Enzymatic resolution and base pairing properties of D- and L-cyclohexenyl nucleic acids (CeNA)

An enzymatic transesterification reaction afforded large scale resolution of the cyclohexenol precursor needed for preparation of both series of CeNA building blocks. CeNA oligos of "D-like" chirality display a strong and selective interaction with RNA, while preserving RNase H activity, and therefore have potential as antisense constructs. CeNAs of opposite chirality form a self-pairing system on their own.     

Base pairing properties of D- and L-cyclohexene nucleic acids (CeNA)

Cyclohexene nucleic acids (CeNA) with a D-like configuration form very stable self-complementary duplexes and stable duplexes with RNA. An increased duplex stability with Delta T(m)/mod of +1.2 degrees C is observed. The duplex with DNA is less stable. Excellent mismatch discrimination has been observed as well for the duplex with DNA as for the duplex with RNA. The results obtained with mixed CeNA sequences warrant antisense studies with CeNA. The CeNAs of opposite chirality constitute a self-pairing system on their own, resembling L-RNA sequences.     

CYCLOHEXENE NUCLEIC ACIDS (CeNA) FORM STABLE DUPLEXES WITH RNA AND INDUCE RNASE H ACTIVITY

Cyclohexene nucleic acids (CeNA) were synthesized using classical phosporamidite chemistry. Incorporation of a cyclohexene nucleo-side in a DNA chain leads to an increase in stability of the DNA/RNA duplex. CeNA is stable against degradation in serum. A CeNA/RNA hybrid is able to activate E. Coli RNase H, resulting in cleavage of the RNA strand.     

Cyclohexene nucleic acids (CeNA) form stable duplexes with RNA and induce RNase H activity

Cyclohexene nucleic acids (CeNA) were synthesized using classical phosporamidite chemistry. Incorporation of a cyclohexene nucleo-side in a DNA chain leads to an increase in stability of the DNA/RNA duplex. CeNA is stable against degradation in serum. A CeNA/RNA hybrid is able to activate E. Coli RNase H. resulting in cleavage of the RNA strand.     

RNase H mediated cleavage of RNA by cyclohexene nucleic acid (CeNA)

Cyclohexene nucleic acid (CeNA) forms a duplex with RNA that is more stable than a DNA–RNA duplex (ΔT_m per modification: +2°C). A cyclohexenyl A nucleotide adopts a 3′-endo conformation when introduced in dsDNA. The neighbouring deoxynucleotide adopts an O4′-endo conformation. The CeNA:RNA duplex is cleaved by RNase H. The V_max and K_m of the cleavage reaction for CeNA:RNA and DNA:RNA is in the same range, although the k_cat value is about 600 times lower in the case of CeNA:RNA.     

Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG)

Cyclohexene nucleic acids (CeNA), which are characterized by the presence of a cyclohexene moiety instead of a natural (deoxy)ribose sugar, are known to increase the thermal and enzymatic stability when incorporated in RNA oligonucleotides. As it has been demonstrated that even a single cyclohexenyl nucleoside, when incorporated in an oligonucleotide, can have a profound effect on the biological activity of the oligonucleotide, further research is warranted to study the complex of such oligonucleotides with target proteins. In order to analyse the influence of CeNA residues onto the helix conformation and hydration of natural nucleic acid structures, a cyclohexenyl-adenine building block (xAr) was incorporated into the Dickerson sequence CGCGA(xAr)TTCGCG. The crystal structure of this sequence determined to a resolution of 1.90 Å. The global helix belongs to the B-type family and shows a water spine, which is partially broken up by the apolar cyclohexene residue. The cyclohexene ring adopts the ²E-conformation allowing a better incorporation of the residue in the dodecamer sequence. The crystal packing is stabilized by cobalt hexamine residues and belongs to space group P222₁, never before reported for nucleic acids.     

