Native DNA electronics: is it a matter of nanoscale assembly?

The genomic DNA is enveloped by nanotubes formed by the nuclear aggregates of polyamines (NAPs) that induce DNA conformational changes and provide protection and increased interaction abilities for the double strands. In a physiological environment, the nanotube arrangement is initiated by spontaneous interaction among the terminal amino groups of the polyamines and the phosphate ions, with the consequent formation of cyclic monomers that hook at the DNA grooves. The polymer thus formed has the morphological features of an organic semiconductor and therefore, it can be considered to be able to conduct electric charges. Phosphate ions positioned on the NAP external surface could regulate, as in a physical electric circuit, both linear and rotational (histones) protein motion, in accordance with the basilar principles of the electronics. A model of a carrier system for protein motion along the polymer wrapping the DNA strands, based on the phosphate-phosphate complexation, is proposed.

DNA-HMGB1 interaction: The nuclear aggregates of polyamine mediation.

Nuclear aggregates of polyamines (NAPs) are supramolecular compounds generated by the self-assembly of protonated nuclear polyamines (spermine, spermidine and putrescine) and phosphate ions. In the presence of genomic DNA, the hierarchical process of self-structuring ultimately produces nanotube-like polymers that envelop the double helix. Because of their modular nature and their aggregation-disaggregation dynamics, NAPs confer plasticity and flexibility to DNA. Through the disposition of charges, NAPs also enable a bidirectional stream of information between the genome and interacting moieties. High mobility group (HMG) B1 is a non-histone chromosomal protein that binds to DNA and that influences multiple nuclear processes. Because genomic DNA binds to either NAPs or HMGB1 protein, we explored the ability of in vitro self-assembled NAPs (ivNAPs) to mediate the DNA-HMGB1 interaction. To this end, we structured DNA-NAPs-HMGB1 and DNA-HMGB1-NAPs ternary complexes in vitro through opportune sequential incubations. Mobility shift electrophoresis and atomic force microscopy showed that the DNA-ivNAPs-HGMB1 complex had conformational assets supposedly more suitable those of the DNA-HGMB1-ivNAPs to comply with the physiological and functional requirements of DNA. Our findings indicated that ivNAPs act as mediators of the DNA-HMGB1 interaction.

Mass spectrometric analysis of in vitro nuclear aggregates of polyamines.

RATIONALE: In the nuclei of eukaryotic cells, polyamines and phosphate ions self-assemble via ionic interactions and hydrogen bonding, generating three families of supramolecular compounds that have been named large (l-), medium (m-) and small (s-) nuclear aggregates of polyamines (NAPs). In a simulated nuclear environment, polyamines and phosphate ions generate the in vitro NAPs (ivNAPs) that share strict structural and functional analogies with their cellular cognates. Mass spectrometric data are expected to provide important structural details of NAPs/ivNAPs. METHODS: We used both electrospray ionization (ESI) and nitrocellulose (NC) matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to support a variety of analytical techniques previously addressed to structurally characterize NAPs/ivNAPs. RESULTS: The dominant m/z values of s-ivNAP (m/z 735, 749, 761) are compatible with a defined set of cyclic or linear aggregates. On the basis of the experimental molecular mass (a cluster centred at m/z 2980), the m-ivNAP corresponds to the supramolecular assembly of four modules of s-ivNAPs. No informative mass spectra were obtained for the l-ivNAP. CONCLUSIONS: MS data support the models of NAPs that have been inferred by using an array of analytical techniques. NC MALDI-MS contributed much more effectively than ESI-MS to the structural characterization of ivNAPs.

Nuclear aggregates of polyamines in a radiation-induced DNA damage model.

Polyamines (PA) are believed to protect DNA minimizing the effect of radiation damage either by inducing DNA compaction and aggregation or acting as scavengers of free radicals. Using an in vitro pDNA double strand breakage assay based on gel electrophoretic mobility, we compared the protective capability of PA against γ-radiation with that of compounds generated by the supramolecular self-assembly of nuclear polyamines and phosphates, named Nuclear Aggregates of Polyamines (NAPs). Both unassembled PA and in vitro produced NAPs (ivNAPs) were ineffective in conferring pDNA protection at the sub-mM concentration. Single PA showed an appreciable protective effect only at high (mM) concentrations. However, concentrations of spermine (4+) within a critical range (0.481 mM) induced pDNA precipitation, an event that was not observed with NAPs-pDNA interaction. We conclude that the interaction of individual PA is ineffective to assure DNA protection, simultaneously preserving the flexibility and charge density of the double strand. Furthermore, data obtained by testing polyamine and ivNAPS with the current radiation-induced DNA damage model support the concept that PA-phosphate aggregates are the only forms through which PA interact with DNA.

DNA and nuclear aggregates of polyamines.

