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It is well known that multivalent cations cause free DNA in solution to condense into nanometer-scale particles with toroidal and rod-like morphologies. However, it has not been shown to what degree kinetic factors (e.g., condensate nucleation) versus thermodynamic factors (e.g., DNA bending energy) determine experimentally observed relative populations of toroids and rods. It is also not clear how multimolecular DNA toroids and rods interconvert in solution. We have conducted a series of condensation studies in which DNA condensate morphology statistics were measured as a function of time and DNA structure. Here, we show that in a typical in vitro DNA condensation reaction, the relative rod population 2 min after the initiation of condensation is substantially greater than that measured after morphological equilibrium is reached (ca. 20 min). This higher population of rods at earlier time points is consistent with theoretical studies that have suggested a favorable kinetic pathway for rod nucleation. By using static DNA loops to alter the kinetics and thermodynamics of condensation, we further demonstrate that reported increases in rod populations associated with decreasing DNA length are primarily due to a change in the thermodynamics of DNA condensation, rather than a change in the kinetics of condensate nucleation or growth. The results presented also reveal that the redistribution of DNA from rods to toroids is mediated through the exchange of DNA strands with solution.

▪ Abstract Toroidal DNA condensates have attracted the attention of biophysicists, biochemists, and polymer physicists for more than thirty years. In the biological community, the quest to understand DNA toroid formation has been motivated by its relevance to gene packing in certain viruses and by the potential use of DNA toroids in artificial gene delivery (e.g., gene therapy). In the physical sciences, DNA toroids are appreciated as a superb model system for studying particle formation by the collapse of a semiflexible, polyelectrolyte polymer. This review focuses on experimental studies from the past few years that have significantly increased our understanding of DNA toroid structure and the mechanism of their formation. Highlights include structural studies that show the DNA strands within toroids to be packed in an ideal hexagonal lattice, and also in regions with a nonhexagonal lattice that are required by the topological constraints associated with winding DNA into a toroid. Recent studies of DNA toroid formation have also revealed that toroid size limits result from a complex interplay between kinetic and thermodynamic factors that govern both toroid nucleation and growth. The work discussed in this review indicates that it will ultimately be possible to obtain substantial control over DNA toroid dimensions.

Structures formed by human telomere sequence (HTS) DNA are of interest due to G-quadruplex forming HTS DNA that has recently generated a tremendous interest due to its involvement in aging process and cancer. The present study examines HTS in anhydrous, exceptionally viscous deep eutectic solvent (DES), comprised of choline, chloride, and urea. Under these conditions, HTS adopts an extremely stable “parallel-propeller” form of G-quadruplex, consistent with the previously observed effects of diminished water activity. Additionally, the high solvent friction of DES slows the dynamics of HTS folding on the order of months, as opposed to milliseconds in aqueous solution, and allows the entrapment of kinetic intermediates. Moreover, analogous transition studies of the quadruplex converting from the aqueous buffer structure to the parallel form in 90% DES (w/v) and 40% PEG 200 (v/v) differ from hours to days scaling inversely with viscosity ∼ 1/ƞ1.4. This diffusion control over the HTS folding is consistent wit...

The fine structure of the DNA double helix and a number of its physical properties depend upon nucleotide sequence. This includes minor groove width, the propensity to undergo the B-form to A-form transition, sequence-directed curvature, and cation localization. Despite the multitude of studies conducted on DNA, it is still difficult to appreciate how these fundamental properties are linked to each other at the level of nucleotide sequence. We demonstrate that several sequence-dependent properties of DNA can be attributed, at least in part, to the sequence-specific localization of cations in the major and minor grooves. We also show that effects of cation localization on DNA structure are easier to understand if we divide all DNA sequences into three principal groups: A-tracts, G-tracts, and generic DNA. The A-tract group of sequences has a peculiar helical structure (i.e., B*-form) with an unusually narrow minor groove and high base-pair propeller twist. Both experimental and theoretical studies have provided evidence that the B*-form helical structure of A-tracts requires cations to be localized in the minor groove. G-tracts, on the other hand, have a propensity to undergo the B-form to A-form transition with increasing ionic strength. This property of G-tracts is directly connected to the observation that cations are preferentially localized in the major groove of G-tract sequences. Generic DNA, which represents the vast majority of DNA sequences, has a more balanced occupation of the major and minor grooves by cations than A-tracts or G-tracts and is thereby stabilized in the canonical B-form helix. Thus, DNA secondary structure can be viewed as a tug of war between the major and minor grooves for cations, with A-tracts and G-tracts each having one groove that dominates the other for cation localization. Finally, the sequence-directed curvature caused by A-tracts and G-tracts can, in both cases, be explained by the cation-dependent mismatch of A-tract and G-tract helical structures with the canonical B-form helix of generic DNA (i.e., a cation-dependent junction model).

