Base Pairing (base + pairing)

Distribution by Scientific Domains


Selected Abstracts


Oligonucleotides Containing 7-Deaza-2,-deoxyinosine as Universal Nucleoside: Synthesis of 7-Halogenated and 7-Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne,Azide ,Click' Reaction

HELVETICA CHIMICA ACTA, Issue 7 2008
Frank Seela
Abstract Oligonucleotides containing 7-deaza-2,-deoxyinosine derivatives bearing 7-halogen substituents or 7-alkynyl groups were prepared. For this, the phosphoramidites 2b,2g containing 7-substituted 7-deaza-2,-deoxyinosine analogues 1b,1g were synthesized (Scheme,2). Hybridization experiments with modified oligonucleotides demonstrate that all 2,-deoxyinosine derivatives show ambiguous base pairing, as 2,-deoxyinosine does. The duplex stability decreases in the order Cd>Ad>Td>Gd when 2b,2g pair with these canonical nucleosides (Table,6). The self-complementary duplexes 5,-d(F7c7I-C)6, d(Br7c7I-C)6, and d(I7c7I-C)6 are more stable than the parent duplex d(c7I-C)6 (Table,7). An oligonucleotide containing the octa-1,7-diyn-1-yl derivative 1g, i.e., 27, was functionalized with the nonfluorescent 3-azido-7-hydroxycoumarin (28) by the Huisgen,Sharpless,Meldal cycloaddition ,click' reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme,3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ,click' chemistry. ii) Space demanding residues introduced in the 7-position of the 7-deazapurine base does not interfere with duplex structure and stability (Table,8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology. [source]


Replacement of Canonical DNA Nucleobases by Benzotriazole and 1,2,3-Triazolo[4,5- d]pyrimidine: Synthesis, Fluorescence, and Ambiguous Base Pairing

HELVETICA CHIMICA ACTA, Issue 4 2005
Frank Seela
The syntheses and the fluorescence properties of 7H -3,6-dihydro-1,2,3-triazolo[4,5- d]pyrimidin-7-one 2,-deoxy- , - D -ribonucleosides (=2,-deoxy-8-azainosine) 3 (N3), 15 (N2), and 16 (N1) as well as of 1,2,3-benzotriazole 2,- O -methyl- , - or - , - D -ribofuranosides 6 (N1) and 24 (N1) are described. Also the fluorescence properties of 1,2,3-benzotriazole 2,-deoxy- , - D -ribofuranosides 4 (N1) and 5 (N2) are evaluated. From the nucleosides 3,6, the phosphoramidites 19, 26a, 26b, and 28 are prepared and employed in solid-phase oligonucleotide synthesis. In 12-mer DNA duplexes, compound 3 shows similar ambiguous base-pairing properties as 2,-deoxyinosine (1), while the nucleosides 4,6 show strong pairing with each other and discriminate very little the four canonical DNA constituents. [source]


Incorporation of Thymine Nucleotides by DNA Polymerases through T,HgII,T Base Pairing

ANGEWANDTE CHEMIE, Issue 37 2010
Hidehito Urata Prof.
DNA in schlechter Gesellschaft: In Gegenwart von HgII -Ionen führten DNA-Polymerasen Thymidin-5,-triphosphat (TTP) gegenüber einem Thyminrest im Templatstrang ein bildeten zur Verlängerung des Primerstrangs eine Phosphodiesterbindung. DNA-Polymerasen erkannten dieses ungewöhnliche, durch ein Metallion verknüpfte Basenpaar und synthetisierten darüber hinweg das Volllängenprodukt (siehe Bild). [source]


Oligonucleotides Incorporating 8-Aza-7-deazapurines: Synthesis and Base Pairing of Nucleosides with Nitrogen-8 as a Glycosylation Position.