Polyamines (PAs) are linear polycations that are involved in many biological functions. Putrescine, spermidine and spermine are highly represented in the nucleus of eukaryotic cells and have been the subject of decades of extensive research. Nevertheless, their capability to modulate the structure and functions of DNA has not been fully elucidated. We found that polyamines self-assemble with phosphate ions in the cell nucleus and generate three forms of compounds referred to as Nuclear Aggregates of Polyamines (NAPs), which interact with genomic DNA. In an in vitro setting that mimics the nuclear environment, the assembly of PAs occurs within well-defined ratios, independent of the presence of the DNA template. Strict structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their cellular homologues. Atomic force microscopy showed that ivNAPs, as theoretically predicted, have a cyclic structure, and in the presence of DNA, they form a tube-like arrangement around the double helix. Features of the interaction between ivNAPs and genomic DNA provide evidence for the decisive role of "natural" NAPs in regulating important aspects of DNA physiology, such as conformation, protection and packaging, thus suggesting a new vision of the functions that PAs accomplish in the cell nucleus.

DNA is wrapped by the nuclear aggregates of polyamines: the imaging evidence.

In the cell nucleus, putrescine, spermidine, and spermine self-assemble with phosphate ions to generate three forms of compounds, named nuclear aggregates of polyamines (NAPs), which may interact with DNA. In an in vitro setting mimicking the cell nucleus milieu, this molecular aggregation occurs within well-defined ratios. Structural and functional analogies exist between the in vitro NAPs (ivNAPs) and their extractive homologues. The present Article reports images of ivNAPs at different resolution levels. Independent of the DNA template, ivNAPs become hierarchically stacked to produce ultimately macroscopic filamentous structures. The ivNAP-DNA complexes arranged in long and repetitive structures that displayed the self-similar features of natural fractals when dehydrated onto glass slides. Atomic force microscopy showed that ivNAPs have a cyclic structure and dispose around the DNA in a tube-like arrangement. Overall, the images indicate that these aggregates envelope the genomic DNA, thus proving that NAPs play a crucial role in DNA compaction and functioning.

The in vitro nuclear aggregates of polyamines.

Natural polyamines (putrescine, spermidine, and spermine) self-assemble in a simulated physiological environment (50 mm sodium phosphate buffer, pH 7.2), generating in vitro nuclear aggregates of polyamines (ivNAPs). These supramolecular compounds are similar in structure and molecular mass to naturally occurring cellular nuclear aggregates of polyamines, and they share the ability of NAPs to interact with and protect the genomic DNA against nuclease degradation. Three main ivNAP compounds were separated by gel permeation chromatography. Their elution was carried out with 50 mm sodium phosphate buffer supplemented with 150 mm NaCl. Freezing and thawing of selected chromatographic fractions obtained by GPC runs in which the mobile phase was sodium phosphate buffer not supplemented with NaCl yielded three different microcrystallites, specifically corresponding to the ivNAPs, all of which were able to bind DNA. In this study, we demonstrated that in vitro self-assembly of polyamines and phosphates is a spontaneous, reproducible and inexpensive event, and provided the indications for the production of the ivNAPs as a new tool for manipulating the genomic DNA machinery.

Increased left ventricular mass in pre-liver transplantation cirrhotic patients.

OBJECTIVE: Severe liver disease is associated with abnormalities in cardiac geometry and function. We aimed to assess the prevalence of these abnormalities and to determine if they represent an adaptation of the heart to the haemodynamic overload associated with liver dysfunction. METHODS: Seventy cirrhotic patients underwent standard Doppler echocardiography, as a screening evaluation for liver transplantation, and were compared with 70 normal subjects matched for age and sex. The values of echocardiographically measured left ventricular mass (LVM) were compared with those predicted from individual haemodynamic load, sex and height, which represent the compensatory values. LVM was considered inappropriately high when the observed/predicted LVM ratio was >128%. RESULTS: Cirrhotic patients had higher LVM index (40.6 +/- 11.2 vs. 36.3 +/- 7.7 g/m; P = 0.009)), similar values of ejection fraction, but lower intrinsic wall mechanics (P < 0.01) compared to controls. The observed/predicted LVM ratio was also significantly increased (117.7 +/- 30.2 vs. 106.5 +/- 16.8%; P < 0.01) and prevalence of inappropriate LVM was almost three-fold higher in cirrhotic patients (27.7 vs. 10.0%; P < 0.05) than in controls. Cirrhotic patients also presented mild impairment of left ventricular systolic function, documented by lower values of midwall shortening. CONCLUSIONS: Patients with severe liver disease have LVM values exceeding the compensatory needs to sustain haemodynamic overload, associated with subclinical systolic dysfunction.

Nuclear aggregates of polyamines.

