-
Journal of the American Chemical Society Jan 2024DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based...
DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic-inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single- or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarse-grained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic-inorganic nanomaterials.
Topics: Nucleic Acid Conformation; Polynucleotides; DNA; Nanostructures; Silicon Dioxide
PubMed: 38117542
DOI: 10.1021/jacs.3c09310 -
The Biochemical Journal Aug 1989[5'-32P]pdT8d(-)dT7, containing an AP (apurinic/apyrimidinic) site in the ninth position, and [d(-)-1',2'-3H, 5'-32P]DNA, containing AP sites labelled with 3H in the 1'...
[5'-32P]pdT8d(-)dT7, containing an AP (apurinic/apyrimidinic) site in the ninth position, and [d(-)-1',2'-3H, 5'-32P]DNA, containing AP sites labelled with 3H in the 1' and 2' positions of the base-free deoxyribose [d(-)] and with 32P 5' to this deoxyribose, were used to investigate the yields of the beta-elimination and delta-elimination reactions catalysed by spermine, and also the yield of hydrolysis, by the 3'-phosphatase activity of T4 polynucleotide kinase, of the 3'-phosphate resulting from the beta delta-elimination. Phage-phi X174 RF (replicative form)-I DNA containing AP (apurinic) sites has been repaired in five steps: beta-elimination, delta-elimination, hydrolysis of 3'-phosphate, DNA polymerization and ligation. Spermine, in one experiment, and Escherichia coli formamidopyrimidine: DNA glycosylase, in another experiment, were used to catalyse the first and second steps (beta-elimination and delta-elimination). These repair pathways, involving a delta-elimination step, may be operational not only in E. coli repairing its DNA containing a formamido-pyrimidine lesion, but also in mammalian cells repairing their nuclear DNA containing AP sites.
Topics: Apurinic Acid; Bacteriophage phi X 174; DNA Ligases; DNA Polymerase I; DNA Repair; DNA, Viral; Polynucleotide 5'-Hydroxyl-Kinase; Polynucleotides; Spermine
PubMed: 2529848
DOI: 10.1042/bj2610707 -
Analytical Biochemistry Jun 2011The ability to monitor and characterize DNA mismatch repair activity in various mammalian cells is important for understanding mechanisms involved in mutagenesis and...
The ability to monitor and characterize DNA mismatch repair activity in various mammalian cells is important for understanding mechanisms involved in mutagenesis and tumorigenesis. Since mismatch repair proteins recognize mismatches containing both normal and chemically altered or damaged bases, in vitro assays must accommodate a variety of mismatches in different sequence contexts. Here we describe the construction of DNA mismatch substrates containing G:T or O(6)meG:T mismatches, the purification of recombinant native human MutSĪ± (MSH2-MSH6) and MutLĪ± (MLH1-PMS2) proteins, and in vitro mismatch repair and excision assays that can be adapted to study mismatch repair in nuclear extracts from mismatch repair proficient and deficient cells.
Topics: Base Sequence; Cell Line; DNA Mismatch Repair; DNA Repair Enzymes; DNA-Binding Proteins; Humans; MutL Proteins; Polynucleotides; Recombinant Proteins
PubMed: 21329650
DOI: 10.1016/j.ab.2011.02.017 -
International Journal of Molecular... Oct 2022It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that...
The Ring World: Eversion of Small Double-Stranded Polynucleotide Circlets at the Origin of DNA Double Helix, RNA Polymerization, Triplet Code, Twenty Amino Acids, and Strand Asymmetry.
It is not entirely clear why, at some stage in its evolution, terrestrial life adopted double-stranded DNA as the hereditary material. To explain this, we propose that small, double-stranded, polynucleotide circlets have special catalytic properties. We then use this proposal as the basis for a 'view from here' that we term the Circlet hypothesis as part of a broader Ring World. To maximize the potential explanatory value of this hypothesis, we speculate boldly about the origins of several of the fundamental characteristics and briefly describe the main methods or treatments applied. The principal prediction of the paper is that the highly constrained, conformational changes will occur preferentially in dsDNA, dsRNA and hybrid RNA-DNA circlets that are below a critical size (e.g., 306 bp) and that these will favor the polymerization of precursors into RNA and DNA. We conclude that the Circlet hypothesis and the Ring World therefore have the attraction of offering the same solution to the fundamental problems probably confronting both the earliest cells and the most recent ones.
