Vaccinia DNA topoisomerase forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at a pentapyrimidine target site 5'-C(+5)C(+4)C(+3)T(+2)T(+1)p downward arrow in duplex DNA. The enzyme engages the target site within a C-shaped protein clamp. Here we mapped the interface of topoisomerase with the DNA minor groove by introducing chiral C-10 R and S 7,8-diol 9,10-epoxide adducts of benzo[a]...

A period from 1890 to 1930's roughly corresponds to active investigations in the United States into grooves on the occlusal surface of the teeth by such men as BLACK [5], BODECKER [6-9], HYATT [12-20] and DIAMOND[11]. Our concept of the morphology of the occlusal grooves has been developed and fostered by these pioneering workers. The occlusal grooves are usually of twofold : one is what is ter...

The width of the DNA minor groove varies with sequence and can be a major determinant of DNA shape recognition by proteins. For example, the minor groove within the center of the Fis-DNA complex narrows to about half the mean minor groove width of canonical B-form DNA to fit onto the protein surface. G/C base pairs within this segment, which is not contacted by the Fis protein, reduce binding a...

The major and minor groove in duplex DNA are sites of specific molecular recognition by DNA-binding agents such as proteins, drugs and metal complexes and have functional significance. In view of this, understanding of the inherent differences in their environment and the allosteric information transfer between them induced by DNA-binding agents assumes importance. Site-specific incorporation o...

We describe sequence-specific alkylation in the minor groove of double-stranded DNA by a hybridization-triggered reactive group conjugated to a triplex forming oligodeoxyribonucleotide (TFO) that binds in the major groove. The 24 nt TFOs (G/A motif) were designed to form triplexes with a homopurine tract within a 65 bp target duplex. They were conjugated to an N 5-methyl-cyclopropapyrroloindole...

Important classes of graph grammars have infinite state spaces and therefore cannot be verified with traditional model checking techniques. One way to address this problem is to perform graph abstraction, which allows us to generate a finite abstract state space that over-approximates the original one. In previous work we developed the theory of neighbourhood abstraction. In this paper, we pres...

Tumors of the olfactory groove may cause unilateral optic atrophy with contralateral papilledema and anosmia (Foster Kennedy syndrome). We describe a case of a young pregnant woman with Foster Kennedy syndrome due to an olfactory groove meningioma.

The “groove” of a song correlates with enjoyment and bodily movement. Recent work has shown that humans often agree whether a song does or does not have groove and how much groove a song has. It is therefore useful to develop algorithms that characterize the quality of groove across songs. We evaluate three unsupervised tempo-invariant models for measuring pairwise musical groove similarity: A ...

BACKGROUND The B-DNA major and minor groove dimensions are crucial for DNA-protein interactions. It has long been thought that the groove dimensions depend on the DNA sequence, however this relationship has remained elusive. Here, our aim is to elucidate how the DNA sequence intrinsically shapes the grooves. METHODOLOGY/PRINCIPAL FINDINGS The present study is based on the analysis of datasets...

Based on the waveguide mode (WGM) method, coupling interaction of electromagnetic wave in a groove doublet configuration is studied. The formulation obtained by WGM method for a single groove [Prog. Electromagn. Res. 18, 1-17 (1998)] is extended to two grooves. By exploring the total scattered field of the configuration, coupling interaction ratios are defined to describe the interaction betwee...