Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Nucleic Acids”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources
PubMed1991

DNA probes: applications of the principles of nucleic acid hybridization.

Nucleic acid hybridization with a labeled probe is the only practical way to detect a complementary target sequence in a complex nucleic acid mixture. The first section of this article covers quantitative aspects of nucleic acid hybridization thermodynamics and kinetics. The probes considered are oligonucleotides or polynucleotides, DNA or RNA, single- or double-stranded, and natural or modified, either in the nucleotide bases or in the backbone. The hybridization products are duplexes or triplexes formed with targets in solution or on solid supports. Additional topics include hybridization acceleration and reactions involving branch migration. The second section deals with synthesis or biosynthesis and detection of labeled probes, with a discussion of their sensitivity and specificity limits. Direct labeling is illustrated with radioactive probes. The discussion of indirect labels begins with biotinylated probes as prototypes. Reporter groups considered include radioactive, fluorescent, and chemiluminescent nucleotides, as well as enzymes with colorimetric, fluorescent, and luminescent substrates.

Base Sequence↗
PubMed2003

Enhanced nucleic acid capture and flow cytometry detection with peptide nucleic acid probes and tunable-surface microparticles.

New methods for automated, direct nucleic acid purification and detection are required for the next generation of unattended environmental monitoring devices. In this study we investigated whether tunable-surface bead chemistry and peptide nucleic acids (PNA) could enhance the recovery and detection of intact rRNA in both test tube and automated suspension array hybridization formats. Intact rRNA was easily captured and detected on PNA-coated Lumavidin beads from 0.1 ng total RNA with a 15-min hybridization in pH 7 buffer, representing 1.7 x 10(3) cell equivalents of total RNA. DNA-conjugated beads in pH 5 hybridization buffer required an overnight hybridization to achieve a detectable signal at 0.1 ng target RNA. Standard DNA hybridization conditions (pH 7) were one order of magnitude less sensitive than the tunable-surface (pH 5) condition. The PNA-conjugated particles were 100x more sensitive than the tunable-surface DNA particles in the automated format, with a detection limit of 0.1 ng total RNA. The detection limits for total RNA on PNA-conjugated microparticles is immediately conducive to the detection and characterization of microorganisms in low-biomass environments or to the identification of rare sequences in a complex sample mixture, without using PCR.

Bacillus↗
PubMedDate not supplied

In situ nucleic acid hybridization.

Nucleic acid hybridization is a recently developed laboratory technique that allows identification of the genetic material in tissue specimens. The role of the nucleic acids DNA and RNA in cellular function and disease is reviewed, followed by discussion of nucleic acid detection techniques. Earlier methods used to detect nucleic acids were slow and time-consuming. Current in situ detection techniques allow rapid characterization of pathogenic organisms in tissue sections and localization of the pathologic genetic material to specific cellular regions. This technology has been useful in the understanding of viral ocular diseases including herpes keratitis and cytomegalovirus retinitis and also has great potential in the understanding of the pathogenesis of human cancers, genetic disorders and endocrine and immunologic diseases.

DNA↗
PubMed2004

The alpha-helical peptide nucleic acid concept: merger of peptide secondary structure and codified nucleic acid recognition.

A novel platform for nucleic acid recognition that integrates the alpha-helix secondary structure of peptides with the codified base-pairing capability of nucleic acids is reported. The resulting alpha-helical peptide nucleic acids (alpha PNAs) are composed of a repeating tetrapeptidyl unit, aa(1)-aa(2)-aa(3)-Ser(B), where aa(1) through aa(3) represent generic ancillary amino acids and B = nucleobases linked to Ser via a methylene bridge. Effective syntheses of constituent Fmoc-protected nucleoamino acids (Fmoc-Ser(B)-OH, where B = thymine, cytosine, and uracil) are described along with a protocol for the solid-phase synthesis of 21mer alpha PNAs containing five such nucleobases. By varying the ancillary amino acids, two distinct classes of alpha PNAs were constructed, having a net charge of -1 or +6, respectively, at physiological pH. The modular nature of the alpha PNA platform was illustrated by the synthesis of symmetrical disulfide-bridged alpha PNA dimers containing 10 nucleobases. Hybridization of these alpha PNAs with ssDNA has been examined by thermal denaturation, gel electrophoresis, and circular dichroism (CD) and the data indicated that alpha PNA binds to ssDNA in a cooperative manner with high affinity and sequence specificity. In general, b2 alpha PNAs bind faster and more strongly with ssDNA than do the corresponding b1 alpha PNAs. Parallel alpha PNA-DNA complexes are more stable than their antiparallel counterparts. CD studies also revealed that the hybridization event involves the folding of both species into their helical conformations. Finally, NMR experiments provided conclusive evidence of Watson-Crick base pairing in alpha PNA-ssDNA hybrids.