We propose that a molecular midwife , a flat molecule approximately 10 A×10 A with two hydrophobic faces, was essential to the origin of life. This molecule was positively charged, water soluble and did not strongly associate with itself in solution. It may have been a derivative of phthalocyanine that no longer exists on the Earth today, and might have been formed solely from hydrogen cyanide and formaldehyde. The midwife tended to intercalate between side groups (bases, similar to those in RNA) of polymers to form stacks , which incorporated bare bases. The midwife alternated in these stacks with hydrogen-bonded tetrads of bases. Under conditions of low water activity, as in a desert during the day, bare bases in the stacks were joined together by neutral and chemically heterogeneous backbones of no fixed chirality. The components of the backbones were the products of the formose reaction of formaldehyde, and were involved in the reversible formation of N -glycosides and acetals catalysed by divalent metal ions. The final product of this assemblage was a fully intercalated quadruplex of four information-containing polymer strands (four proto -RNA molecules). This process constituted replication of the original polymer that had seeded the formation of the stack. The stack structure ensured that the polymer's base sequence was replicated faithfully despite the lack of both homochirality and chemical homogeneity in the backbone. At night, water from condensing dew would suddenly come in contact with these products, quenching all chemical reactions and releasing midwife molecules and single- or double-stranded proto-RNA. Evaporation of water during the day then gave new stacks containing one or two proto-RNA strands, bare bases, and midwife molecules, which could begin a new replication cycle. Our model also allows for the generation of new stacks and the extension of existing ones, without restricting the base sequence of either, thereby providing a source of genetic information. The proto-RNA replication cycle is driven purely by concentration changes caused by the Sun and the rotation of the Earth. We propose that this system as a whole could have gradually evolved into the RNA World.

The DNA sequence d(G(4)T(4)G(4)) [Oxy-1.5] consists of 1.5 units of the repeat in telomeres of Oxytricha nova and has been shown by NMR and X-ray crystallographic analysis to form a dimeric quadruplex structure with four guanine-quartets. However, the structure reported in the X-ray study has a fundamentally different conformation and folding topology compared to the solution structure. In order to elucidate the possible role of different counterions in this discrepancy and to investigate the conformational effects and dynamics of ion binding to G-quadruplex DNA, we compare results from further experiments using a variety of counterions, namely K(+), Na(+)and NH(4)(+). A detailed structure determination of Oxy-1.5 in solution in the presence of K(+)shows the same folding topology as previously reported with the same molecule in the presence of Na(+). Both conformations are symmetric dimeric quadruplexes with T(4)loops which span the diagonal of the end quartets. The stack of quartets shows only small differences in the presence of K(+)versus Na(+)counterions, but the T(4)loops adopt notably distinguishable conformations. Dynamic NMR analysis of the spectra of Oxy-1.5 in mixed Na(+)/K(+)solution reveals that there are at least three K(+)binding sites. Additional experiments in the presence of NH(4)(+)reveal the same topology and loop conformation as in the K(+)form and allow the direct localization of three central ions in the stack of quartets and further show that there are no specific NH(4)(+)binding sites in the T(4)loop. The location of bound NH(4)(+)with respect to the expected coordination sites for Na(+)binding provides a rationale for the difference observed for the structure of the T(4)loop in the Na(+)form, with respect to that observed for the K(+)and NH(4)(+)forms.

