Structural polymorphism of telomere DNA: interquadruplex and duplex-quadruplex conversions probed by Raman spectroscopy

Features in short guanine-rich sequences that stimulate DNA polymerization in vitro

We have discovered that short guanine-rich oligonucleotides are able to self-associate into higher order structures that stimulate DNA synthesis in vitro without the addition of a conventional template [Ying, J., Bradley, R. K., Jones, L. B., Reddy, M. S., Colbert, D. T., Smalley, R. E., and Hardin, S. H. (1999) Biochemistry 38, 16461-16468]. Our initial analysis indicated the importance of the presence of three contiguous guanines (G) in an oligonucleotide that stimulates DNA polymerization. To gain insight into and to refine sequence requirements for the unexpected DNA synthesis, we analyzed a 231-member guanine-rich octamer library in a fluorescent nucleotide polymerization assay. We observe that, in addition to three contiguous Gs, the presence of a secondary G cluster within the octamer is essential. Furthermore, the location of the primary G cluster in the center of the molecule is most stimulatory. The majority of the octamers that form extended DNA products have a single non-G base separating the primary and secondary G clusters, the identity of which is predominantly thymine (T). Further, a T 5' or 3' of the primary G cluster positively influences the stimulatory function of the oligonucleotide. Overall, the occurrence of bases in the octamer is in the descending order of G > T > A > C. Our studies demonstrate that structures stabilized by noncanonical base pairings are recognized by a DNA polymerase in vitro, and these findings may have relevance within the cell. In particular, the features of these G-rich stimulatory sequences show striking similarities to telomeric sequences that form diverse G-quartet structures in vitro.

Human telomeric DNA: G-quadruplex, i-motif and Watson-Crick double helix

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson-Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C*C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding.

Secondary structure polymorphism in Oxytricha nova telomeric DNA

Tandem repeats of the telomeric DNA sequence d(T4G4) of Oxytricha nova are capable of forming unusually stable secondary structures incorporating Hoogsteen hydrogen bonding interactions. The biological significance of such DNA structures is supported by evidence of specific recognition of telomere end-binding proteins in the crystal state. To further characterize structural polymorphism of Oxytricha telomeric DNAs, we have obtained and interpreted Raman, ultraviolet resonance Raman (UVRR) and circular dichroism (CD) spectra of the tandem repeats d(G4T4G4) (Oxy1.5), d(T4G4)2 (Oxy2) and dT6(T4G4)2 (T6Oxy2) and related non-telomeric isomers in aqueous salt solutions. Raman markers of Oxy1.5 identify both C2'-endo/anti and C2'-endo/syn conformations of the deoxyguanosine residues and Hoogsteen hydrogen bonded guanine quartets, consistent with the quadruplex fold determined previously by solution NMR spectroscopy. Raman, UVRR and CD signatures and Raman dynamic measurements, to monitor imino NH-->ND exchanges, show that the Oxy1.5 antiparallel quadruplex fold is distinct from the hairpin structures of Oxy2 and T6Oxy2, single-stranded structures of d(TG)8 and dT6(TG)8 and previously reported quadruplex structures of d(T4G4)4 (Oxy4) and dG12. Spectral markers of the telomeric and telomere-related DNA structures are tabulated and novel Raman and UVRR indicators of thymidine and deoxyguanosine conformations are identified. The results will be useful for probing structures of Oxytricha telomeric repeats in complexes with telomere end-binding proteins.

Characterization and thermodynamic properties of quadruplex/duplex competition

Structural characteristics and thermodynamic properties of dG(3)(T(2)AG(3))(3), d(C(3)TA(2))(3)C(3) and dG(3)(T(2)AG(3))(3)/d(C(3)TA(2))(3)C(3) were intensively investigated. It was indicated that metal ions greatly affected the conformation and stability of the G-quadruplex. A competition of a structure transition among the G-quadruplex, I-motif, and the duplex was confirmed to be dependent on both cation species and pH values. The structural competitive mechanism is discussed for the first time. This study shows an intriguing potential in modulating DNA structures in vivo, which is of great importance in drug design and cancer chemotherapy.

Quadruplex structures in nucleic acids

DNA oligonucleotides that have repetitive tracts of guanine bases can form G-quadruplex structures that display an amazing polymorphism. Structures of several new G-quadruplexes have been solved recently that greatly expand the known structural motifs observed in nucleic acid quadruplexes. Base triads, base hexads, and quartets that contain cytosine have recently been identified stacked over the familiar G-quartets. The current status of the diverse array of structural features in quadruplexes is described and used to provide insight into the polymorphism and folding pathways. This review also summarizes recent progress in the techniques used to probe the structures of G-quadruplexes and discusses the role of ion binding in quadruplex formation. Several of the quadruplex structures featured in this review can be accessed in the online version of this review as CHIME representations.