CHEMINFORM, Issue 37 2003
Junlin He
No abstract is available for this article. [source]


Assessment of adenyl residue reactivity within model nucleic acids by surface enhanced Raman spectroscopy

BIOPOLYMERS, Issue 1 2006
Lydie Grajcar
Abstract We rank the reactivity of the adenyl residues (A) of model DNA and RNA molecules with electropositive subnano size [Ag] sites as a function of nucleic acid primary sequences and secondary structures and in the presence of biological amounts of Cl, and Na+ or Mg2+ ions. In these conditions A is markedly more reactive than any other nucleic acid bases. A reactivity is higher in ribo (r) than in deoxyribo (d) species [pA > pdA and (pA)n , (pdA)n]. Base pairing decreases A reactivity in corresponding duplexes but much less in r than in d. In linear single and paired dCAG or dGAC loci, base stacking inhibits A reactivity even if A is bulged or mispaired (A.A). dA tracts are highly reactive only when dilution prevents self-association and duplex structures. In d hairpins the solvent-exposed A residues are reactive in CAG and GAC triloops and even more in ATC loops. Among the eight rG1N2R3A4 loops, those bearing a single A (A4) are the least reactive. The solvent-exposed A2 is reactive, but synergistic structural transitions make the initially stacked A residues of any rGNAA loop much more reactive. Mg2+ cross-bridging single strands via phosphates may screen A reactivity. In contrast d duplexes cross-bridging enables "A flipping" much more in rA.U pairs than in dA.T. Mg2+ promotes A reactivity in unpaired strands. For hairpins Mg2+ binding stabilizes the stems, but according to A position in the loops, A reactivity may be abolished, reduced, or enhanced. It is emphasized that not only accessibility but also local flexibility, concerted docking, and cation and anion binding control A reactivity. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 6,28, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source]


Oligonucleotides Containing 7-Deaza-2,-deoxyinosine as Universal Nucleoside: Synthesis of 7-Halogenated and 7-Alkynylated Derivatives, Ambiguous Base Pairing, and Dye Functionalization by the Alkyne,Azide ,Click' Reaction

HELVETICA CHIMICA ACTA, Issue 7 2008
Frank Seela
Abstract Oligonucleotides containing 7-deaza-2,-deoxyinosine derivatives bearing 7-halogen substituents or 7-alkynyl groups were prepared. For this, the phosphoramidites 2b,2g containing 7-substituted 7-deaza-2,-deoxyinosine analogues 1b,1g were synthesized (Scheme,2). Hybridization experiments with modified oligonucleotides demonstrate that all 2,-deoxyinosine derivatives show ambiguous base pairing, as 2,-deoxyinosine does. The duplex stability decreases in the order Cd>Ad>Td>Gd when 2b,2g pair with these canonical nucleosides (Table,6). The self-complementary duplexes 5,-d(F7c7I-C)6, d(Br7c7I-C)6, and d(I7c7I-C)6 are more stable than the parent duplex d(c7I-C)6 (Table,7). An oligonucleotide containing the octa-1,7-diyn-1-yl derivative 1g, i.e., 27, was functionalized with the nonfluorescent 3-azido-7-hydroxycoumarin (28) by the Huisgen,Sharpless,Meldal cycloaddition ,click' reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme,3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal CC bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ,click' chemistry. ii) Space demanding residues introduced in the 7-position of the 7-deazapurine base does not interfere with duplex structure and stability (Table,8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology. [source]


Oligonucleotide Analogues with Integrated Bases and Backbone.

HELVETICA CHIMICA ACTA, Issue 4 2007
Part 1
Abstract The self-complementary tetrameric propargyl triols 8, 14, 18, and 21 were synthesized to investigate the duplex formation of self-complementary, ethynylene-linked UUAA, AAUU, UAUA, and AUAU analogues with integrated bases and backbone (ONIBs). The linear synthesis is based on repetitive Sonogashira couplings and C -desilylations (34,72% yield), starting from the monomeric propargyl alcohols 9 and 15 and the iodinated nucleosides 3, 7, 11, and 13. Strongly persistent intramolecular H-bonds from the propargylic OH groups to N(3) of the adenosine units prevent the gg -type orientation of the ethynyl groups at C(5,). As such, an orientation is required for the formation of cyclic duplexes, this H-bond prevents the formation of duplexes connected by all four base pairs. However, the central units of the UAUA and AAUU analogues 18 and 14 associate in CDCl3/(D6)DMSO 10,:,1 to form a cyclic duplex characterized by reverse Hoogsteen base pairing. The UUAA tetramer 8 forms a cyclic UU homoduplex, while the AUAU tetramer 21 forms only linear associates. Duplex formation of the O -silylated UUAA and AAUU tetramers is no longer prevented. The self-complementary UUAA tetramer 22 forms Watson,Crick - and Hoogsteen -type base-paired cyclic duplexes more readily than the sequence-isomeric AAUU tetramer 23, further illustrating the sequence selectivity of duplex formation. [source]


