TY - JOUR TI - Eigenvector mapping: a method for discerning solvent effects on vibrational spectra AU - Lappi, S. E. AU - Franzen, S. T2 - Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy. AB - This paper reports a density functional theory (DFT) analysis of the adenine spectra in a hydrogen-bonding environment. We compare the theoretical vibrational spectra of 26 model systems in which water has been hydrogen bonded to adenine with the experimental frequencies of the solid state infrared spectra (150-1700 cm(-1)) of polycrystalline adenine and the experimental frequencies observed in matrix isolation spectra of adenine [J. Phys. Chem. 100 (1996) 3527]. The vibrational eigenvectors of adenine are compared by taking the dot product to determine how the normal modes of the 15-adenine atoms are affected by different hydrogen bonding geometries. Using the isolated adenine molecule as a reference permits a comparison of different calculated spectra in terms of the projections of various normal modes and the determination of the potential energy redistribution among normal modes. This method creates a map of the normal modes using the isolated adenine molecule as a reference. Improvement in agreement between the polycrystalline data and a model of adenine with four waters is most striking. The improvement in the fit between matrix isolation data and a model of adenine with a single water was not as dramatic as the fit seen for the polycrystalline data, but the fact that a single hydrogen-bonded water shifted the spectra of the model to a closer fit than that of isolated adenine is important. We call this method eigenvector mapping. The eigenvector mapping method can be used to extract the normal modes of a parent molecule from a solvent model system. The application of this method is important because it aids in the interpretation of complex molecular interactions in terms of the spectrum of an isolated molecule. The eigenvector mapping procedure will be shown to greatly improve the correspondence between the model and the experimental data. DA - 2004/// PY - 2004/// DO - 10.1016/S1386-1425(03)00248-8 VL - 60 IS - 02-Jan SP - 357-370 ER - TY - JOUR TI - Characterization of single- and double-stranded DNA on gold surfaces AU - Moses, S AU - Brewer, SH AU - Lowe, LB AU - Lappi, SE AU - Gilvey, LBG AU - Sauthier, M AU - Tenent, RC AU - Feldheim, DL AU - Franzen, S T2 - LANGMUIR AB - Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5‘-C6H12SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation−infrared reflection absorption spectroscopy (PM−IRRAS). The formation of dsDNA on the surface was identified by PM−IRRAS by a dsDNA IR signature at ∼1678 cm-1 that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 °C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au−S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces. DA - 2004/12/7/ PY - 2004/12/7/ DO - 10.1021/la0492815 VL - 20 IS - 25 SP - 11134-11140 SN - 0743-7463 ER - TY - JOUR TI - Infrared spectra of (H2O)-O-16, (H2O)-O-18 and D2O in the liquid phase by single-pass attenuated total internal reflection spectroscopy AU - Lappi, SE AU - Smith, B AU - Franzen, S T2 - SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY AB - Mid-infrared attenuated total internal reflection (ATR) spectra of H216O, H218O and D216O in the liquid state were obtained and normal coordinate analysis was performed based on the potential energy surface obtained from density functional theory (DFT) calculations. Fits of the spectra to multiple Gaussians showed a consistent fit of three bands for the bending region and five bands for the stretching region for three isotopomers, H216O, H218O and D216O. The results are consistent with previous work and build on earlier studies by the inclusion of three isotopomers and mixtures using the advantage of single-pass ATR to obtain high quality spectra of the water stretching bands. DFT calculation of the vibrational spectrum of liquid water was conducted on seven model systems, two systems with periodic boundary conditions (PBC) consisting of four and nine H216O molecules, and five water clusters consisting of 4, 9, 19, 27 and 32 H216O molecules. The PBC and cluster models were used to obtain a representation of bulk water for comparison with experiment. The nine-water PBC model was found to give a good fit to the experimental line shapes. A difference is observed in the broadening of the water bending and stretching vibrations indicative of a difference in the rate of pure dephasing. The nine-water PBC calculation was also used to calculate the wavenumber shifts observed in the water isotopomers. DA - 2004/9// PY - 2004/9// DO - 