Nuclear aggregates of polyamines (NAPs) are cyclic supramolecular compounds made of polyamines and phosphate groups. Three different aggregates, s-NAP, m-NAP and l-NAP, with a molecular weight of 1035, 5175 and 9552 Da, respectively, are described. These molecules interact with genomic DNA. In consequence of this interaction, NAPs not only protect DNA from nucleases with extraordinarily greater efficiency than single polyamines (spermine, spermidine and putrescine), but also induce noticeable changes in DNA condensation status, as shown by temperature-dependent modifications of DNA electrophoretic properties. The biochemical characterization of these compounds has allowed the definition of a structural model for each NAP. According to this model, five s-NAPs assemble together to form a m-NAP unit. We hypothesize that the complexation of s-NAP into m-NAP favours the transition to Z-DNA through the progressive widening of DNA strands and the exposure of bases. We propose that NAPs, by wrapping the DNA helixes, form supramolecular tunnel-like structures that confer efficient protection without affecting DNA elasticity.

Nuclear aggregates of polyamines are supramolecular structures that play a crucial role in genomic DNA protection and conformation.

In a previous study we showed that natural polyamines interact in the nuclear environment with phosphate groups to form molecular aggregates [nuclear aggregates of polyamines (NAPs)] with estimated molecular mass values of 8000, 4800 and 1000 Da. NAPs were found to interact with genomic DNA, influence its conformation and interfere with the action of nucleases. In the present work, we demonstrated that NAPs protect naked genomic DNA from DNase I, whereas natural polyamines (spermine, spermidine and putrescine) fail to do so. In the context of DNA protection, NAPs induced noticeable changes in DNA conformation, which were revealed by temperature-dependent modifications of DNA electrophoretic properties. In addition, we presented, for NAPs, a structural model of polyamine aggregation into macropolycyclic compounds. We believe that NAPs are the sole biological forms by which polyamines efficiently protect genomic DNA against DNase I, while maintaining its dynamic structure.

Increased IGF-I : IGFBP-3 ratio in patients with hepatocellular carcinoma.

BACKGROUND: The development of hepatocellular carcinoma in liver cirrhosis is associated with altered synthesis and secretion of several growth factors. AIM: The aim of this prospective study was to investigate the potential implication of IGF-I and its major binding protein (IGFBP-3) in the development of hepatocellular carcinoma. PATIENTS AND METHODS: IGF-I and IGFBP-3 were measured in 150 healthy subjects, 40 patients with liver cirrhosis and 63 with liver cirrhosis and untreated hepatocellular carcinoma. The ratio between IGF-I and IGFBP-3 was also calculated. RESULTS: Serum IGF-I (70 +/- 10 and 65 +/- 7 vs. 185 +/- 6.4 microg/l, P < 0.001) and IGFBP-3 levels (1225 +/- 113 and 984 +/- 67 vs. 3017 +/ -80 microg/l, P < 0.001) were lower in patients with liver cirrhosis, without or with hepatocellular carcinoma, than in controls. Age was negatively correlated with IGF-I levels in patients with liver cirrhosis (r = -0.6; P = 0.0002) as well as in controls (r = -0.8, P < 0.0001), but not in patients with hepatocellular carcinoma (r = -0.2; P = 0.2). Additionally, in patients with liver cirrhosis (r = -0.54; P = 0.0003) and more weakly in those with hepatocellular carcinoma (r = -0.24; P = 0.04) IGF-I levels were negatively correlated with liver failure measured according with Child class. Despite patients with class C hepatocellular carcinoma being older than those in the same functional class with cirrhosis (64 +/- 2 vs. 57 +/- 12 years, P < 0.01), they had a significantly increased IGF-I : IGFBP-3 ratio (0.18 +/- 0.05 vs. 0.41 +/- 0.09, P = 0.04), due mostly to increased IGF-I levels (27.1 +/- 5.6 vs. 42 +/- 6.2 microg/l) as IGFBP-3 levels were similar to patients with cirrhosis (734 +/- 81 vs. 679 +/- 83 microg/l). CONCLUSIONS: Hepatocellular carcinoma is associated with a higher IGF-I : IGFBP-3 ratio than that found in patients with liver cirrhosis and a similar degree of liver failure.

Polyamines interact with DNA as molecular aggregates.

New compounds, named nuclear aggregates of polyamines, having a molecular mass of 8000, 4800 and < 1000 Da, were found in the nuclear extracts of several replicating cells. Their molecular structure is based on the formation of ionic bonds between polyamine ammonium and phosphate groups. The production of the 4800 Da compound, resulting from the aggregation of five or more < 1000 Da units, was increased in Caco-2 cells treated with the mitogen gastrin. Dissolving single polyamines in phosphate buffer resulted in the in vitro aggregation of polyamines with the formation of compounds with molecular masses identical to those of natural aggregates. After the interaction of the 4800 Da molecular aggregate with the genomic DNA at 37 degrees C, both the absorbance of DNA in phosphate buffer and the DNA mobility in agarose gel increased greatly. Furthermore, these compounds were able to protect the genomic DNA from digestion by DNase I, a phosphodiesterasic endonuclease. Our data indicate that the nuclear aggregate of polyamines interacts with DNA phosphate groups and influence, more efficaciously than single polyamines, both the conformation and the protection of the DNA.