Multiple forms of U2 snRNA coexist in the silk moth Bombyx mori

INSECT MOLECULAR BIOLOGY, Issue 1 2002
J. M. Sierra-Montes
Abstract Eight U2 snRNA variants were isolated from several Bombyx mori U2-specific RT-PCR libraries. U2 sequences and secondary structures were generated and examined in terms of potential RNA and protein interactions. Analysis indicated that nucleotide changes occurred in both stem/loop and single-stranded areas. Changes in the double stranded areas were either compensatory, single substitutions (e.g. C , U) or prevented the double-stranded formation of one or two base pairs. The polymorphisms were clustered in moderately conserved regions. Some of the changes observed generated stronger base pairing. Inter-species conserved protein or RNA-binding sites were relatively unaffected. No polymorphic sites were found in known functional sequences. Bombyx mori and Drosophila melanogaster U2 sequences are 95% and 70% similar at the 5,- and the 3,-ends of the molecule, respectively. Phylogenetic analysis of the U2 sequences demonstrates remarkable conservation across species. [source]


Computational characterization of nucleotide bases: Molecular surface electrostatic potentials and local ionization energies, and local polarization energies

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3-4 2001
Jane S. Murray
Abstract Electrostatic potentials and local ionization energies have been computed at the HF/6-31G* level on the molecular surfaces of the five nucleotide bases. The potentials are analyzed in terms of their most positive and negative values as well as several statistically defined quantities that reflect their patterns over the entire surface. Considerable charge separation and variability are found for all five molecules. The results are consistent with the base pairing that is known to occur. The observed reactive behavior toward electrophiles can be interpreted in terms of the complementary roles of the surface potential and the local electron lability. Local polarization energies, corresponding to a test charge being placed at specific points above the molecules, are also calculated (HF/6-31+G*), and their relationship to the local ionization energies is examined. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 245,254, 2001 [source]


Antisense applications for biological control

JOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2006
Wei-Hua Pan
Abstract Although Nature's antisense approaches are clearly impressive, this Perspectives article focuses on the experimental uses of antisense reagents (ASRs) for control of biological processes. ASRs comprise antisense oligonucleotides (ASOs), and their catalytically active counterparts ribozymes and DNAzymes, as well as small interfering RNAs (siRNAs). ASOs and ribozymes/DNAzymes target RNA molecules on the basis of Watson-Crick base pairing in sequence-specific manner. ASOs generally result in destruction of the target RNA by RNase-H mediated mechanisms, although they may also sterically block translation, also resulting in loss of protein production. Ribozymes and DNAzymes cleave target RNAs after base pairing via their antisense flanking arms. siRNAs, which contain both sense and antisense regions from a target RNA, can mediate target RNA destruction via RNAi and the RISC, although they can also function at the transcriptional level. A considerable number of ASRs (mostly ASOs) have progressed into clinical trials, although most have relatively long histories in Phase I/II settings. Clinical trial results are surprisingly difficult to find, although few ASRs appear to have yet established efficacy in Phase III levels. Evolution of ASRs has included: (a) Modifications to ASOs to render them nuclease resistant, with analogous modifications to siRNAs being developed; and (b) Development of strategies to select optimal sites for targeting. Perhaps the biggest barrier to effective therapies with ASRs is the "Delivery Problem." Various liposomal vehicles have been used for systemic delivery with some success, and recent modifications appear to enhance systemic delivery, at least to liver. Various nanoparticle formulations are now being developed which may also enhance delivery. Going forward, topical applications of ASRs would seem to have the best chances for success. In summary, modifications to ASRs to enhance stability, improve targeting, and incremental improvements in delivery vehicles continue to make ASRs attractive as molecular therapeutics, but their advance toward the bedside has been agonizingly slow. J. Cell. Biochem. 98: 14,35, 2006. © 2006 Wiley-Liss, Inc. [source]


Motifs in nucleic acids: Molecular mechanics restraints for base pairing and base stacking