10.1016/j.saa.2003.12.042 VL - 60 IS - 11 SP - 2611-2619 SN - 1386-1425 KW - IR KW - attenuated total reflection KW - (H2O)-O-16 KW - (H2O)-O-18 KW - (D2O)-O-16 KW - density functional theory calculations ER - TY - JOUR TI - Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome AU - Shapkina, T AU - Lappi, S AU - Franzen, S AU - Wollenzien, P T2 - NUCLEIC ACIDS RESEARCH AB - Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10–40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 × 109 W m–2, to determine strand breakage yields and the frequency and pattern of RNA–RNA cross‐ linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 × 10–3 over the incident intensity range studied. The yield for RNA–RNA cross‐linking was 3 × 10–4 cross‐links/photon at the intensity of 4.5 × 109 W m–2, an ∼4‐fold higher yield per photon than obtained with a transilluminator. The cross‐link yield/photon decreased at higher light intensities, probably due to intensity‐dependent photoreversal. The pattern of cross‐linking was similar to that observed with low intensity irradiation but with four additional long‐range cross‐links not previously seen in E.coli ribosomes. Cross‐ linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation. DA - 2004/2// PY - 2004/2// DO - 10.1093/nar/gkh320 VL - 32 IS - 4 SP - 1518-1526 SN - 1362-4962 ER - TY - JOUR TI - Infrared detection of a phenylboronic acid terminated alkane thiol monolayer on gold surfaces AU - Brewer, SH AU - Allen, AM AU - Lappi, SE AU - Chasse, TL AU - Briggman, KA AU - Gorman, CB AU - Franzen, S T2 - LANGMUIR AB - Polarization modulation infrared reflectance absorption spectroscopy (PM-IRRAS) and infrared reflectance absorption spectroscopy (IRRAS) have been used to characterize the formation of a self-assembled monolayer of N-(3-dihydroxyborylphenyl)-11-mercaptoundecanamide) (abbreviated PBA) on a gold surface and the subsequent binding of various sugars to the PBA adlayer through the phenylboronic acid moiety to form a phenylboronate ester. Vibrationally resonant sum frequency generation (VR-SFG) spectroscopy confirmed the ordering of the substituted phenyl groups of the PBA adlayer on the gold surface. Solution FTIR spectra and density functional theory were used to confirm the identity of the observed vibrational modes on the gold surface of PBA with and without bound sugar. The detection of the binding of glucose on the gold surface was confirmed in part by the presence of a C−O stretching mode of glucose and the observed O−H stretching mode of glucose that is shifted in position relative to the O−H stretching mode of boronic acid. An IR marker mode was also observed at 1734 cm-1 upon the binding of glucose. Additionally, changes in the peak profile of the B−O stretching band were observed upon binding, confirming formation of a phenylboronate ester on the gold surface. The binding of mannose and lactose were also detected primarily through the IR marker mode at ∼1736 to 1742 cm-1 depending on the identity of the bound sugar. DA - 2004/6/22/ PY - 2004/6/22/ DO - 10.1021/la035037m VL - 20 IS - 13 SP - 5512-5520 SN - 0743-7463 ER - TY - JOUR TI - Covalent attachment of a nickel nitrilotriacetic acid group to a germanium attenuated total reflectance element AU - Smith, BM AU - Lappi, SE AU - Brewer, SH AU - Dembowy, S AU - Belyea, J AU - Franzen, S T2 - LANGMUIR AB - The surface of a germanium internal reflectance element (IRE) was modified to bind 6X-histidine (his)-tagged biomolecules. The step-by-step surface modification was monitored via single-pass attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FT-IR). Initially an adlayer of 7-octenyltrimethoxysilane (7-OTMS) was formed on the Ge crystal through the surface hydroxyl groups, which were produced via ozonolysis of the Ge surface. The vinyl moiety of 7-OTMS was oxidized to a carboxylic acid, which was activated by 1,1'-carbonydiimidazole (CDI) to produce a labile imidazole. The labile imidazole that resulted from the CDI coupling was then displaced by the primary amine of nitrilotriacetic acid (NTA). Nickel sulfate was added to the system, and it coordinated with the three carbonyl groups and the nitrogen on NTA, thus leaving the ability of Ni to coordinate with two adjacent histidine residues. Binding of his-tagged biotin to nickel nitrilotriacetic acid (Ni-NTA) was observed by ATR-FT-IR spectroscopy. The surface modification method presented in this paper had minimal nonspecific binding, the Ni-NTA surface was reusable if stored properly, and complete removal of the organic surface was achievable. DA - 2004/2/17/ PY - 2004/2/17/ DO - 10.1021/la034194i VL - 20 IS - 4 SP - 1184-1188 SN - 0743-7463 ER -