yDNA versus xDNA pyrimidine nucleobases: computational evidence for dependence of duplex stability on spacer location

The structural and binding properties of the natural and x- and y-pyrimidines were compared using computational methods. Our calculations show that although the x-pyrimidines favor different orientations about the glycosidic bond compared to the natural pyrimidines, which could have implications for the formation and resulting stability of xDNA duplexes and jeopardize the selectivity of expanded nucleobases, y-pyrimidines have rotational profiles more similar to the natural bases. Increasing the pyrimidine size using a benzene spacer leads to relatively minor changes in the hydrogen-bond strength of isolated Watson-Crick base pairs. However, differences in the anomeric carbon distances in pairs composed of x- or y-pyrimidines suggest yDNA may yield a more optimal expanded structure. By stacking two monomers via their centers of mass, we find that the expanded nucleobases stack much stronger than the natural bases. Additionally, although replacing xT by yT changes the stacking energy by less than 5 kJ mol (-1), replacing xC by yC significantly strengthens complexes with the natural nucleobases (by up to 30%). Calculations on larger duplex models composed of four nucleobases reveal that x- and y-pyrimidines can increase duplex stability of natural helices by strengthening both the intra and interstrand stacking interactions. Furthermore, when the total stability (sum of all hydrogen-bonding and (intrastrand and interstrand) stacking interactions) of the larger models is considered, y-pyrimidines lead to more stable complexes than x-pyrimidines for all but three duplex sequences. Thus, through analysis of a variety of properties, our calculations suggest that the location of the benzene spacer affects the properties of expanded nucleobases and the stability of expanded duplexes, and therefore should be carefully considered when designing future expanded analogues.     

Enhancement of protein sensitivity for MALDI imaging mass spectrometry after chemical treatment of tissue sections

MALDI imaging mass spectrometry (IMS) has become a valuable tool for the investigation of the content and distribution of molecular species in tissue specimens. Numerous methodological improvements have been made to optimize tissue section preparation and matrix deposition protocols, as well as MS data acquisition and processing. In particular for proteomic analyses, washing the tissue sections before matrix deposition has proven useful to improve spectral qualities by increasing ion yields and the number of signals observed. We systematically explore here the effects of several solvent combinations for washing tissue sections. To minimize experimental variability, all of the measurements were performed on serial sections cut from a single mouse liver tissue block. Several other key steps of the process such as matrix deposition and MS data acquisition and processing have also been automated or standardized. To assess efficacy, after each washing procedure the total ion current and number of peaks were counted from the resulting protein profiles. These results were correlated to on-tissue measurements obtained for lipids. Using similar approaches, several selected washing procedures were also tested for their ability to extend the lifetime as well as revive previously cut tissue sections. The effects of these washes on automated matrix deposition and crystallization behavior as well as their ability to preserve tissue histology were also studied. Finally, in a full-scale IMS study, these washing procedures were tested on a human renal cell carcinoma biopsy.     

Time-resolved studies of CN radical reactions and the role of complexes in solution

Time-resolved studies using 100 fs laser pulses generate CN radicals photolytically in solution and probe their subsequent reaction with solvent molecules by monitoring both radical loss and product formation. The experiments follow the CN reactants by transient electronic spectroscopy at 400 nm and monitor the HCN products by transient vibrational spectroscopy near 3.07 microm. The observation that CN disappears more slowly than HCN appears shows that the two processes are decoupled kinetically and suggests that the CN radicals rapidly form two different types of complexes that have different reactivities. Electronic structure calculations find two bound complexes between CN and a typical solvent molecule (CH(2)Cl(2)) that are consistent with this picture. The more weakly bound complex is linear with CN bound to an H atom through the N atom, and the more strongly bound complex has a structure in which the CN bridges Cl and H atoms of the solvent. Fitting the transient absorption data with a kinetic model containing two uncoupled complexes reproduces the data for seven different chlorinated alkane solvents and yields rate constants for the reaction of each type of complex. Depending on the solvent, the linear complex reacts between 2.5 and 12 times faster than the bridging complex and is the primary source of the HCN reaction product. Increasing the Cl atom content of the solvents decreases the reaction rate for both complexes.     

Development and assessment of scoring functions for protein identification using PMF data

PMF is one of the major methods for protein identification using the MS technology. It is faster and cheaper than MS/MS. Although PMF does not differentiate trypsin-digested peptides of identical mass, which makes it less informative than MS/MS, current computational methods for PMF have the potential to improve its detection accuracy by better use of the information content in PMF spectra. We developed a number of new probability-based scoring functions for PMF protein identification based on the MOWSE algorithm. We considered a detailed distribution of matching masses in a protein database and peak intensity, as well as the likelihood of peptide matches to be close to each other in a protein sequence. Our computational methods are assessed and compared with other methods using PMF data of 52 gel spots of known protein standards. The comparison shows that our new scoring schemes have higher or comparable accuracies for protein identification in comparison to the existing methods. Our software is freely available upon request. The scoring functions can be easily incorporated into other proteomics software packages.     