The problem of β-nucleoside formation under prebiotic conditions represents one of the most significant challenges to the RNA world hypothesis and to many of its proposed precursors. The possibility exists that alternative bases may have come before the contemporary bases (i.e., A, G, C, and U), including bases that more readily form nucleosides. In a search for pyrimidine bases that are able to form nucleosides in plausible prebiotic reactions, it was discovered that the drying and heating of 2-pyrimidinone with ribose produces a β-furanosyl ribonucleoside in approximately 12% yield. At least two other chemical isomers of zebularine are also produced in the condensation reaction. This work represents the first successful synthesis of a pyrimidine nucleoside from a free base and a nonactivated sugar in a plausible prebiotic reaction. A comparison of 2-pyrimidinone with the purine bases that have also been demonstrated to form nucleosides in plausible prebiotic reactions provides insights regarding what ch...

Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.

Elucidating the physiochemical principles that govern molecular self-assembly is of great importance for understanding biological systems and may provide insight into the emergence of the earliest macromolecules of life, an important challenge facing the RNA World hypothesis. Self-assembly results from a delicate balance between multiple noncovalent interactions and solvent effects, but achieving efficient self-assembly in aqueous solution with synthetic molecules has proven particularly challenging. Here, we demonstrate how two physical properties – monomer solubility and large hydrophobic surfaces of intermediate structures – are key elements to achieving supramolecular polymers in aqueous solution (Cafferty et al., 2013). Applying these two principles, we report the highly cooperative self-assembly of two weakly interacting, low molecular weight monomers [cyanuric acid and a modified triaminopyrimidine] into a water-soluble supramolecular assembly (see scheme below). The observed equilibrium between on...

A variant of lactate dehydrogenase (LDHB∗GUA1) was previously identified among the Guaymi Indians of Panama and Costa Rica. The LDHB∗GUA1 variant is enzymatically inactive; however, the variant subunits alter the electrophoresic mobility of the tetramers that include active LDHA and LDHB subunits. The kinetic properties of the tetramerc enzyme, comprised of inactive B plus active A subunits, are similar to properties of the heterotetramers with active B subunits, except for the reduced specific activity. We have determined that a single C · G to T · A transition changes an Arg to a Trp at amino acid residue 106. This substitution explains the increase in net negative charge observed by protein electrophoresis. This Arg 106 residue is absolutely conserved throughout evolution. Published high-resolution crystal structures of LDH reveal that this residue is within the hinge of a loop that closes over the active site of the subunit upon binding of substrate and cofactor and also has a direct role in catalysis. Computer modeling of the variant enzyme suggests that replacement of this Arg residue with a Trp does not induce significant change in the structure of the active site. However, this substitution would result in disruption of enzyme activity through the inability of the uncharged tryptophan side-chain to polarize the substrate carbonyl bond. This would explain the loss of catalytic function with maintenance of normal kinetic properties in the heterotetramers containing the variant subunits. The ability to maintain normal, tissue-specific kinetic properties could explain the absence of clinical manifestations in the homozygous LDHB∗GUA1 individuals.

Molecules that reversibly bind DNA and trigger the formation of non-Watson-Crick secondary structures would be useful in the design of dynamic DNA nanostructures and as potential leads for new therapeutic agents. We demonstrate that coralyne, a small crescent-shaped molecule, promotes the formation of a duplex secondary structure from homo-adenine oligonucleotides. AFM studies reveal that the staggered alignment of homo-adenine oligonucleotides upon coralyne binding produces polymers of micrometers in length, but only 2 nm in height. A DNA duplex was also studied that contained eight A.A mismatches between two flanking 7-bp Watson-Crick helices. CD spectra confirm that the multiple A.A mismatches of this duplex bind coralyne in manner similar to that of homo-adenine oligonucleotides. Furthermore, the melting temperature of this hybrid duplex increases by 13 degrees C upon coralyne binding. These observations illustrate that the helical structure of the homo-adenine-coralyne duplex is compatible with the B-form DNA helix.