Amino Acids↗
PubMed1971

Nucleic Acid Metabolism in Germinating Onion: I. Changes in Root Tip Nucleic Acid during Germination.

Nucleic acid synthesis in the G(1) cell population of the 1-millimeter apex of the Allium cepa embryo was studied during the initial 73 hours of germination. Quantitative data indicate that the total amount of RNA per cell began to increase after 18 hours of germination while the initial DNA per cell increase did not occur until some 20 hours later. Polyacrylamide gel electrophoresis patterns of (3)H-uridine-labeled total nucleic acid samples indicated that synthesis of all detectable RNA fractions present in the pre-emergent 1-millimeter apex (i.e., cytoplasmic and "chloroplast-like" RNA) began at approximately the same time (18 hours). Synthesis of the various cytoplasmic RNA fractions continued throughout the germination period. Data indicating synthesis of the "chloroplast-like" RNA were obtained only for the initial 36 hours of germination. Specific radioactivity of (3)H-uridine-labeled total nucleic acid increased during the first 41.5 hours of germination but then decreased while the accumulation of RNA per cell continued to increase throughout the 73-hour period. In addition, a method is described which reduced the bacterial contamination of Allium seed to a level not detectable by incorporation of radioactive precursors into bacterial ribosomal RNA.

Journal Article↗
PubMed1995

A novel yeast gene product, G4p1, with a specific affinity for quadruplex nucleic acids.

G4 nucleic acids are four-stranded helical structures that are formed in vitro by nucleic acids that contain guanine tracts. These structures anneal readily under physiological conditions and are unusually stable once formed. G4 nucleic acids are thought to participate in telomere function, retroviral genome dimerization, chromosome alignment during homologue pairing, and mitotic recombination, although the in vivo demonstration of these structures in any of these situations has not yet been achieved. Here we purify and characterize an activity from yeast, G4p1, which has a high and specific affinity for G4 nucleic acids. G4p1 prefers substrates containing multiple G4 domains, has an equal affinity for parallel and antiparallel G4 structures, and binds equivalently to RNA and DNA in G4 form. The Keq for G4p1 binding to a G4 DNA oligomer is 5.0 x 10(8) M-1, under near physiological conditions. G4p1 was purified and shown to derive from a 42-kDa protein (p42). We have cloned and sequenced the gene encoding p42 and show it to encode a novel protein with a region significantly homologous to bacterial methionyl-tRNA synthetase dimerization domains. We have reconstituted the G4p1 binding activity with recombinant p42 and present evidence that G4p1 is a homodimer of p42.

Amino Acid Sequence↗
PubMed2001

Contribution of individual amino acids to the nucleic acid binding activities of the Xenopus zinc finger proteins TFIIIIA and p43.

Xenopus transcription factor IIIIA (TFIIIA) binds to both 5S RNA and the 5S RNA gene in immature oocytes, an interaction mediated by nine zinc fingers. To determine the role of the central zinc fingers of the protein in these nucleic acid binding activities, a series of substitution mutants of TFIIIA were constructed and expressed as recombinant proteins in Escherichia coli. The mutant proteins were purified to homogeneity and analyzed for DNA and RNA binding activities using a nitrocellulose filter binding assay. Finger 5, but not finger 4, 6, or 7, is involved in sequence-specific binding to the 5S RNA gene. A TWT amino acid motif in finger 6 makes a significant contribution to the binding of TFIIIA to 5S RNA, while mutations in fingers 4, 5, and 7 have little or no effect on RNA binding by TFIIIA. In striking contrast, a TWT motif in finger 6 of p43, another Xenopus zinc finger protein that binds to 5S RNA, is not necessary for 5S RNA binding by this protein. Evidence for the presence of inhibitory finger-finger interactions that limit the nucleic acid binding properties of individual zinc fingers within TFIIIA and p43 is discussed.