A study of piperidinium structure-directing agents in the synthesis of silica molecular sieves under fluoride-based conditions

This study is a continuation of our efforts to understand the interplay in the self-assembly chemistry for formation of molecular sieves from guest organocations and inorganic silicon oxide. In this particular study we focus on the competitive interplay of the organocations and the synthesis cofactor fluoride anion. The anions play a key role in structure determination, as a function of net solution concentration. They compete with the role for the space-filling organocation in determining which molecular sieve host structure will be specified. In this study we look at this competition in the synthesis for a series of 33 different organocations derived from the piperidine ring system. Derivatives were prepared which both fixed substituents on the carbon and nitrogen centers on the ring. Results were discussed in terms of product selectivity from synthesis as a function of solution concentration for the reactants. A total of 17 different host topologies were found in this series, and a correlation was seen for (a) open-framework lattices (low framework densities) under the most concentrated reaction conditions and then (b) high framework density products once the conditions were more dilute. Some surprising synthesis differences are seen in comparing the performance of these structure directing agents (SDAs) in fluoride media vs hydroxide media (the more conventional environment for zeolite/molecular sieve syntheses involving silicate chemistry). Finally molecular modeling was used to understand some of the trends in product selectivity for closely related guest (SDA) candidates.     

Environmental effects on the enhancement in natural and damaged DNA nucleobase acidity because of discrete hydrogen-bonding interactions

The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.     

Steps along the path to dihydrogen activation at [FeFe] hydrogenase structural models: dependence of the core geometry on electrocatalytic proton reduction

Differences in the rate of electrocatalytic proton reduction by Fe2(mu-PPh2)2(CO)6, DP, and the linked phosphido-bridged analogue Fe2(mu,mu-PPh(CH2)3PPh)(CO)6, 3P, suggest that dihydrogen elimination proceeds through a bridging hydride. The reaction path was examined using electrochemical, spectroscopic, and in silico studies where reduction of 3P gives a moderately stable monoanion [Kdisp(3P-) = 13] and a distorted dianion. The monomeric formulation of 3P- is supported by the form of the IR and EPR spectra. EXAFS analysis of solutions of 3P, 3P-, and 3P2- indicates a large increase in the Fe-Fe separation following reduction (from 2.63 to ca. 3.1-3.55 A). DFT calculations of the 3P, 3P-, 3P2- redox series satisfactorily reproduce the IR spectra in the nu(CO) region and the crystallographic (3P) and EXAFS-derived Fe-Fe distances. Digital simulation of the electrocatalytic response for proton reduction indicates a low rate of dihydrogen evolution from the two-electron, two-proton product of 3P (H23P), with more rapid dihydrogen evolution following further reduction of H23P. Because dihydrogen evolution is not observed upon formation of H2DP, dihydrogen evolution at the two-electron-reduced level does not involve protonation of a hydridic Fe-H ligand. The rates of dihydrogen elimination from H2DP, H23P, and H2Fe2(mu,mu-S(CH2)3S)(CO)6 (H23S) are related to the DFT-calculated H-H distances [H23S (1.880 A) < H23P (2.064 A) < H2DP (3.100 A)], and this suggests a common reaction path for the thiolato- and phosphido-bridged diiron carbonyl compounds.     

ALD resist formed by vapor-deposited self-assembled monolayers

A new process of applying molecular resists to block HfO2 and Pt atomic layer deposition has been investigated. Monolayer films are formed from octadecyltrichlorosilane (ODTS) or tridecafluoro-1,1,2,2-tetrahydrooctyltrichlorosilane (FOTS) and water vapor on native silicon oxide surfaces and from 1-octadecene on hydrogen-passivated silicon surfaces through a low-pressure chemical vapor deposition process. X-ray photoelectron spectroscopy data indicates that surfaces blocked by these monolayer resists can prevent atomic layer deposition of both HfO2 and Pt successfully. Time-dependent studies show that the ODTS monolayers continue to improve in blocking ability for as long as 48 h of formation time, and infrared spectroscopy measurements confirm an evolution of packing order over these time scales.     

How do size-expanded DNA nucleobases enhance duplex stability? Computational analysis of the hydrogen-bonding and stacking ability of xDNA bases

Computational chemistry (B3LYP, MP2) is used to study the properties of size-expanded DNA nucleobases generated by inserting a benzene spacer into the natural nucleobases. Although the addition of the spacer does not significantly affect the hydrogen-bonding properties of natural nucleobases, the orientation of the base about the glycosidic bond necessary for Watson-Crick binding is destabilized, which could have implications for the selectivity of expanded bases, as well as the stability of expanded duplexes. Consideration of the (stacked) binding energies in the preferred relative orientation of natural and expanded nucleobases aligned according to their centers of mass reveals that the stacking within natural dimers can be increased by up to 50% upon expansion of one nucleobase and up to 90% upon expansion of two nucleobases. The implications of these findings to the stability of expanded duplexes were revealed by considering simplified models of natural and mixed duplexes composed of four nucleobases. Although intra- and interstrand interactions within double helices are typically less than those predicted when nucleobases are stacked according to their centers of mass, some nucleobases utilize their full stacking potential within double helices, where both intra- and interstrand interactions can be significant. Most importantly, increasing the size of nucleobases within the duplex significantly increases both intra- and interstrand stacking interactions. Specifically, some interactions are double the magnitude of the corresponding intrastrand interactions in natural helices, and even greater increases in interstrand interactions are sometimes found. Thus, our work suggests that mixed duplexes composed of natural bases hydrogen bound to expanded bases may exploit the increase in the inherent stacking ability of the expanded bases in more than one way and thereby afford duplexes with greater stability than natural DNA.