Synthesis and Triple-Helix-Stabilization Properties of Branched Oligonucleotides Carrying 8-Aminoadenine Moieties

The synthesis of several branched oligonucleotides, i.e., of the parallel hairpins 5-8 and the Y-shaped 9 is described, together with their use in the formation of pyrimidine purine triple helices. Special attention was paid to the optimization of the assembly of the second strand from asymmetric branching molecules. The presence of 8-aminoadenine moieties in the Watson-Crick purine strand and 2′-O-methyl-RNA in the Hoogsteen pyrimidine strand produced strong stabilization of the triplex.Peer reviewe

Self-association of short DNA loops through minor groove C:G:G:C tetrads

In addition to the better known guanine-quadruplex,four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson–Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson–Crick duplexes.Peer reviewe

Locked nucleic acid (LNA) mediated improvements in siRNA stability and functionality

Therapeutic application of the recently discovered small interfering RNA (siRNA) gene silencing phenomenon will be dependent on improvements in molecule bio-stability, specificity and delivery. To address these issues, we have systematically modified siRNA with the synthetic RNA-like high affinity nucleotide analogue, Locked Nucleic Acid (LNA). Here, we show that incorporation of LNA substantially enhances serum half-life of siRNA's, which is a key requirement for therapeutic use. Moreover, we provide evidence that LNA is compatible with the intracellular siRNA machinery and can be used to reduce undesired, sequence-related off-target effects. LNA-modified siRNAs targeting the emerging disease SARS, show improved efficiency over unmodified siRNA on certain RNA motifs. The results from this study emphasize LNA's promise in converting siRNA from a functional genomics technology to a therapeutic platform

Why Are Regulations Changed? A Parcel Analysis of Upzoning in Los Angeles

Planners, officials, and neighborhood groups often debate zoning changes, yet there is little empirical evidence explaining why zoning and other land use regulations are changed. I use logistic regression models to examine density-enabling rezoning (“upzoning”) in Los Angeles. I find that upzoning occurs where there are development opportunities combined with limited political resistance. Upzoning is most likely on well-located parcels zoned for low-intensity, nonresidential uses. Meanwhile, homeowners—and particularly homeowners with access to valuable amenities—are associated with regulatory stasis. I conclude by recommending strategies for addressing homeowners’ concerns about higher density housing

Convenient synthesis of 8-amino-2′-deoxyadenosine

We studied the behaviour of 8-azido-2′-deoxyadenosine and 8-bromo-2′-deoxyadenosine in aqueous solutions of ammonia and primary and secondary amines. Unexpectedly, 8-Azido-2′-deoxyadenosine is converted to 8-amino-2′-deoxyadenosine in excellent yields. The use of this reaction for the preparation of 8-aminoadenine derivatives needed for the preparation of oligonucleotides carrying 8-aminoadenine is discussed.We thank the Dirección General de Investigación Científica y Técnica (grants BQU2000-0649 and CAL01-058-C2-2), the Generalitat de Catalunya (2000-SGR-0018 and 2001-SGR-0049) and Cygene Inc. for financial support.Peer reviewe

Synthesis of oligonucleotide-peptide conjugates carrying the c-myc peptide epitope as recognition system

Oligonucleotide-peptide conjugates 1-3 were prepared by sequential addition of the appropriate Boc-protected amino acids, followed by nucleoside phosphoramidites in the same support. These molecules are designed to be used for triplex formation and for the directed assembly of nanomaterials. The structures of the desired oligonucleotide-peptide conjugates were confirmed by mass spectrometry on small oligonucleotide-peptide conjugates, by gel electrophoresis, and by hybridization with complementary oligonucleotides. Oligonucleotides carrying the c-myc peptide were specifically recognized by the anti-c-myc monoclonal antibody.Peer reviewe

Parallel-stranded hairpins containing 8-aminopurines. Novel efficient probes for triple-helix formation

We describe novel oligomers with a greater propensity to form triplexes than oligomers containing only natural bases. They consist of a polypyrimidine sequence linked head-to-head with a polypurine sequence carrying one or several 8-aminoadenine or 8-aminoguanines. The presence of 8-aminopurines also stabilised the parallel-stranded duplex structure. © 2001 Elsevier Science Ltd.The authors thank the Dirección General de Investigación Cientı́fica y Técnica (projects PB98-1222, PM99-0046 and BQU2000-0649), the Generalitat de Catalunya (project 2000-SGR-0018) and CyGene, Inc. for financial supportPeer Reviewe

LNA guanine and 2,6-diaminopurine. Synthesis, characterization and hybridization properties of LNA 2,6-diaminopurine containing oligonucleotides

Christoph Rosenbohm, Daniel Sejer Pedersen, Miriam Frieden, Flemming R. Jensen, Susan Arent, Sine Larsen and Troels Kochhttp://www.elsevier.com/wps/find/journaldescription.cws_home/129/description#descriptio