NMR at 900 MHz

An important factor in the development of solution state NMR has always been th e ability to produce stable and homogeneous magnetic fields. As higher and higher field strengths are reached the pressure is growing on manufacturers to produce NMR systems with greatly improved spectral resolution and signal to noise ratio. The introduction of the Varian 900 MHz INOVA system in August 2000 featuring Oxford Instruments 21.1 T magnet represents the latest pioneering development in NMR technology.     

Nucleobase‐Modified PNA Suppresses Translation by Forming a Triple Helix with a Hairpin Structure in mRNA In Vitro and in Cells

Compounds that bind specifically to double‐stranded regions of RNA have potential as regulators of structure‐based RNA function; however, sequence‐selective recognition of double‐stranded RNA is challenging. The modification of peptide nucleic acid (PNA) with unnatural nucleobases enables the formation of PNA–RNA triplexes. Herein, we demonstrate that a 9‐mer PNA forms a sequence‐specific PNA–RNA triplex with a dissociation constant of less than 1 nm at physiological pH. The triplex formed within the 5′ untranslated region of an mRNA reduces the protein expression levels both in vitro and in cells. A single triplet mismatch destabilizes the complex, and in this case, no translation suppression is observed. The triplex‐forming PNAs are unique and potent compounds that hold promise as inhibitors of cellular functions that are controlled by double‐stranded RNAs, such as RNA interference, RNA editing, and RNA localization mediated by protein–RNA interactions.     

Total synthesis of 3',5'-C-branched nucleosides

[reaction: see text] A novel total synthesis of 3',5'-C-branched uridine azido acid has been accomplished using stereoselective aldehyde alkynylation, Ireland-Claisen rearrangement, and iodolactonization as the key reactions. Compared to traditional routes that start from carbohydrates, the present methodology is more efficient, flexible for future optimization, and provides access to both enantiomers of the products. Because the key chemistry does not involve the 3'- and 5'-C substituents, our route is a general approach to 3',5'-C alkyl nucleoside analogues.     

Synthesis and properties of RNA analogues having amides as interuridine linkages at selected positions

Oligoribonucleotide analogues having amide internucleoside linkages (AM1: 3'-CH(2)CONH-5' and AM2: 3'-CH(2)NHCO-5') at selected positions have been synthesized and the thermal stability of duplexes formed by these analogues with complementary RNA fragments has been evaluated by UV melting experiments. Two series of oligomers with either 2'-OH or 2'-OMe vicinal to the amide linkages were studied. Monomeric synthons (3' and 5'-C amines and carboxylic acids) were synthesized as follows: For synthesis of the AM1 analogue, the known sequence of radical allylation followed by the cleavage of the double bond was adopted. For synthesis of the AM2 analogue, novel routes via addition of nitromethane followed by conversion of the nitro function to either amino or carboxyl groups were developed. Coupling of monomeric amines and carboxylic acids followed by protecting group manipulation and phosphonylation gave dimeric 3'-hydrogenphosphonate building blocks for oligonucleotide synthesis. Monomeric model compounds having 3'-amide and 2'-OH or 2'-OMe groups were also prepared and their conformational equilibrium was determined by (1)H NMR. The AM1 and AM2 models showed equal preferences for the North conformers (at 40 degrees C, 88-89% with 2'-OH, and 92-93% with 2'-OMe). At physiological salt concentration (0.1 M NaCl) the duplexes between AM1 modified oligonucleotides and RNA had stability similar to unmodified RNA-RNA duplexes (Delta t(m)= -0.2 to +0.7 degrees C per modification). However, the AM2 modification resulted in substantial stabilization of duplexes: Delta t(m)= +1 to +2.4 degrees C per modification compared to all RNA. A 2'-O-methyl vicinal to the AM2 linkage further increased the duplex stability. Our results suggest that RNA analogues having amide internucleoside bonds are very promising candidates for medicinal applications.     