The histone octamer influences the wrapping direction of DNA on it: Brownian dynamics simulation of the nucleosome chirality

In eukaryote nucleosome, DNA wraps around a histone octamer in a left-handed way. We study the process of chirality formation of nucleosome with Brownian dynamics simulation. We model the histone octamer with a quantitatively adjustable chirality: left-handed, right-handed or non-chiral, and simulate the dynamical wrapping process of a DNA molecule on it. We find that the chirality of a nucleosome formed is strongly dependent on that of the histone octamer, and different chiralities of the histone octamer induce its different rotation directions in the wrapping process of DNA. In addition, a very weak chirality of the histone octamer is quite enough for sustaining the correct chirality of the nucleosome formed. We also show that the chirality of a nucleosome may be broken at elevated temperature.     

Heart and gut chiralities are controlled independently from initial heart position in the developing zebrafish

A fundamental problem in developmental biology is how left-right (LR) asymmetry is generated, both on the whole organism level and at the level of an individual organ or structure. To investigate the relationship of organ sidedness to organ chirality, we examined 12 zebrafish mutants for initial heart tube position and later heart looping direction (chirality). Anomalous initial heart position was found in seven mutants, which also demonstrated loss of normal LR asymmetry in lateral plate mesoderm (LPM) antivin/lefty-1 and Pitx2 expression. Those with a relatively normal notochord (cyc(b16), din, and spt) displayed a predictive correlation between initial heart position and heart chirality, whereas initial heart position and heart chirality were independently randomized in those with a defective notochord (flh, boz, ntl, and mom). The predictability of heart chirality in spt, din, and b16 embryos, even in the absence of normal antivin/lefty-1 and Pitx2 expression, strongly suggests that heart chirality is controlled by a process distinct from that which controls appropriate left-sided LPM expression of antivin-Pitx2 signaling pathway molecules. In addition, there was correlation of initial heart position with gut chirality (and also between heart chirality and gut chirality) in the first class of mutants with normal notochord, but not in the second class, which appears to model human heterotaxy syndrome.     

Ligand distortion modes leading to increased chirality content of Katsuki-Jacobsen catalysts

The "chirality content" of Katsuki-Jacobsen epoxidation catalysts are computed with the Avnir continuous chirality measure (CCM). An assessment of Mn(salen) molecules from the Cambridge Structural Database shows there exist some variation in CCM and the chirality content for several triplet state complexes of these catalysts purported in the literature to be the active species show even larger CCM values. Several deformation modes were analyzed to examine how chirality content changes as catalyst distortion is induced. The deformations studied include in-plane deformations, cup-shaped puckering, ligand twisting motions, and step-like deformations. Some distortions lead to increases of chirality while others lead to a decrease in chirality content. The most influential distortion modes that can be used for ligand design are twisting and step induction.     

Chirality: A Relational Geometric‐Physical Property

The definition of the term chirality by Lord Kelvin in 1893 and 1904 is analyzed by taking crystallography at that time into account. This shows clearly that chirality is a relational geometric‐physical property, i.e., two relations between isometric objects are possible: homochiral or heterochiral. In scientific articles the relational term chirality is often mistaken for the two valued measure for the individual (absolute) sense of chirality, an arbitrary attributive term. Chirality 25:684–685, 2013. © 2013 Wiley Periodicals Inc.     

Corolla chirality does not contribute to directed pollen movement in Hypericum perforatum (Hypericaceae): mirror image pinwheel flowers function as radially symmetric flowers in pollination