Protamine is a small protein that packages DNA in the sperm of most vertebrates. Shortly after its synthesis, the serine and threonine residues in each protamine are phosphorylated and the modified proteins are deposited onto DNA, displacing the histones and other chromatin proteins. We have hypothesized that the phosphorylation of protamine 1 induces protamine dimerization and these dimers are required for efficient histone displacement. Histone displacement by protamines in late-step spermatids appears to be essential for the production of fertile sperm in man and other mammals, and the disruption of this process could provide a new approach for male contraception. As a first step towards testing this theory, we have initiated a set of in vitro experiments to determine whether of not protamine phosphorylation is essential for histone displacement. Thee results of these experiments, although incomplete, confirm that unphosphorylated protamine cannot effectively displace histone from DNA. Polyarginine molecules twice the size of a protamine molecule and salmine dimer were found to be more effective. These results are consistent with the theory that the disruption of protamine phosphorylation may prove to be a useful new approach for male contraception if it can be shown to facilitate or induce protamine dimerization.

Mg²⁺ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe²⁺ in the absence of free oxygen as a replacement for Mg²⁺ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg²⁺ in RNA folding and function can indeed be served by Fe²⁺. The results of quantum mechanical calculations show that the geometry of coordination of Fe²⁺ by RNA phosphates is similar to that of Mg²⁺. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4-P6 domain RNA is conserved between complexes with Fe²⁺ or Mg²⁺. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg²⁺, and the hammerhead ribozyme are enhanced in the presence of Fe²⁺ compared to Mg²⁺. All chemical footprinting and ribozyme assays in the presence of Fe²⁺ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe²⁺. The combined biochemical and paleogeological data are consistent with a role for Fe²⁺ in an RNA World. RNA and Fe²⁺ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg²⁺ alone.

A self-organizing process is described that combines DNA template association thermodynamics and kinetic reductive amination to translate polymer sequence information into amine nucleoside polymers. The developed kinetic model analyses allowed this process to be extended to the translation of templates as long as catalytic ribozymes.

Isolated DNA fibers complexed with protamine (the chromosomal protein that packages DNA in mammalian sperm) have been produced by partially decondensing the highly compacted mouse sperm chromatin particle on a glass coverslip. These DNA fibers were then scanned with the atomic force microscope (AFM). While the smallest of the fibers appear in AFM images as ribbon-like structures 250–350 A wide and 10–25 A high, experiments indicate that these images are the result of a convolution of the imaging-tip's shape with the object's actual shape. In such convolutions the height of the object is affected only by the compressibility of the object, while the width is affected in addition by the sharpness of the tip. Images of polyamidoamine particles also appear to show this artifact. We have also deduced the tip's radius of curvature from images of sharp steps and attempt to demonstrate the artifacts associated with a relatively large imaging tip.

Packaging inside Bacteriophages and Compaction inside Bacteria.The presence of polyvalent cations such as spermine and spermidine in DNA solutions leads to the formation of DNA condensates. This phenomenon has been experimentally observed for DNA confined inside bacteriophages and upon its release into bacterial cells. It has been shown that the topology of DNA in condensates depends not only on the concentration of polycations but also on the presence of small proteins that induce DNA binding such as HU and IHF (Sarkar, 2007, Nuc. Acids Res. 35, 951). In the absence of these proteins the morphology of DNA condensates resembles toroidal structures, whereas the presence of these proteins leads to the formation of rod-like conformations. In this study we present simulations of DNA condensation using a coarse-grained model of DNA under attractive conditions. The first group of simulations describes the condensation of DNA upon its packaging inside bacteriophages lambda and P4. Both systems reveal formation of toroidal condensates inside the capsids. We also show that the forces required to pack the genomes in the presence of polyamines are significantly lower than those observed under repulsive conditions (in the absence of polycations). In the second group of simulations we characterize the effect of binding proteins (modeled by randomly introducing flexible sites along DNA) on the morphology of free (unconfined) DNA condensates. The results show that in the absence of binding proteins the fraction of rod-like structures is 48%. With the flexible sites introduced it becomes 74%. The simulations semi-quantitatively reproduce the experimental data, which supports the proposed model of the role of binding proteins. The formation of toroidal and rod-like condensates in the presence of polyvalent cations and binding proteins also strongly backs the push-pull mechanism of genome injection from bacteriophages inside bacterial cells.

