Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.

We have subjected several analogs of DNA that have been widely used as antisense oligonucleotide (ASO) inhibitors of gene expression to comparative molecular dynamics (MD) calculations of their ability to form duplexes with DNA and RNA. The analogs included in this study are the phosphorothioate (PS), peptide nucleic acid (PNA), locked nucleic acid (LNA), morpholino nucleic acid (PMO), the 2'-OMe, 2'-F, 2'-methoxyethyl (2'-MOE) and the constrained cET analogs, as well as the natural phosphodiester (PO) as control, for a total of nine structures, in both XNA-DNA and XNA-RNA duplexes. This is intended as an objective criterion for their relative ability to duplex with an RNA complement and their comparative potential for antisense applications.

Molecular dynamics simulations of acyclic analogs of nucleic acids for antisense inhibition.

For antisense applications, oligonucleotides must be chemically modified to be resistant to endogenous nucleases. Until now, antisense oligonucleotide (ASO) analogs have been synthesized and then tested for their ability to duplex with a target nucleic acid, usually RNA. In this work, using molecular dynamics calculations simulations, we systematically tested a series of chemically modified analogs in which the 2-deoxyribose was substituted for by one or two methylene groups on each side of the phosphate backbone, producing four compounds, of which three were previously unknown.

31P-magnetic resonance spectra of ovarian cancer cells exposed to chemotherapy within a three-dimensional Matrigel construct.

We aimed to determine the metabolic profile and effects of chemotherapy on ovarian cancer cell metabolism in a three-dimensional (3D) vs. a two-dimensional (2D) construct using 31P-magnetic resonance spectroscopy (MRS). Three ovarian cancer cell lines were embedded in a 3D perfused Matrigel construct or grown in a 2D monolayer.

Oxidative stress causes membrane phospholipid rearrangement and shedding from RBC membranes--an NMR study.

Nuclear Magnetic Resonance (NMR) spectroscopy was used to investigate the relationship between oxidative stress experienced by RBCs and their phospholipid content and shedding. Using 1H-NMR, we demonstrated a higher lactate/pyruvate ratio, an indicator of oxidative stress, in normal RBCs treated with oxidants (t-butylhydroxyperoxide and H2O2) as well as in beta-thalassemic RBCs. Using 31P-NMR, we found 30% more phosphatidylcholine (PC), and unexpectedly, 35% less phosphatidylserine (PS) in the thalassemic RBCs.

Specific lipoplex-mediated antisense against Bcl-2 in breast cancer cells: a comparison between different formulations.

G3139 is an antisense oligonucleotide (ODN) that can down-regulate bcl-2, thus potentially acting as a potent anticancer drug. However, effective therapy requires efficient ODN delivery, which may be achieved by employing G3139 lipoplexes. Yet, lipofection is a complex, multifactorial process that is still poorly understood.

Hormone sensitivity is reflected in the phospholipid profiles of breast cancer cell lines.

We have found that the profiles of total phospholipids in malignant breast cancer cell lines change going from hormone sensitive to highly hormone resistant cells lines. In particular, two phospholipid components that were absent or at very low levels in hormone sensitive MCF7 cells and moderately hormone sensitive cell lines (MIII, LCC2) were found in relatively high proportions in highly hormone resistant cell lines (MB435, MB231). These two components were shown to be the alkylacylphosphatidylcholine (AAPtdC) and the unsaturated analog plasmenylphosphatidylethanolamine (plasmenyl-PtdE).

High-b-value diffusion-weighted MR imaging for pretreatment prediction and early monitoring of tumor response to therapy in mice.

Purpose: To evaluate the use of diffusion-weighted magnetic resonance (MR) imaging with standard and high b values for pretreatment prediction and early detection of tumor response to various antineoplastic therapies in an animal model.

Materials And Methods: Mice bearing C26 colon carcinoma tumors were treated with doxorubicin (n = 25) and with aminolevulinic acid-based photodynamic therapy (n = 23). Fourteen mice served as controls.

Determination of intracellular pH and compartmentation using diffusion-weighted NMR spectroscopy with pH-sensitive indicators.

The intracellular pH (pHi) of a series of cancer cell lines was determined using the pH-sensitive indicators imidazole (Im) or histidine (His) and diffusion-weighted (DW) proton NMR spectroscopy. The DW method allows the observation at high magnetic field gradient values of only the slow-moving (intracellular) components, thus ensuring complete separation between intra- and extracellular components. Using the chemical shift difference (deltadelta) between the imidazole ring C2-H and C4(5)-H peaks, we were able to measure the pHi independently of chemical shift standardization.

Early detection of response to radiation therapy in patients with brain malignancies using conventional and high b-value diffusion-weighted magnetic resonance imaging.

Purpose: To study the feasibility of using diffusion-weighted magnetic resonance imaging (DWMRI), which is sensitive to the diffusion of water molecules in tissues, for detection of early tumor response to radiation therapy; and to evaluate the additional information obtained from high DWMRI, which is more sensitive to low-mobility water molecules (such as intracellular or bound water), in increasing the sensitivity to response.

Patients And Methods: Standard MRI and DWMRI were acquired before and at regular intervals after initiating radiation therapy for 10 malignant brain lesions in eight patients.

Results: One week posttherapy, three of six responding lesions showed an increase in the conventional DWMRI parameters.