Corolla chirality, the pinwheel arrangement of petals within a flower, is found throughout the core eudicots. In 15 families, different chiral type flowers (i.e., right or left rotated corolla) exist on the same plant, and this condition is referred to as unfixed/enantiomorphic corolla chirality. There are no investigations on the significance of unfixed floral chirality on directed pollen movement even though analogous mirror image floral designs, for example, enantiostyly, has evolved in response to selection to direct pollinator and pollen movement. Here, we examine the role of corolla chirality on directing pollen transfer, pollinator behavior, and its potential influence on disassortative mating. We quantified pollen transfer and pollinator behavior and movement for both right and left rotated flowers in two populations of Hypericum perforatum. In addition, we quantified the number of right and left rotated flowers at the individual level. Pollinators were indifferent to corolla chirality resulting in no difference in pollen deposition between right and left flowers. Corolla chirality had no effect on pollinator and pollen movement between and within chiral morphs. Unlike other mirror image floral designs, corolla chirality appears to play no role in promoting disassortative mating in this species.     

Chirality as a tool in nucleic acid recognition: principles and relevance in biotechnology and in medicinal chemistry

The understanding of the interaction of chiral species with DNA or RNA is very important for the development of new tools in biology and of new drugs. Several cases in which chirality is a crucial point in determining the DNA binding mode are reviewed and discussed, with the aim of illustrating how chirality can be considered as a tool for improving the understanding of mechanisms and the effectiveness of nucleic acid recognition. The review is divided into two parts: the former describes examples of chiral species interacting with DNA: intercalators, metal complexes, and groove binders; the latter part is dedicated to chirality in DNA analogs, with discussion of phosphate stereochemistry and chirality of ribose substitutes, in particular of peptide nucleic acids (PNAs) for which a number of works have been published recently dealing with the effect of chirality in DNA recognition. The discussion is intended to show how enantiomeric recognition originates at the molecular level, by exploiting the enormous progresses recently achieved in the field of structural characterization of complexes formed by nucleic acid with their ligands by crystallographic and spectroscopic methods. Examples of application of the DNA binding molecules described and the role of chirality in DNA recognition relevant for biotechnology or medicinal chemistry are reported.     

Fundamental symmetry aspects of chirality

Physical systems which exhibit distinguishable enantiomers under space inversion are not necessarily chiral. A new definition of chirality is proposed that enables true and false chirality to be distinguished. Although spatial enantiomorphism is sufficient to guarantee chirality in a stationary object, enantiomorphous systems are not necessarily chiral when motion is involved. Only a truly chiral influence can induce absolute asymmetric synthesis in a reaction mixture at thermodynamic equilibrium, but false chirality might suffice if equilibrium is not attained. Parity violation lifts only the degeneracy of enantiomers of truly chiral systems, the true enantiomers (i.e. strictly degenerate) being interconverted by space inversion together with charge conjugation. The time-independence of optical activity arising from parity violation is contrasted with the time-dependence of that arising from spontaneous parity breaking.     

Geometrical and algebraic approach to central molecular chirality: a chirality index and an Aufbau description of tetrahedral molecules

On the basis of empirical Fischer projections, we develop an algebraic approach to the central molecular chirality of tetrahedral molecules. The elements of such an algebra are obtained from the 24 projections which a single chiral tetrahedron can generate in S and R absolute configurations. They constitute a matrix representation of the O4 orthogonal group. According to this representation, given a molecule with n chiral centres, it is possible to define an "index of chirality chi identical with {n, p}", where n is the number of stereogenic centres of the molecule and p the number of permutations observed under rotations and superimpositions of the tetrahedral molecule to its mirror image. The chirality index not only assigns the global chirality of a given tetrahedral chain, but indicates also a way to predict the same property for new compounds, which can be built up consistently.     

Spiral galaxies as enantiomers: Chirality,an underlying feature in chemistry and astrophysics

Spiral galaxies are axisymmetric objects showing 2D chirality when projected onto a plane. Features in common with tetrahedral molecules are pointed out, in particular the existence of a preferred chiral modality for genetic galaxies as in amino acids and sugars. Environmental effects can influence the intrinsic chirality of originally isolated stellar systems so that a progressive loss of chirality is recognized in the Hubble morphological sequence of galaxies. © 2005 Wiley‐Liss, Inc. Chirality