Raman spectra were acquired of individual E. coli cells suspended in solution and trapped by a single tightly focused laser beam. Overexpression of MOG(1-120) in transformed E. coli Rosetta-Gami (DE3)pLysS cells was induced by addition of isopropyl thiogalactoside (IPTG). Changes in the peak intensities of the Raman spectra from a population of cells were monitored and analyzed over a total duration of three hours. Data was also collected for concentrated purified MOG(1-120) protein in solution, and the spectra compared with that obtained for the MOG(1-120) expressing cells. Raman spectra of individual, living E. coli cells exhibit signatures due to DNA and protein molecular vibrations. Characteristic Raman markers associated with protein vibrations, such as 1257 cm{sup -1}, 1340 cm{sup -1}, 1453 cm{sup -1} and 1660 cm{sup -1}, are shown to increase as a function of time following the addition of IPTG. Comparison of these spectra and the spectra of purified MOG protein indicates that the changes are predominantly due to the induction of MOG protein expression. Protein expression was found to occur mostly within the second hour, with a 470% increase relative to the protein expressed in the first hour. A 230% relative increase between the second and third hour indicates that protein expression begins to level off within the third hour. It is demonstrated that LTRS has sufficient sensitivity for real-time, nondestructive, and quantitative monitoring of biological processes, such as protein expression, in single living cells. Such capabilities, which are not currently available in flow cytometry, open up new possibilities for analyzing cellular processes occurring in single microbial and eukaryotic cells

Ultra-fast Laser Synthesis of Nanopore Arrays in Silicon for Bio-molecule Separation and Detection

We demonstrate that interference of ultra-fast pulses of laser light can create regular patterns in thin silicon membranes that are compatible with the formation of a uniform array of nanopores. The spacing and size of these pores can be tuned by changing the laser energy, wavelength and number of ultra-short pulses. Short pulses and wavelengths ({approx}550 nm and smaller) are needed to define controllable nanoscale features in silicon. Energy must be localized in time and space to produce the etching, ablation or amorphization effects over the {approx}100 nm length scales appropriate for definition of single pores. Although in this brief study pattern uniformity was limited by laser beam quality, a complementary demonstration reported here used continuous-wave interferometric laser exposure of photoresist to show the promise of the ultra-fast approach for producing uniform pore arrays. The diameters of these interferometrically-defined features are significantly more uniform than the diameters of pores in state-of-the-art polycarbonate track etch membranes widely used for molecular separations

Evidence that Localized Variation in Primate Sequence Divergence Arises from an Influence of Nucleosome Placement on DNA Repair

Understanding the origins of localized substitution rate heterogeneity has important implications for identifying functional genomic sequences. Outside of gene regions, the origins of rate heterogeneity remain unclear. Experimental studies establish that chromatin compaction affects rates of both DNA lesion formation and repair. A functional association between chromatin status and 5-methyl-cytosine also exists. These suggest that both the total rate and the type of substitution will be affected by chromatin status. Regular positioning of nucleosomes, the building block of chromatin, further predicts that substitution rate and type should vary spatially in an oscillating manner. We addressed chromatin's influence on substitution rate and type in primates. Matched numbers of sites were sampled from Dnase I hypersensitive (DHS) and closed chromatin control flank (Flank). Likelihood ratio tests revealed significant excesses of total and of transition substitutions in Flank compared with matched DHS for both intergenic and intronic samples. An additional excess of CpG transitions was evident for the intergenic, but not intronic, regions. Fluctuation in substitution rate along ∼1,800 primate promoters was measured using phylogenetic footprinting. Significant positive correlations were evident between the substitution rate and a nucleosome score from resting human T-cells, with up to ∼50% of the variance in substitution rate accounted for. Using signal processing techniques, a dominant oscillation at ∼200 bp was evident in both the substitution rate and the nucleosome score. Our results support a role for differential DNA repair rates between open and closed chromatin in the spatial distribution of rate heterogeneity

Vasopressin V2R-Targeting Peptide Carrier Mediates siRNA Delivery into Collecting Duct Cells

Internalization of receptor proteins after interacting with specific ligands has been proposed to facilitate siRNA delivery into the target cells via receptor-mediated siRNA transduction. In this study, we demonstrated a novel method of vasopressin V2 receptor (V2R)-mediated siRNA delivery against AQP2 in primary cultured inner medullary collecting duct (IMCD) cells of rat kidney. We synthesized the dDAVP conjugated with nine D-arginines (dDAVP-9r) as a peptide carrier for siRNA delivery. The structure of synthetic peptide carrier showed two regions (i.e., ligand domain to V2R (dDAVP) and siRNA carrying domain (nine D-arginine)) bisected with a spacer of four glycines. The results revealed that 1) synthesized dDAVP-9r peptides formed a stable polyplex with siRNA; 2) siRNA/dDAVP-9r polyplex could bind to the V2R of IMCD cells and induced AQP2 phosphorylation (Ser 256); 3) siRNA/dDAVP-9r polyplex was stable in response to the wide range of different osmolalities, pH levels, or to the RNases; 4) fluorescein-labeled siRNA was delivered into V2R-expressing MDCK and LLC-PK1 cells by siRNA/dDAVP-9r polyplex, but not into the V2R-negative Cos-7 cells; and 5) AQP2-siRNA/dDAVP-9r polyplex effectively delivered siRNA into the IMCD cells, resulting in the significant decrease of protein abundance of AQP2, but not AQP4. Therefore, for the first time to our knowledge, we demonstrated that V2R-mediated siRNA delivery could be exploited to deliver specific siRNA to regulate abnormal expression of target proteins in V2R-expressing kidney cells. The methods could be potentially used in vivo to regulate abnormal expression of proteins associated with disease conditions in the V2R-expressing kidney cells

Sexual Selection Halts the Relaxation of Protamine 2 among Rodents

Sexual selection has been proposed as the driving force promoting the rapid evolutionary changes observed in some reproductive genes including protamines. We test this hypothesis in a group of rodents which show marked differences in the intensity of sexual selection. Levels of sperm competition were not associated with the evolutionary rates of protamine 1 but, contrary to expectations, were negatively related to the evolutionary rate of cleaved- and mature-protamine 2. Since both domains were found to be under relaxation, our findings reveal an unforeseen role of sexual selection: to halt the degree of degeneration that proteins within families may experience due to functional redundancy. The degree of relaxation of protamine 2 in this group of rodents is such that in some species it has become dysfunctional and it is not expressed in mature spermatozoa. In contrast, protamine 1 is functionally conserved but shows directed positive selection on specific sites which are functionally relevant such as DNA-anchoring domains and phosphorylation sites. We conclude that in rodents protamine 2 is under relaxation and that sexual selection removes deleterious mutations among species with high levels of sperm competition to maintain the protein functional and the spermatozoa competitive