Double-stranded DNA molecules which contain runs of four to eight consecutive adenine or thymine residues without a 5′TA-3′ step (i.e., A-tracts) exhibit a significant curvature of the helical axis. In spite of numerous investigations, the origin of A-tract bending remains unresolved.1 A hallmark of curved DNA is an electrophoretic mobility in polyacrylamide gels that is anomalously large with respect to straight DNA (i.e., DNA without static curvature).2 The magnitude of this anomaly for A-tract DNA, and presumably its curvature, depends upon the concentration and species of cation(s) present in the running buffer of the gel.3 Surprisingly, we find no reports of experimental investigations which address the possibility of sitespecific interactions between cations and A-tract DNAs. We have initiated such a study by monitoring line broadening in 1H NMR spectra of oligonucleotides containing A-tracts in the presence of the paramagnetic cation manganese(II). Here, we report what is, to our knowledge, the first experimental evidence of cations localized in the minor groove of DNA in the solution state. Oneand two-dimensional 1H NMR spectra of the selfcomplementary dodecamers d(GCA4T4GC) [A4T4] and d(CGT4A4CG) [T4A4] have been collected as a function of MnCl2 concentration. It has previously been shown that DNAs containing the sequence 5′-A4T4-3′ exhibit bending typical of A-tract DNA, while DNAs containing the sequence 5′-T4A4-3′ are either straight or perhaps only slightly curved.4 1D 1H NMR spectra of the aromatic resonances of representative MnCl2 titrations of the A-tract oligonucleotides are shown in Figure 1. While all aromatic resonances are affected to some extent by the presence of Mn2+, which is expected considering the polyanionic nature of DNA, specific 1H resonances in both sequences are preferentially broadened with respect to others. This indicates that both duplex oligonucleotides contain sites where Mn2+ association is relatively high and/or relatively close to the bases.5 In A4T4, the minor groove A3H2 and A4H2 resonances are the most broadened of the nonexchangeable aromatic resonances upon the addition of MnCl2, indicating a favored site for Mn2+ association in the minor groove. Consistent with this observation is the selective line broadening of the minor groove H4′ resonances. Because of spectral overlap in the 1D 1H spectra, broadening of the H4′ resonances can be appreciated more easily by a comparison of the H1′-H4′ cross peaks from 2D 1H NOESY spectra in the absence and presence of MnCl2. Reduction in the intensities of H1′-H4′ NOESY cross peaks accurately reflects the line broadening of the H4′ resonances because the H1′ resonances are far less affected by the presence

Studies of the organization of double-stranded DNA within bacteriophage heads during the past four decades have produced a wealth of data. However, despite the presentation of numerous models, the true organization of DNA within phage heads remains unresolved. The observations of toroidal DNA structures in electron micrographs of phage lysates have long been cited as support for the organization of DNA in a spool-like fashion. This particular model, like all other models, has not been found to be consistent will all available data. Recently we proposed that DNA within toroidal condensates produced in vitro is organized in a manner significantly different from that suggested by the spool model. This new toroid model has allowed the development of an alternative model for DNA organization within bacteriophage heads that is consistent with a wide range of biophysical data. Here we propose that bacteriophage DNA is packaged in a toroid that is folded into a highly compact structure.

Several neurodegenerative diseases have been found to be strongly associated with proteins containing a polyglutamine stretch which is greatly expanded from approximately 20 glutamines in normal individuals to more than 40 in affected individuals. A conformational change in the expanded polyglutamine stretch has been suggested to form the molecular basis for disease onset. Model peptides containing polyglutamine tend to aggregate and become insoluble. We have synthesized readily water-soluble monomeric peptides by flanking polyglutamine stretches with sequences rich in alanine and lysine. Circular dichroism measurements show that polyglutamine stretches of length 9 or 17 adopt a random coil configuration in aqueous solution. We think that in the disease-associated peptides for normal individuals the stretches of approximately 20 glutamines are in a random coil conformation, whereas in affected individuals the polyglutamine stretch may be in some other conformation. Our method to design soluble monomeric peptides containing extended polyglutamine stretches may be generally useful in studying other highly aggregating peptides.