Two-dimensional spectroscopy with parallel acquisition of 1H-X and 19F-X correlations

Two-dimensional NMR spectra correlating both (1)H and (19)F nuclei with either (13)C or (15)N, are recorded at the same time, using a 600-MHz broadband radio frequency probe feeding independent (1)H and (19)F receiver channels. This technique, known as parallel acquisition NMR spectroscopy (PANSY), speeds up multidimensional NMR and is compatible with other fast-acquisition schemes. The method is illustrated with single-bond (HSQC) and multiple-bond (HMBC) experiments on 2-bromophenyl-3-trifluoromethyl-5-methylpyrazole, giving simultaneous (1)H-X and (19)F-X correlation spectra (X = (13) C or (15)N).     

Fast multidimensional NMR by polarization sharing

The speed of multidimensional NMR spectroscopy can be significantly increased by drastically shortening the customary relaxation delay between scans. The consequent loss of longitudinal magnetization can be retrieved if 'new' polarization is transferred from nearby spins. For correlation spectroscopy involving heteronuclei (X=13C or 15N), protons not directly bound to X can repeatedly transfer polarization to the directly bound protons through Hartmann-Hahn mixing. An order of magnitude increase in speed has been observed for the 600 MHz two-dimensional HMQC spectra of amikacin and strychnine using this technique, and it also reduces the noisy F1 ridges that degrade many heteronuclear correlation spectra recorded with short recovery times.     

Molecular structure from a single NMR experiment

A procedure is described for determining the structure of a small molecule from a single NMR experiment. Several standard NMR sequences are combined so that the essential structural information is obtained in just one pass. Two-dimensional (13)C-(13)C correlations ("INADEQUATE"), single- and multiple-bond (13)C-(1)H correlations, and the conventional (13)C spectrum are recorded in parallel, making use of separate receiver channels for acquisition of (13)C and (1)H signals. The natural-abundance (13)C-(13)C correlation measurements employ a high-sensitivity cryogenically cooled probe, optimized for (13)C detection. An extension of this "all-in-one" sequence with three parallel receivers permits the corresponding natural-abundance (15)N spectra to be included.     

Second harmonic generation in selenium-metal structures

Results of second harmonic (SH) generation in amorphous and crystalline selenium films and selenium-metal (Ga, Zn, In, Sb, Bi) sandwich structures induced by titan-sapphire femtosecond laser (wavelength λ – 690–1040 nm) are presented. It is found that the highest intensity of SH is provided by fundamental wave at wavelength 1000 nm and it reaches maximum in approximately 100 s. The intensity of transmitted SH depends on film thickness while that of reflected does not. The highest SH intensities in selenium-metal structures are provided by Se–Ga and Se–Zn films. A possible mechanism for central symmetry breaking in amorphous films also is proposed.     

Toward amide-linked RNA mimics: total synthesis of 3'-C branched uridine azido acid via an ene-iodolactonization approach

[reaction: see text] A novel synthesis of 3'-C branched uridine azido acid has been accomplished by a sequence of stereoselective ene and iodolactonization reactions. Compared to traditional routes that start from carbohydrates, the present methodology is more flexible and can be further optimized by incorporation of novel future developments of synthetic chemistry. Because the key chemistry does not involve the 3'-C substituent, our route is a general approach to 3'-C alkyl nucleoside analogues.     

Electron beam induced surface modification of amorphous Sb2Se3 thin film

The change in the surface morphology of amorphous Sb₂Se₃ thin films during the electron beam irradiation has been studied mainly by atomic force microscopy (AFM). Electron beam at accelerating voltages 30 kV is focused onto the surface of the specimens of 100-μm thickness, and then the surface morphology of each specimen has been observed by AFM in air. The modification of the film surface includes lateral and vertical resizing which is typically in the micrometer and sub-micrometer range. Protrusions above the surface as high as 90 nm are observed at 180 pA electron beam current, whilst trenches as deep as 97 nm are observed at 800 pA electron beam current (total thickness of thin film is 100 nm). The dependence of patterns characteristics on irradiation parameters such as exposure time and beam current has also been studied. Physical mechanisms for trench and mound formation are proposed.