Biological aspects of DNA/RNA quadruplexes

Among the many unusual conformations of DNA and RNA, quadruplex structures, based on the guanine quartet, possess several unique properties. These properties, along with the general features of guanine quadruplexes, are described in the context of possible roles for these structures in biological systems. A variety of experimental observations supporting the notion that quadruplexes are important in vivo is presented, including proteins known to specifically bind to quadruplex structures, guanine-rich DNA, and RNA sequences endowed with the potential for forming quartet-based structures in telomeres and regulatory regions, such as gene promoters, quadruplexes as DNA aptamer folding motifs arising from in vitro selection experiments, and potential chemotherapeutic, quadruplex-forming oligonucleotides. Taken together, all of these observations argue cogently not only for the presence of quadruplexes in biological systems but also for their significance in terms of their roles in various biological processes.

Raman spectroscopy of protein and nucleic acid assemblies

The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.

Fluorescence resonance energy transfer as a probe for G-quartet formation by a telomeric repeat

The secondary structure of guanine-rich oligodeoxynucleotides has been investigated with fluorescent probes. Intramolecular folding of a telomeric oligonucleotide into a quadruplex led to fluorescence resonance energy transfer (FRET) between a donor (fluorescein) and an acceptor (tetramethylrhodamine) covalently attached to the 5' and 3' ends of the DNA, respectively. Depending on oligonucleotide length, quenching efficiency varied between 0.45 and 0.72 at 20 degrees C. The conjugation of the dyes to the oligonucleotide had a limited, but significant, influence on the thermodynamics of G-quartet formation. Intramolecular folding was demonstrated from the concentration independence of fluorescence resonance energy transfer over a wide concentration range. Folding of the oligonucleotide was confirmed by UV absorption, UV melting, and circular dichroism experiments. The folding of the G-quartet could be followed at concentrations as low as 100 pM. Fluorescence resonance energy transfer can thus be used to reveal the formation of multistranded DNA structures.

The third zinc finger of TFIIIA stabilizes a hairpin structure of the non-coding strand in the internal control region of 5S RNA gene

The structures of non-coding and coding strands in box C of the internal control region (ICR) of Xenopus laevis somatic 5S RNA gene have been examined by circular dichroism (CD) and Raman spectroscopy in the absence and presence of the third zinc finger of transcription factor IIIA (TFIIIA), which binds to the ICR. The non-coding strand exhibits CD signals assignable to a hairpin and an unfolded structure. The presence of the hairpin structure is supported by Raman spectra, gel electrophoresis, and nucleotide deletion experiments. Binding of the zinc finger to the non-coding strand increases the CD signal of hairpin structure, indicating stabilization of the hairpin structure by the zinc finger. In contrast, the corresponding coding strand remains unfolded even in the presence of the zinc finger. The TFIIIA-ICR complex is not only required for initiation of transcription but also lasts during many rounds of transcription of the 5S RNA gene including the ICR (Bogenhagen et al., Cell 28 (1982) 413). TFIIIA may play a role in promoting the transcription by maintaining the unwound non-coding strand in the hairpin structure and leaving the coding strand available for transcription by RNA polymerase.

G-quadruplex DNA: a potential target for anti-cancer drug design

In addition to the familiar duplex DNA, certain DNA sequences can fold into secondary structures that are four-stranded; because they are made up of guanine (G) bases, such structures are called G-quadruplexes. Considerable circumstantial evidence suggests that these structures can exist in vivo in specific regions of the genome including the telomeric ends of chromosomes and oncogene regulatory regions. Recent studies have demonstrated that small molecules can facilitate the formation of, and stabilize, G-quadruplexes. The possible role of G-quadruplex-interactive compounds as pharmacologically important molecules is explored in this article.

Intramolecular quadruplex formation of the G-rich strand of the mouse hypervariable minisatellite Pc-1

The minisatellite Pc-1, isolated from the mouse genome consisting of a tandem repeat of d(GGCAG), is hypervariable with a mutation rate of 0.15/generation. Here we describe a structural characterization of the G-rich strand of Pc-1 by biochemical and physicochemical methods. It was found to be comparatively resistant to both single-stranded DNA-binding protein binding and digestion by single-stranded DNA-specific nuclease and to cause arrest of DNA synthesis. The guanine imino proton NMR signals observed on the Pc-1 G-rich strand and their slow (1)H/(2)H exchange profiles pointed to a quadruplex structure with guanine quartets. The melting temperature of the quadruplex determined by CD was not dependent on DNA concentration. These results indicate that the G-rich strand of Pc-1 forms an intramolecular folded-back quadruplex structure under physiological conditions. Possible mechanisms of the Pc-1 mutations implicated with the formation of the quadruplex structure are discussed.