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2003
Stephen C. Harvey
Abstract In building and refining nucleic acid structures, it is often desirable to enforce particular base pairing and/or base stacking interactions. Energy-based modeling programs with classical molecular mechanics force fields do not lend themselves to the easy imposition of penalty terms corresponding to such restraints, because the requirement that two bases lie in or near the same plane (pairing) or that they lie in parallel planes (stacking) cannot be easily expressed in terms of traditional interactions involving two atoms (bonds), three atoms (angles), or four atoms (torsions). Here we derive expressions that define a collection of pseudobonds and pseudoangles through which molecular mechanics restraints for base pairing and stacking can be imposed. We have implemented these restraints into the JUMNA package for modeling DNA and RNA structures. JUMNA scripts can specify base pairing with a variety of standard geometries (Watson,Crick, Hoogsteen, wobble, etc.), or with user-defined geometries; they can also specify stacking arrangements. We have also implemented "soft-core" functions to modify van der Waals and electrostatic interactions to avoid steric conflicts in particularly difficult refinements where two backbones need to pass through one another. Test cases are presented to show the utility of the method. The restraints could be adapted for implementation in other molecular mechanics packages. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 1,9, 2003 [source]


An ab initio theoretical study of electronic structure and properties of 2,-deoxyguanosine in gas phase and aqueous media

JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2002
S. K. Mishra
Abstract Molecular geometries of two structural forms of 2,-deoxyguanosine (keto-N9R and keto-N7R, R = the sugar moiety) considering both the C2,-endo and C3,-endo conformations of the sugar ring and those of the complexes of these species with two water molecules each were optimized employing the ab initio RHF procedure. A mixed basis set consisting of the 6-311+G* basis set for the nitrogen atom of the amino group and the 4-31G basis set for all the other atoms was used. The RHF calculations were followed by correlation correction of the total energy at the MP2 level. Both the structural forms of 2,-deoxyguanosine were solvated using the polarized continuum model (PCM) of the self-consistent reaction field (SCRF) theory and the corresponding RHF optimized geometries at the RHF and MP2 levels. Geometry optimization was also performed in aqueous media using the Onsager model at the RHF level using the above-mentioned mixed basis set, and subsequently, using the reoptimized geometries, single-point MP2 calculations were performed. It is found that both the keto-N9R and keto-N7R forms of 2,-deoxyguanosine as well as their complexes with two water molecules each would occur, particularly at the water,air interface. Though the normal Watson,Crick-type base pairing would not be possible with the keto-N7R form of 2,-deoxyguanosine(G*), two other (G*-C and G*-T) base pairing schemes may occur with this form of the nucleoside, which may cause mutation. The present calculated geometry of the keto-N9R form of the anti -conformation of 2,-deoxyguanosine including the dihedral angle ,CN agree satisfactorily with the available crystallographic results. The present results also agree satisfactorily with those obtained by other authors earlier for the keto-N9R form of 2,-deoxyguanosine using B3LYP and MP2 methods employing the 6-31G* basis set. Using transition state calculations, it is shown that tautomerism of guanine and other similar molecules where the tautomers would coexist would be facilitated by the occurrence of the H+ and OH, fragments of water molecules. Further, this coexistence of the two tautomers appears to make the C8 carbon atom located between the N7 and N9 nitrogen atoms susceptible to attack by the OH, group. Thus, an explanation is obtained for the efficient formation of the reaction product 8-hydroxy-2,-deoxyguanosine, which serves as a biomarker for oxidative damage to DNA in biological systems. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 530,540, 2002; DOI 10.1002/jcc.10046 [source]


The hidden code in genomics: a tool for gene discovery

JOURNAL OF MOLECULAR RECOGNITION, Issue 5 2001
Heinz Kohler
Abstract Among new insights coming from the completion of sequencing of the human genome, reported in Nature and Science, are clues of how evolution has increased the complexity of species, and in particular how the genetic code has enabled this process. It is clear that life has not only evolved by increasing the number of genes, but also by ingeniously evolving an efficient code for expressing diversity in the building blocks (i.e. the amino acids). The rules of nucleic acid base pairing and the classification of amino acids according to hydrophobicity/hydrophilicity relationships define a binary DNA code, which determines the general biophysical characteristics of proteins. Sense and antisense strands can encode protein segments having inverted and complementary hydropathy. The underlying binary code controls association and dissociation of proteins and presumably represents a primordial code that might have emerged in the early stages of self-organizing biochemical cycles. It is the purpose of this communication to provide a perspective of the code in the context of a binary language from its primordial origin to its present day format and to propose to use this code as a genomic mining tool. Copyright © 2001 John Wiley & Sons, Ltd. [source]