Topics: Polynucleotides; Amino Acids; Polymerization; DNA; RNA, Double-Stranded
PubMed: 36361702
DOI: 10.3390/ijms232112915 -
Journal of Virology Oct 1993Sequence motifs within the nonstructural protein NS3 of members of the Flaviviridae family suggest that this protein possesses nucleoside triphosphatase (NTPase) and RNA... (Comparative Study)
Comparative Study
Sequence motifs within the nonstructural protein NS3 of members of the Flaviviridae family suggest that this protein possesses nucleoside triphosphatase (NTPase) and RNA helicase activity. The RNA-stimulated NTPase activity of this protein from prototypic members of the Pestivirus and Flavivirus genera has recently been established and enzymologically characterized. Here, we experimentally demonstrate that the NS3 protein from a member of the third genus of Flaviviridae, human hepatitis C virus (HCV), also possesses a polynucleotide-stimulated NTPase activity. Characterization of the purified HCV NTPase activity showed that it exhibited reaction condition optima with respect to pH, MgCl2, and salt identical to those of the representative pestivirus and flavivirus enzymes. However, each NTPase also possessed several unique properties when compared with one another. Notably, the profile of polynucleotide stimulation of the NTPase activity was distinct for the three enzymes. The HCV NTPase was the only one whose activity was significantly enhanced by a deoxyribopolynucleotide. Additional distinguishing features among the three enzymes relating to the kinetic properties of their NTPase activities are discussed. These studies provide a foundation for investigation of the putative RNA helicase activity of these proteins and for further study of the role of the NS3 proteins of members of the Flaviviridae in the replication cycle of these viruses.
Topics: Adenosine Triphosphatases; Base Sequence; Cloning, Molecular; Deoxyribonucleotides; Escherichia coli; Flavivirus; Hepacivirus; Kinetics; Molecular Sequence Data; Nucleoside-Triphosphatase; Oligodeoxyribonucleotides; Pestivirus; Phosphoric Monoester Hydrolases; Polymerase Chain Reaction; Polynucleotides; RNA Helicases; Recombinant Proteins; Serine Endopeptidases; Species Specificity; Substrate Specificity; Viral Nonstructural Proteins
PubMed: 8396675
DOI: 10.1128/JVI.67.10.6152-6158.1993 -
The Biochemical Journal Aug 1974X-ray-diffraction analysis of oriented, partially crystalline fibres of polyinosinic acid has resulted in a new molecular model. This model consists of four identical...
X-ray-diffraction analysis of oriented, partially crystalline fibres of polyinosinic acid has resulted in a new molecular model. This model consists of four identical polynucleotide chains related to one another by a fourfold rotation axis. The coaxial helices are righthanded (screw symmetry 23(2)) and have an axial translation per residue h=0.341nm and a rotation per residue t=31.3 degrees . Incorporated in the model are standard bond lengths, bond angles and C-2-endo furanose rings. The nucleotide conformation angles, determined by linked-atom least-squares methods, are orthodox and the fit with the X-ray intensities is good. Each hypoxanthine base is linked to two others by hydrogen bonds involving O-6 and N-1. Further stability may arise from intrachain hydrogen bonds between each ribose hydroxyl group and the phosphate oxygen O-3. If guanine were to be substituted for hypoxanthine in an isogeometrical molecular structure, additional hydrogen bonds could be made between every N-2 and N-7.
Topics: Guanine Nucleotides; Guanosine Monophosphate; Hypoxanthines; Inosine Monophosphate; Inosine Nucleotides; Models, Molecular; Nucleic Acid Conformation; Polynucleotides; X-Ray Diffraction
PubMed: 4375981
DOI: 10.1042/bj1410537 -
Infection and Immunity Nov 1981Two series of interferon-inducing complexes containing polyriboinosinic and polyribocytidylic acids, poly-L-lysine, and carboxymethyl cellulose were prepared. One series...
Two series of interferon-inducing complexes containing polyriboinosinic and polyribocytidylic acids, poly-L-lysine, and carboxymethyl cellulose were prepared. One series contained carboxymethyl cellulose, 27,000-molecular-weight poly-L-lysine, and either 4S, 6S, or 9S polyriboinosinic and polyribocytidylic acids. The other series contained carboxymethyl cellulose, 9S polyriboinosinic and polyribocytidylic acids, and poly-L-lysine, whose molecular weights ranged from 2,000 to 27,000. The homogeneity of these double-stranded polynucleotide complexes was confirmed by single-step thermal denaturation profiles and by single peaks in sucrose gradient velocity sedimentation. The complexes have a greater resistance to hydrolysis by ribonuclease than does polyriboinosinic-polyribocytidylic acid. The resistance to ribonuclease increased with the increasing size of polynucleotide homopolymers and poly-L-lysine. In monkeys and, to a lesser extent, in mice, serum interferon levels induced by the different complexes were related to the degree of resistance of the complexes to hydrolysis by ribonuclease. In mice, 4S, 6S, and 9S complexes of polyriboinosinic-polyribocytidylic acid, poly-L-lysine, and carboxymethyl cellulose had a higher level of toxicity than did polyriboinosinic-polyribocytidylic acid as measured by 50% lethal dose. The toxicity was parallel to the ribonuclease resistance of the complexes. It was concluded that an increase in the size of the polynucleotides and the polyamino acids in these complexes leads to higher resistance to hydrolysis by ribonuclease and to greater interferon responses in mice and rhesus monkeys.