Probing the structure of multi-stranded guanine-rich DNA complexes by Raman spectroscopy and enzymatic degradation

The multi-stranded DNA complexes formed by the oligonucleotides d(T15G4T2G4), Tel, and d(T15G15), TG, were examined by nuclease digestion and Raman spectroscopy. Both Tel and TG can aggregate to form structures consisting of multiple, parallel-oriented DNA strands with two independent structural domains. Overall, the structures of the TG and Tel aggregates appear similar. According to the Raman data, the majority of bases are in C2'-endo/anti conformation. The interaction of guanines at the 3'-ends in both complexes stabilizes the complexes and protects them from degradation by exonuclease III. The 5'-extensions remain single-stranded and the thymines are accessible to single-strand-specific nuclease digestion. The extent of enzymatic cleavage at the junction at the 5' end of the 15 thymines implies a conformational change between this part of the molecule and the guanine-rich region. The differential enzymatic sensitivity of the complexes suggests there are variations in backbone conformations between TG and Tel aggregates. TG aggregates were more resistant to digestion by DNase I, Mung Bean nuclease, and S1 nuclease than Tel complexes. It is proposed that the lower DNase I sensitivity may be partly due to the more stable backbone exhibited by TG than Tel complexes. Structural uniformity along the guanine core of TG is suggested, as there is no indication of structural discontinuities or protected sites in the guanine-rich regions of TG aggregates. The lower extent of digestion by Mung Bean nuclease at the 3' end implies that these bases are inaccessible to the enzyme. This suggests that there is minimal fraying at the ends, which is consistent with the extreme thermal stability of the TG aggregates.

Fluorescent dyes specific for quadruplex DNA

Fluorescent dyes which are specific for duplex DNA have found a wide range of applications from staining gels to visualization of chromosomes. Porphyrin dyes have been found which are highly fluorescent in the presence of quadruplex but not duplex DNA. These dyes may offer a route to the specific detection of quadruplex DNA under biologically important conditions. There are three types of DNA quadruplex structures, and these may play important roles in telomere, centromere, triplet repeat, integration sites and other DNAs, and this first set of porphyrin dyes show some selectivity between the quadruplex types.

A hairpin conformation for the 3' overhang of Oxytricha nova telomeric DNA

The solution secondary structure of the Oxytricha nova telomeric 3' overhang, d(T4G4)2, has been investigated by Raman spectroscopy, hydrogen-deuterium exchange kinetics and gel electrophoresis. The electrophoretic mobility of d(T4G4)2 in non-denaturing gels indicates a highly compact conformation, consistent with a hairpin secondary structure. Raman markers show that the d(T4G4)2 hairpin contains equal numbers of C2'-endo/syn and C2'-endo/anti deoxyguanosine conformers, as well as G.G base-pairs of the Hoogsteen type. The hydrogen-deuterium exchange kinetics of d(T4G4)2, monitored by time-resolved Raman spectroscopy, reveal two kinetically distinct classes of guanine imino (N1H) protons. The more slowly exchanging fraction (kN1H(1)=4.6x10(-3) min-1), which represents 50% of N1H groups, is attributed to Hoogsteen-paired residues. The more rapidly exchanging fraction (kN1H(2)>/=0.3 min-1) is attributable to solvent-exposed residues. Raman dynamic probe of the kinetics of guanine C8H-->C8(2)H exchange in d(T4G4)2 reveals modest retardation vis-à-vis dGMP, which rules out quadruplex formation by the telomeric repeat and confirms an ordered secondary structure consistent with a Hoogsteen-paired hairpin. Similar Raman, hydrogen-isotope exchange and electrophoretic mobility experiments on the related telomeric model, dT6(T4G4)2, also reveal a hairpin stabilized by Hoogsteen G.G pairs. Presence of the 5' thymidine tail preceding the Oxytricha telomeric repeat has no apparent effect on the hairpin secondary structure. We propose a molecular model for the hairpin conformation of the Oxytricha nova telomeric repeat and consider its possible roles in mechanisms of telomeric DNA interaction in vitro and telomere function in vivo.