Amino Acid Motifs↗
PubMed2003

Parallel nucleic acid recognition by the LNA (locked nucleic acid) stereoisomers beta-L-LNA and alpha-D-LNA; studies in the mirror image world.

Two LNA (locked nucleic acid) stereoisomers (beta-L-LNA and alpha-D-LNA) are evaluated in the mirror-image world, that is by the study of two mixed sequences of LNA and alpha-L-LNA and their L-DNA and L-RNA complements. Both are found to display high-affinity RNA-recognition by the formation of duplexes with parallel strand orientation.

Base Sequence↗
PubMed2001

At nonzero temperatures, stacked structures of methylated nucleic acid base pairs and microhydrated nonmethylated nucleic acid base pairs are favored over planar hydrogen-bonded structures: a molecular dynamics simulations study.

The dynamic structure of all ten possible nucleic acid (NA) base pairs and methylated NA base pairs hydrated by a small number of water molecules (from 1 to 16) was determined by using molecular dynamics simulations in the NVE microcanonical and NVT canonical ensembles with the Cornell force field (W. D. Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. E. Caldwell, P. Kollman, J. Am. Chem. Soc. 1995, 117, 5179). The presence of one water molecule does not affect the structure of any hydrogen-bonded (H-bonded) nonmethylated base pair. An equal population of H-bonded and stacked structures of adenine...adenine, adenine...guanine and adenine... thymine pairs is reached if as few as two water molecules are present, while obtaining equal populations of these structures in the case of adenine...cytosine, cytosine...thymine, guanine... guanine and guanine...thymine required the presence of four water molecules, and in the case of guanine...cytosine, six. A comparable population of planar, H-bonded and stacked structures for cytosine...cytosine and thymine... thymine base pairs was only obtained if at least eight water molecules hydrated a pair. Methylation of bases changed the situation dramatically and stacked structures were favoured over H-bonded ones even in the absence of water molecules in most cases. Only in the case of methyl cytosine...methyl cytosine, methyl guanine...methyl guanine and methyl guanine...methyl cytosine pairs were two, two or six water molecules, respectively, needed in order to obtain a comparable population of planar, H-bonded and stacked structures. We believe that these results give clear evidence that the preferred stacked structure of NA base pairs in the microhydrated environment, and also apparently in a regular solvent, is due to the hydrophilic interaction of a small number of water molecules. In the case of methylated bases, it is also due to the fact that the hydrogen atoms most suitable for the formation of H-bonds have been replaced by a methyl group. A preferred stacked structure is, thus, not due to a hydrophobic interaction between a large bulk of water molecules and the base pair, as believed.

Base Pairing↗
PubMed1990

Acidic domains around nucleic acids.

The hydrogen ion concentration in the vicinity of DNA was mapped out within the Poisson-Boltzmann approximation. Experimental conditions were modeled by assuming Na-DNA to be solvated in a buffer solution containing 45 mM Tris and 3 mM Mg cations at pH 7.5. Three regions of high H+ concentration (greater than 10 microM) are predicted: one throughout the minor groove of DNA and two localized in the major groove near N7 of guanine and C5 of cytosine for a G.C base pair. These acidic domains correlate well with the observed covalent binding sites of benzo[a]pyrene epoxide (N2 of guanine) and of aflatoxin B1 epoxide (N7 of guanine), chemical carcinogens that presumably undergo acid catalysis to form highly reactive carbocations that ultimately bind to DNA. It is suggested that these regions of high H+ concentration may also be of concern in understanding interactions involving proteins and noncarcinogenic molecules with or near nucleic acids.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1999

Antisense properties of peptide nucleic acid.

Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose phosphate backbone has been replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNA-oligomers can be synthesized in relatively large amounts, are highly stable in biological environments, and bind complementary DNA and RNA targets with remarkably high affinity and specificity. Thus PNA possesses many of the properties desired for a good antisense agent. Until recently, limited uptake of PNA into cells has been the major obstacle for applying PNA as an antisense agent in cell cultures and in vivo. Here, the antisense properties of PNA in vitro and in vivo will be reviewed. In particular, we will focus on recent observations indicating that PNA equipped with or without various uptake moieties may function as an efficient and gene-specific inhibitor of translation in Escherichia coli and in certain mammalian cell types.

Animals↗