Topics: Animals; Carboxymethylcellulose Sodium; Centrifugation, Density Gradient; Female; Interferons; Macaca mulatta; Male; Methylcellulose; Mice; Molecular Weight; Peptides; Poly I-C; Polylysine; Ribonucleases; Temperature
PubMed: 6171519
DOI: 10.1128/iai.34.2.416-421.1981 -
Biophysical Journal Feb 2009Key biological and nano-technological processes require the partial or complete association and dissociation of complementary DNA strands. We present a variant of the...
Key biological and nano-technological processes require the partial or complete association and dissociation of complementary DNA strands. We present a variant of the Poland-Scheraga model for DNA melting where we introduce a local, sequence-dependent salt correction of the nearest-neighbor parameters. Furthermore, our formulation accounts for capping and interfacial energies of helical and coiled chain sections. We show that the model reproduces experimental data for melting temperatures over the full experimental range of strand length, strand concentration, and ionic strength of the solution. In particular, we reproduce a phenomenological relation by Frank-Kamenetskii for very long chains using a parameterization based on melting curves for short oligomers. However, we also show that the parameters of the Poland-Scheraga model are still not known with sufficient precision to quantitatively predict the fine structure of melting curves. This formulation of the Poland-Scheraga model opens the possibility to overcome this limitation by optimizing parameters with respect to an extended base of experimental data for short-, medium-, and long-chain melting. We argue that the often-discarded melting data for longer oligomers exhibiting non-two-state transitions could play a particularly important role.
Topics: Computer Simulation; DNA; Models, Chemical; Models, Genetic; Monte Carlo Method; Nucleic Acid Denaturation; Polynucleotides; Salts; Transition Temperature
PubMed: 18849409
DOI: 10.1529/biophysj.108.134031 -
Nucleic Acids Research Dec 1974The known methods of enzymatic phosphorylation with [(32)P]phosphate of the 3'- or 5'-hydroxyl group of an oligonucleotide have been applied to oligonucleotides derived...
The known methods of enzymatic phosphorylation with [(32)P]phosphate of the 3'- or 5'-hydroxyl group of an oligonucleotide have been applied to oligonucleotides derived from Mycoplasma tRNA(Phe). The fingerprints obtained by both methods are very similar to each other and to that of uniformly labelled tRNA. The sequence of some oligonucleotides was determined by partial digestion of the 3'-phosphorylated fragment with spleen phosphodiesterase and of the corresponding 5'-phosphorylated fragment with venom phosphodiesterase.
Topics: Base Sequence; Micrococcus; Mycoplasma; Phenylalanine; Phosphorus Radioisotopes; Phosphotransferases; Polynucleotides; Polyribonucleotide Nucleotidyltransferase; RNA, Bacterial; RNA, Transfer; Ribonucleotides
PubMed: 4449733
DOI: 10.1093/nar/1.12.1733 -
Journal of Virology Oct 1975Two new human papovavirus isolates (JMV and MMV) from the urines of patients with Wiskott-Aldrich syndrome were morphologically and serologically identical to BK virus... (Comparative Study)
Comparative Study
Two new human papovavirus isolates (JMV and MMV) from the urines of patients with Wiskott-Aldrich syndrome were morphologically and serologically identical to BK virus (BKV). The genomes of these two new isolates were found to be indistinguishable from prototype BKV DNA in a variety of nucleic acid hybridization experiments. Like BKV DNA, JMV and MMV DNAs share approximately 20% of their polynucleotide sequences with simian virus 40 DNA. The genome of JMV was indistinguishable from that of BKV by restriction endonuclease analysis; MMV DNA contained three instead of four R-Hind cleavage sites and one rather than no R-HpaII cleavage sites. Physical maps of the BKV and MMV genomes were constructed using restriction endonucleases, and these maps were oriented to the map of simian virus 40 DNA.
Topics: BK Virus; Base Sequence; Chromosome Mapping; DNA Restriction Enzymes; DNA, Circular; DNA, Viral; Genes; Humans; Molecular Weight; Nucleic Acid Conformation; Polynucleotides; Polyomavirus; Simian virus 40; Urine; Wiskott-Aldrich Syndrome
PubMed: 170425
DOI: 10.1128/JVI.16.4.959-973.1975