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Thermodynamic models for the interaction between specific and nonspecific DNA sequences and Fpg protein reveal that Fpg interacts nonspecifically with all the base-pair units within its DNA-binding cleft with a 7 orders of magnitude of affinity for DNA. However, with 8-oxoguanine unit of the substrate Fpg exhibits 6-8 orders of magnitude affinity for specific oligodeoxynucleotides.

Research has been conducted on Escherichia coli's formamidopyrimidine-DNA-glycosylase which repairs oxidative DNA damage. The kinetic mechanism for the 8-oxoguanine excision from DNA substrate with Fpg protein has been investigated via the tryptophan fluorescence application and the results are reported.

Researchers describe inhibitors of ribonuclease P that bind to the substrate rather than the enzyme and are the strongest inhibitors known. They bind to the D and T loops of tRNA.

Copper(II) ions can activate the 3,4,5-trihydroxyphenyl analog of the DNA minor groove ligand Hoechst 33258 at low concentration to cleave DNA effectively. The 3,4-catecholic analog of Hoechst 33258 is unable to cleave DNA in the presence of copper(II) ions. These are determined by NMR spectroscopy in combination with molecular dynamics. The distance restraints obtained from NMR spectroscopy are used in the molecular modeling.

Molecular modeling of meta-Hoechst/DNA complex using molecular mechanics and distance constraints provided by intermolecular NOEs reveals that the m-OH group of meta-Hoechst and the DNA are involved in hydrogen bond formation. The meta analogue binds tightly to the AATT stretch of DNA complex and the complex has a three-dimensional structure. The high affinity of the meta-Hoechst ligand arises from high frequency resonance of adenine C2 hydrogens.

Octahedral tris-chelate complexes [M(super(bpy)3](super 2+) (M =Ru or Os, bpy =2,2'-bipyridyl), covalently attached to the 3' - 5'- phosphates to two oligonucleotides are juxtaposed when hybridized contiguously to a fully complementary DNA target. Visible metal-to-ligand charge-transfer (MLCT) excitation of the [Ru(super II)(bpy)3](super 2+) unit leads to resonance energy transfer to the MLCT state of the [Os(super II)3](super 2+) moity, with the energy transfer efficiency depending on the degree of hybridization.

Biophysical and structural studies of protein kinase monopolar spindle 1 (Mps1) catalytic domain was carried out in the presence of ATP and the aspecific model kinase inhibitor staurosporine to understand the nucleotide binding site architecture of Mps1. The results for the structure of the Mps1 ATP-binding site provide new biophysical insights into Mps1-ligand interactions that would be useful for the design of specific Mps1 inhibitors, including those employing a therapeutically validated quinazoline template.

Atomic force microscopy has been used to measure the surface profile of a periodic array of 10-nanometer (nm)-diameter holes fabricated by fast-atom beam milling of a smooth graphite surface in which a 3.5-nm-thick titanium oxide screen was used as a mask. The nanostructured titanium oxide mask was itself derived from a protein crystal template. Pattern transfer from the biological crystal to the metal oxide film and finally to the graphite substrate was accomplished entirely by parallel processing., We report the use of atomic force microscopy (AFM) to probe the topography of a periodically nanostructured surface. In these experiments, two-dimensional (2-D) protein crystals are adsorbed to smooth substrates [...]

The preparation and operation of FRET-based quantum dots (QD) bioprobes that are individually able to detect the actions of protease, deoxyribonuclease, DNA polymerase, or changes in pH is described

The stopped-flow kinetics with intrinsic Trp fluorescence detection was used to obtain detailed kinetic schemes for 8-oxoG opposite different bases and for dihydrouracil (DHU) opposite C or G. From the findings it is concluded that rejection of the incorrect substrates occurs mostly at the early stage of formation of the pre-eversion recognition complex, supporting the role of indirect readout in damage recognition.

The self-assembly of heterobinuclear d-f complexes in protic media is reported, using an approach that permits unprecedentedly rapid and effective screening of senstizing chromophores. An attempt is made to address the difficulties using relatively simple heteronuclear complexes to test the feasibility of a given sensitizer, but the approach is limited in scope, since the complexes dissociate in protic solvents.

A study reports on the stereochemical course of the hydrolysis of D-1-Sp-myo-inositol (17O)thiophosphate catalyzed by recombinant bovine myo-inositol monophosphatase. One experimental finding proved highly significant because it re-establishes and reinforces the generalization that single-step phosphoryl-transfer reactions proceed via in-line mechanisms. It also firmly ruled out a mechanism proceeding by a phosphoenzyme intermediate.