Core-shell particles with glycopolymer shell and polynucleoside core via RAFT: From micelles to rods

JOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 6 2009
Samuel Pearson
Abstract Amphiphilic block copolymers were synthesized via the reversible addition fragmentation chain transfer (RAFT) copolymerisation of 2-methacrylamido glucopyranose (MAG) and 5,- O -methacryloyl uridine (MAU). Homopolymerisations of both monomers using (4-cyanopentanoic acid)-4-dithiobenzoate (CPADB) proceeded with pseudo first order kinetics in a living fashion, displaying linear evolution of molecular weight with conversion and low PDIs. A bimodal molecular weight distribution was observed for PMAU at low conversions courtesy of hybrid behavior between living and conventional free radical polymerization. This effect was more pronounced when a PMAG macroRAFT agent was chain extended with MAU, however, in both cases, good control was attained once the main RAFT equilibrium was established. A stability study on PMAU found that its hydrolysis is diffusion controlled, and is accelerated at physiological pH compared with neutral conditions. Self-assembly of four block copolymers with increasing hydrophobic (PMAU) block lengths produced micelles, which demonstrated an increased tendency to form rods as the PMAU block length increased. Interestingly, none of the block copolymers were surface-active. An initial assessment of PMAU's ability to bind the nucleoside adenosine through base pairing was highly promising, with DSC measurements indicating that adenosine is fully miscible in the PMAU matrix. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1706,1723, 2009 [source]


First look at RNA in l -configuration

ACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2004
RNA in l -configuration
Nucleic acid molecules in the mirror image or l -configuration are unknown in nature and are extraordinarily resistant to biological degradation. The identification of functional l -­oligonucleotides called Spiegelmers offers a novel approach for drug discovery based on RNA. The sequence r(CUGGGCGG)·r(CCGCCUGG) was chosen as a model system for structural analysis of helices in the l -configuration as the structure of the d -form of this sequence has previously been determined in structural studies of 5S RNA domains, in particular domain E of the Thermus flavus 5S rRNA [Perbandt et al. (2001), Acta Cryst. D57, 219,224]. Unexpectedly, the results of crystallization trials showed little similarity between the d - and the l -forms of the duplex in either the crystallization hits or the diffraction performance. The crystal structure of this l -RNA duplex has been determined at 1.9,Å resolution with Rwork and Rfree of 23.8 and 28.6%, respectively. The crystals belong to space group R32, with unit-cell parameters a = 45.7, c = 264.6,Å. Although there are two molecules in the asymmetric unit rather than one, the structure of the l -form arranges helical pairs in a head-to-tail fashion to form pseudo-continuous infinite helices in the crystal as in the d -form. On the other hand, the wobble-like G·C+ base pair seen in the D-RNA analogue does not appear in the l -RNA duplex, which forms a regular double-helical structure with typical Watson,Crick base pairing. [source]


Can Copper(II) Mediate Hoogsteen Base-Pairing in a Left-Handed DNA Duplex?

CHEMPHYSCHEM, Issue 3 2010
A Pulse EPR Study
Abstract Pulse EPR spectroscopy is used to investigate possible structural features of the copper(II) ion coordinated to poly(dG-dC),poly(dG-dC) in a frozen aqueous solution, and the structural changes of the polynucleotide induced by the presence of the metal ion. Two different copper species were identified and their geometry explained by a molecular model. According to this model, one species is exclusively coordinated to a single guanine with the N7 nitrogen atom forming a coordinative bond with the copper. In the other species, a guanine and a cytosine form a ternary complex together with the copper ion. A copper crosslink between the N7 of guanine and N3 of cytosine is proposed as the most probable coordination site. Moreover, no evidence was found for an interaction of either copper species with a phosphate group or equatorial water molecules. In addition, circular dichroism (CD) spectroscopy showed that the DNA of the CuII -poly(dG-dC),poly(dG-dC) adducts resembles the left-handed Z-form. These results suggest that metal-mediated Hoogsteen base pairing, as previously proposed for a right-handed DNA duplex, can also occur in a double-stranded left-handed DNA. [source]