Biomedical subjects

M C Wahl

Publications and source records attributed to M C Wahl.

25 records · Page 2Linked to original sources

PubMed1996

Crystal structure of the B-DNA hexamer d(CTCGAG): model for an A-to-B transition.

The crystal structure of the B-DNA hexamer d(CTCGAG) has been solved at 1.9 A resolution by iterative single isomorphous replacement, using the brominated derivative d(CG5BrCGAG), and refined to an R-factor of 18.6% for 120 nonhydrogen nucleic acid atoms and 32 water molecules. Although the central four base pairs form a typical B-form helix, several parameters suggest a transition to an A-like conformation at the termini. Based on this observation, a B-to-A transition was modeled, maintaining efficient base stacking across the junction. The wide minor groove (approximately 6.9 A) is reminiscent of that in the side-by-side double drug-DNA complexes and hosts a double spine of hydration. The global helix axes of the pseudo-continuous helices are at an acute angle of 60 degrees. The pseudocontinuous stacking is reinforced by the minor groove water structure extending between the two duplexes. The crossover point of two pairs of stacked duplexes is at the stacking junction, unlike that observed in the B-DNA decamers and dodecamers. This arrangement may have implications for the structure of a four-way DNA junction. The duplexes are arranged around a large (approximately 20 A diameter) channel centered on a 6(2) screw axis.

Base Sequence↗

PubMed1996

The structure of r(UUCGCG) has a 5'-UU-overhang exhibiting Hoogsteen-like trans U.U base pairs.

The crystal structure of the RNA fragment, 5'-r(UUCGCG)-3', has been determined at 1.4 A resolution by a combination of single isomorphous replacement and molecular search methods. The 3'-terminal CGCG portion of the hexamer engages in Watson-Crick hydrogen bonding while the 5'-terminal UU-overhang forms novel Hoogsteen-like U.U self-base pairs with the overhang of an adjacent duplex. The U.U pairs display a single conventional hydrogen bond between O4 (U1) and N3 (U8) and a CH-O hydrogen bond between C5-H (U1) and O4 (U8), through the Hoogsteen face of the pyrimidine base U1. This unusual arrangement of one of the bases results in a trans U.U pair on antiparallel strands in contrast to the usual cis base pairs. The structure emphasizes the pronounced polymorphism of U.U pairs and has implications for folding of RNA molecules.

Animals↗

PubMed1995

New crystal structures of nucleic acids and their complexes.

In the past year, X-ray crystallographic studies of representatives of all nucleic acid structural types have been reported. Among the most interesting structures are the parallel DNA tetraplex formed by d(TGGGGT), the four-stranded structure formed by d(CCCT) and a double drug bound side by side in an antiparallel orientation to the minor groove of a B-DNA. Certainly, the structure that has received most attention is that of the first complex of a ribozyme with an inhibitor DNA.

Animals↗

PubMed1994

MS/MS with high detection efficiency and mass resolving power for product ions in Fourier transform ion cyclotron resonance mass spectrometry.

We present a new FT-ICR method for MS/MS of trapped ions. Parent ions isolated in the source trap of a dual-trap FT-ICR/MS instrument are subjected to off-resonance dipolar excitation to promote collision-induced dissociation (CID), while product ions are simultaneously axialized by broad-band azimuthal quadrupolar excitation in the presence of argon collision gas. In this way, radial diffusional loss of product ions is greatly reduced; moreover, the axialized product ions may then be efficiently transferred to the analyzer trap for high-resolution detection. Significant improvements in FT-ICR detection efficiency, mass resolving power (m/delta m > or = 20,000 at m/z < or = 1000), and mass accuracy (< or = 50 ppm for peptide fragments of m/z < or = 1000) are demonstrated for CID product ions of the cyclic peptide, gramicidin S.

Amino Acid Sequence↗

PubMed1993

Elimination of frequency drift from Fourier transform ion cyclotron resonance mass spectra by digital quadrature heterodyning: ultrahigh mass resolving power for laser-desorbed molecules.

At sufficiently low pressure, FT-ICR mass resolving power is no longer pressure-limited. Rather, the observed spectral peaks are broadened by ion cyclotron frequency drift during the detection period, due to change in shape of the coherently orbiting ion packet during detection. The frequency drift may be quantitated by Fourier transformation of each of a series of consecutive segments of the time-domain ICR signal, followed by fitting the frequency vs time behavior to a polynomial in time. Correction for that frequency drift is then achieved by a digital quadrature procedure, followed by multiplication by a weight factor which removes the frequency drift. We demonstrate a 750-fold reduction in FT-ICR mass spectral peak width for pseudomolecular (M+K)+ ions of laser-desorbed leucine enkephalin (m/delta m = 1,300,000)! Moreover, correction based on the frequency drift of ions of a given m/z also corrects for frequency drift of ions of other m/z values, as demonstrated for isotopic peaks from (M+K)+ from gramicidin S (m/z 1179). Narrowing of the FT-ICR mass spectral peaks results in a corresponding increase in peak height-to-noise ratio as well. In addition, we propose a theoretical model for frequency drift during detection of the ion cyclotron resonance signal. Simultaneous relaxation of coherent cyclotron motion and compression of the axial distribution of an initially radially coherent ion packet account for ion cyclotron frequency drift during detection. The potential energy generated by mutual ion-ion Coulomb repulsions varies with ion cyclotron orbital radius as ions undergo collisional damping.(ABSTRACT TRUNCATED AT 250 WORDS)

Cyclotrons↗

PubMed1993

Thin gold film-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry of biomolecules.

A new thin gold film-assisted (TGFA) laser desorption/ionization (LDI) technique has been combined with Fourier transform ion cyclotron resonance (FT-ICR) high-resolution mass analysis. A thermally labile organic sample is coated onto a thin gold film deposited on a glass plate and desorbed and ionized by Nd:YAG laser irradiation. The wavelength for maximum light absorption may be tuned by varying the thickness of the metal film; e.g., a 10-nm-thick gold film absorbs maximally near the Nd:YAG fundamental wavelength (1064 nm). A key advantage of the method is the stability of the gold film, which facilitates deposition of samples from any of a variety of solvent systems. Coupled with recently introduced quadrupolar excitation and collisional cooling for ion axialization, TGFA-LDI FT-ICR mass spectra provide high sensitivity (e.g., 100-fmol single-shot detection limit and mass resolving power, m/delta m approximately 113,000, for (M+K)+ ions from gramicidin S at m/z 1180).

Cellobiose↗

PubMed1993

Enhanced mass resolving power, sensitivity, and selectivity in laser desorption Fourier transform ion cyclotron resonance mass spectrometry by ion axialization and cooling.

Ion cooling and axialization produced by azimuthal quadrupolar excitation in the presence of ion-neutral collisions are applied to laser desorption Fourier transform ion cyclotron resonance mass spectrometry (LD/FT/ICR-MS). With this technique, the large kinetic and internal energies of ions generated by laser desorption processes can be cooled effectively by collisions of ions with neutral argon atoms (at > 5 x 10(-7) Torr). After sufficient cooling in the source compartment of a dual ion trap, the axialized ions may be transferred to the analyzer compartment for detection at much lower pressure (and thus much higher mass resolving power). Enhancements in both FT/ICR mass resolving power and sensitivity are observed; moreover, ion isolation with high selectivity at high pressure is also demonstrated.

Argon↗