α-LNA (α-D-Configured Locked Nucleic Acid)

Abstract

Two pyrimidine α-LNA nucleoside monomers have been synthesised and incorporated into α-configured oligonucleotides. A fully modified mixed α-LNA sequence displays unprecedented parallel stranded hybridisation with complementary RNA and a remarkable selectivity for RNA over DNA. Modelling shows α-LNA : RNA to form an extended duplex with a very broad major groove.     

Nucleic Acid Analog Peptide Containing β-Aminoalanine Modified with Nucleobases

Abstract

Oligopeptides containing N^β-(thymin-1-ylacetyl) β-aminoalanine and N^β-(cytosin-1-ylacetyl) β-aminoalanine moieties synthesized on solid phase using standard boc-chemistry showed hybridization properties with single stranded DNA and RNA, and also with double stranded DNA at pH 7.0.     

α-Amylase Formation and Nucleic Acid Metabolism of Bacillus subtilis

The nucleic acid metabolism in washed cells of Bacillus subtilis was investigated with special reference to amylase formation of the bacterium. On incubation of the suspension of the washed cells, purines, pyrimidines and their related compounds were observed in the medium. However, in the medium of the cells incubated with a calcium chelater, where no amylase formation occurred, were detected adenosine- and guanosine-monophosphate in addition to those described above. The addition of a calcium chelater was also found to decrease the quantity of the nucleic acids being involved in the lysozyme-sensitive fraction of the bacterial cells, suggesting the possibility that the metabolism of nucleic acids in this fraction is closely related to amylase formation of the cells.     

Specificity of protein — Nucleic acid interaction and the biochemical evolution

The water soluble carbodiimide mediated condensation of dipeptides of the general form Gly-X was carried out in the presence of mono- and poly-nucleotides. The observed yield of the tetrapeptide was found to be higher for peptide-nucleotide system of higher interaction specificity following mainly the anticodon-amino acid relationship (Basu, H.S. & Podder, S.K., 1981, Ind. J. Biochem. Biophys.,19, 251–253). The yield of the condensation product of L-peptide was more because of its higher interaction specificity. The extent of the racemization during the condensation of Gly-L-Phe, Gly-L-Tyr and Gly-D-Phe was found to be dependent on the specificity of the interaction —the higher the specificity, the lesser the racemization. The product formed was shown to have a catalytic effect on the condensation reaction. These data thus provide a mechanism showing how the specific interaction between amino acids/dipeptides and nucleic acids could lead to the formation of the primitive translation machinery.     

α-cycloPNA: 1-Aminocylopentane-1-carboxylic Acid-Derived Peptide Nucleic Acid

Abstract

All four diastereoisomers of 3-thymine-1-(^tbutoxycarbonyl)aminocyclopentane- 1-carboxylic acid have been synthesised from (S)-dimethyl malate and thymine monomer 12 has been incorporated into an α-cycloPNA oligomer.     

Nucleic acids in circulation: Are they harmful to the host?

It has been estimated that 10(11) -10(12) cells, primarily of haematogenous origin, die in the adult human body daily, and a similar number is regenerated to maintain homeostasis. Despite the presence of an efficient scavenging system for dead cells, considerable amounts of fragmented genetic material enter the circulation in healthy individuals. Elevated blood levels of extracellular nucleic acids have been reported in various disease conditions; such as ageing and age-related degenerative disorders, cancer; acute and chronic inflammatory conditions, severe trauma and autoimmune disorders. In addition to genomic DNA and nucleosomes, mitochondrial DNA is also found in circulation, as are RNA and microRNA. There is extensive literature that suggests that extraneously added nucleic acids have biological actions. They can enter into cells in vitro and in vivo and induce genetic transformation and cellular and chromosomal damage; and experimentally added nucleic acids are capable of activating both innate and adaptive immune systems and inducing a sterile inflammatory response. The possibility as to whether circulating nucleic acids may, likewise, have biological activities has not been explored. In this review we raise the question as to whether circulating nucleic acids may have damaging effects on the host and be implicated in ageing and diverse acute and chronic human pathologies.     

Some X-Ray Diffraction Parameters of Liquid-Crystalline Dispersions of Nucleic Acid–Chitosan Complexes

Liquid-crystalline dispersions of nucleic acid–chitosan complexes (NA–chitosan) possess optical and X-ray diffraction properties different from those of classical cholesterics. It is possible that positive charge distribution (distance between charges, chitosan conformation, etc.) in the chitosan polymeric chain interacting with NA is a factor controlling the spatial structure of the resulting dispersions.     

Nucleic acid testing (NAT) in high prevalence–low resource settings

Blood screening by NAT for major transfusion transmitted viral infections (TTIs) was originally intended to complement serology for detection of infected donations. Reports from developed countries showed limited marginal value to NAT blood screening in improving blood safety. Reports on NAT results from Europe indicated yield of 1:0.6 million donations for HBV, <1:M for HCV and HIV-1-related to low prevalence of TTI. In contrast, prevalence of TTI in resource-limited countries is almost always high. As a result, more incident cases can be expected among first-time blood donors. Most reports of NAT blood donation screening in these countries showed NAT confirmed yield as high as 1/2800 for HBV and 1/3100 blood donations for HCV as reported from Thailand and Egypt, respectively. The issues for low resource countries are mostly the high cost of NAT but also the requirements of staff qualification, adequate facilities, reagent procurement and maintenance of delicate equipment. Alternatives to commercial NAT are the use of combos antigen-antibody for HIV and HCV, anti-HBc for HBV and in-house NAT. Most of these alternatives have been reported but very few comparisons are available. Once yield data is available, models for estimation of feasibility and cost-effectiveness are proposed to help decision-making.     

Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids—TINA

Twisted intercalating nucleic acid (TINA) is a novel intercalator and stabilizer of Hoogsteen type parallel triplex formations (PT). Specific design rules for position of TINA in triplex forming oligonucleotides (TFOs) have not previously been presented. We describe a complete collection of easy and robust design rules based upon more than 2500 melting points (T_m) determined by FRET. To increase the sensitivity of PT, multiple TINAs should be placed with at least 3 nt in-between or preferable one TINA for each half helixturn and/or whole helixturn. We find that ΔT_m of base mismatches on PT is remarkably high (between 7.4 and 15.2°C) compared to antiparallel duplexes (between 3.8 and 9.4°C). The specificity of PT by ΔT_m increases when shorter TFOs and higher pH are chosen. To increase ΔTms, base mismatches should be placed in the center of the TFO and when feasible, A, C or T to G base mismatches should be avoided. Base mismatches can be neutralized by intercalation of a TINA on each side of the base mismatch and masked by a TINA intercalating direct 3′ (preferable) or 5′ of it. We predict that TINA stabilized PT will improve the sensitivity and specificity of DNA based clinical diagnostic assays.     

A Stochastic Model of Nonenzymatic Nucleic Acid Replication: “Elongators” Sequester Replicators

The origin of nucleic acid template replication is a major unsolved problem in science. A novel stochastic model of nucleic acid chemistry was developed to allow rapid prototyping of chemical experiments designed to discover sufficient conditions for template replication. Experiments using the model brought to attention a robust property of nucleic acid template populations, the tendency for elongation to outcompete replication. Externally imposed denaturation-renaturation cycles did not reverse this tendency. For example, it has been proposed that fast tidal cycling could establish a TCR (tidal chain reaction) analogous to a PCR (polymerase chain reaction) acting on nucleic acid polymers, allowing their self-replication. However, elongating side-reactions that would have been prevented by the polymerase in the PCR still occurred in the simulation of the TCR. The same finding was found with temperature and monomer cycles. We propose that if cycling reactors are to allow template replication, oligonucleotide phenotypes that are capable of favorably altering the flux ratio between replication and elongation, for example, by facilitating sequence-specific cleavage within templates, are necessary; accordingly the minimal replicase ribozyme may have possessed restriction functionality.     

Effect of Intercalators on the Properties of Liquid-Crystalline Dispersions of Nucleic Acid–Chitosan Complex

Molecules of deoxyribonucleic acid and synthetic polydeoxyribonucleotides (NA) in the particles of liquid-crystalline dispersions resulting from interaction with chitosan are accessible to interaction with intercalators. The intercalation is accompanied by alteration in the direction of spatial twist of cholesterics of NA–chitosan complexes. This effect is absent in the case of classical cholesterics produced from NA molecules via phase exclusion, i.e., the cholesteric structure of NA–chitosan complex is very labile as distinct from classical cholesteric NA.     

Nucleic acid-like structures III. Oligomerization of 3′-deoxyadenosine 2′,5′-diphosphoimidazolide

Summary The activated dimonophosphate of 3-deoxyadenosine (cordycepin) undergoes oligomerization to produce a new family of pyrophosphate-linked oligomers in which the average repeating unit involves a nine-atom structural group. The presence of a poly(U) template increase the relative yields of higher oligomers, although the template-free reaction is itself extremely efficient.For the previous paper in this series see Schwartz et al. (1987)     

Multiple Functions of Nuclear DNA Helicase Ⅱ （RNA Helicase A） in Nucleic Acid Metabolism

Secondary structures of nucleic acids play an importantrole in regulating their transactions as carriers of thegenetic information, including DNA replication, trans-cription, RNA processing, RNA transport, and translation.Resolving double-stranded (ds) DNA or RNA is usually anenergy-dependent process that can be accomplished byproteins termed DNA or RNA helicases, which are presentin all prokaryotic and eukaryotic organisms. Earlier attemptsto find mammalian helicases led to the detect…     

Structural Explorations of NCp7–Nucleic Acid Complexes Give Keys to Decipher the Binding Process

A comprehensive view of all the structural aspects related to NCp7 is essential to understand how this protein, crucial in many steps of the HIV-1 cycle, binds and anneals nucleic acids (NAs), mainly thanks to two zinc fingers, ZF1 and ZF2. Here, we inspected the structural properties of the available experimental models of NCp7 bound to either DNA or RNA molecules, or free of ligand. Our analyses included the characterization of the relative positioning of ZF1 and ZF2, accessibility measurements and the exhaustive, quantitative mapping of the contacts between amino acids and nucleotides by a recent tessellation method, VLDM. This approach unveiled the intimate connection between NA binding process and the conformations explored by the free protein. It also provided new insights into the functional specializations of ZF1 and ZF2. The larger accessibility of ZF2 in free NCp7 and the consistency of the ZF2/NA interface in different models and conditions give ZF2 the lead of the binding process. ZF1 contributes to stabilize the complexes through various organizations of the ZF1/NA interface. This work outcome is a global binding scheme of NCp7 to DNA and RNA, and an example of how protein–NA complexes are stabilized.     

Polymethylene Derivatives of Nucleic Bases with ω-Functional Groups: V. Pyrimidine- and Purine-Containing γ-Butyrophenones

New polymethylene derivatives of nucleic bases containing a keto function in the ω-position were synthesized by alkylation of nucleic bases with 2-(3-chloropropyl)-2-phenyl-1,3-dioxolane and the subsequent deblocking of the keto group; their physicochemical properties were studied.