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Full-Text Articles in Chemistry
Conserved Geometrical Base-Pairing Patterns In Rna, Neocles B. Leontis, Eric Westhof
Conserved Geometrical Base-Pairing Patterns In Rna, Neocles B. Leontis, Eric Westhof
Chemistry Faculty Publications
RNA molecules fold into a bewildering variety of complex 3D structures. Almost every new RNA structure obtained at high resolution reveals new, unanticipated structural motifs, which we are rarely able to predict at the current stage of our theoretical understanding. Even at the most basic level of specific RNA interactions – base-to-base pairing – new interactions continue to be uncovered as new structures appear. Compilations of possible non-canonical base-pairing geometries have been presented in previous reviews and monographs (Saenger, 1984; Tinoco, 1993). In these compilations, the guiding principle applied was the optimization of hydrogen-bonding. All possible pairs with two standard …
Sequence-Specific Photomodification Of Dna By An Oligonucleotide-Phenanthrodihydrodioxin Conjugate, Kestutis G. Bendinskas, Andreas Harsch, R. Marshall Wilson, W. Robert Midden
Sequence-Specific Photomodification Of Dna By An Oligonucleotide-Phenanthrodihydrodioxin Conjugate, Kestutis G. Bendinskas, Andreas Harsch, R. Marshall Wilson, W. Robert Midden
Chemistry Faculty Publications
We introduce a new member of a family of photochemically active oligonucleotide conjugates. A Phenanthrodihydrodioxin (PDHD)-based agent was synthesized and covalently linked to a 5'-end of the 9-mer oligonucleotide via a hexamethylene linker. The conjugate hybridized to a complementary 30-nucleotide-long target and efficiently cleaved it in a sequence specific manner. Up to 67% of target was specifically damaged (51% cross-links and 16% direct cleavage). While the photosensitizer alone nonspecifically damaged only Gs in a single-stranded target, its conjugate cross-linked to and damaged also A, T, and C sites in a target in agreement with duplex and tripler formation.
The 5s Rrna Loop E: Chemical Probing And Phylogenetic Data Versus Crystal Structure, Neocles B. Leontis, Eric Westhof
The 5s Rrna Loop E: Chemical Probing And Phylogenetic Data Versus Crystal Structure, Neocles B. Leontis, Eric Westhof
Chemistry Faculty Publications
A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of …
Distance Dependence Of Electron Transfer Along Artificial Beta-Strands At 298 And 77 K, S. R. L. Fernando, Gennady V. Kozlov, Michael Y. Ogawa
Distance Dependence Of Electron Transfer Along Artificial Beta-Strands At 298 And 77 K, S. R. L. Fernando, Gennady V. Kozlov, Michael Y. Ogawa
Chemistry Faculty Publications
Photoinduced electron-transfer rate constants were measured for a series of binuclear metallopeptides consisting of a [Ru(bpy)(2)(cmbpy)](2+) electron donor tethered to a Co-III(NH3)(5) electron acceptor by an oligovaline peptide chain (bpy = 2,2'-bipyridine, cmbpy = 4-carboxy-4'-methyl-2,2'-bipyridine). These compounds were shown by H-1 NMR to adopt the conformational properties found within the individual strands of a beta-pleated sheet in both aqueous and methanol solutions. Emission lifetime measurements and HPLC product analysis show that the binuclear donor/acceptor compounds undergo photoinduced electron transfer (ET). The values of k(et) decrease with increasing donor/acceptor distance according to the expression k(et) = k' exp[-beta(r(-)r(0))]. A distance attenuation …