Beyond guanine quartets: cation-induced formation of homogenous and chimeric DNA tetraplexes incorporating iso-guanine and guanine

BACKGROUND

iso-Guanine (iso-G) is the purine component of an isomeric Watson-Crick base pair that may have existed prebiotically. By comparing the abiotic molecular recognition properties of iso-G and its complement, iso-cytosine (iso-C), with those of genomic nucleotide bases, it may be possible to explain the exclusion of the iso-G-iso-C base pair from modern genomes. Whether a nucleobase forms quartets may have a key role in determining its functionality. Biotically, nucleic acid tetraplexes have been implicated in cellular functions; prebiotically, tetraplexes would probably interfere with replication. Recently, in vitro selection has yielded receptors and catalysts that incorporate G quartets. The versatility of these structures could be enhanced by expanding the range of bases that can form the quartet motif.

RESULTS

Native polyacrylamide gel electrophoresis of oligonucleotides bearing runs of iso-G provides strong support for tetraplex formation via cation-promoted DNA strand association. In particular, when strands of different lengths bearing the same iso-G tetrad recognition element were combined, five bands were observed after electrophoresis, corresponding to all possible heterotetraplexes with parallel strand alignment. An analogous experiment with a mixture of strands bearing iso-G or G tetrad recognition domains supports the existence of mixed iso-G/G tetraplexes with antiparallel strand alignment at chimeric junctions. iso-G tetraplex and quartet structure has also been probed by a photo-crosslinking experiment, ultra-violet spectroscopy and theoretical calculations.

CONCLUSIONS

As iso-G and G both have a marked tendency to form tetraplexes, their tandem inclusion in genetic material may be problematic, leading to double-stranded DNA half composed of bases that have a tendency to auto-associate. The resulting density of 'selfish' bases could undermine Watson-Crick pair formation, especially in a prebiotic context devoid of enzymes. Nevertheless, the ability of iso-G to form mixed quartets with G may provide a basis for altering the properties of tetraplexes in the domain of artificial receptors or catalysts from in vitro selections.

The DNA structures at the ends of eukaryotic chromosomes

The sequence organisation of the telomeric regions is extremely similar for all eukaryotes examined to date. Subtelomeric areas may contain large sequence arrays of middle repetitive, complex elements that sometimes have similarities to retrotransposons. In between and within these complex sequences are short, satellite-like repeats. These areas contain very few genes and are thought to be organised into a heterochromatin-like domain. The terminal regions almost invariably consist of short, direct repeats. These repeats usually contain clusters of 2-4 G residues and the strand that contains these clusters (the G strand) always forms the extreme 3'-end of the chromosome. Thus, most telomeric repeats are clearly related to each other which in turn suggests a common evolutionary origin. A number of different structures can be formed by single-stranded telomeric G strand repeats and, as has been suggested recently, by the G strand. Since the main mechanism for the maintenance of telomeric repeats predicts the occurrence of single-stranded extensions of the G strand, the propensity of G-rich DNA to fold into alternative DNA structures may have implications for telomere biology.

A UV resonance Raman study of hairpin dimer helices of d(A-G)10 at neutral pH containing intercalated dA residues and alternating dG tetrads

The structure of the oligonucleotide d(A-G)10 in 0.6 M Na+, pH 7.0 has been investigated with UV resonance Raman (UVRR) spectroscopy. Variable wavelength excitation was used to distinguish the spectral contributions of dG and dA residues. Both classes of residues show UVRR hyperchromism with increasing temperature, reflecting unstacking of the bases. The dG residues melt relatively cooperatively with a Tm of approximately 42 degrees C. Unstacking is non-cooperative for the dA residues, increasing linearly between 4 and 80 degrees C. G-tetrads at low temperature are indicated by UVRR frequency shifts of modes associated with C6=O and C2-NH2 of the dG residues, and of vibrations involving N7, all sites of H-bonding. However, there are no indications of interbase H-bonds for the dA residues, showing they do not form H-bonded tetrads. Most of the bases are oriented anti about the glycosyl bond, but at 4 degrees C a fraction of the residues are syn. These results, together with the findings by Shiber et al. [Shiber,M.C., Braswell,E.H., Klump,H. and Fresco,J.R. (1996) Nucleic Acids Res. 24, 5004-5012] that d(A-G)10 under comparable conditions has the molecular weight of a dimer, support a model in which two hairpins interact to form a helical structure with G-tetrads and intercalated dA residues.

A vibrational spectroscopic study of the metastable form of associated polyinosinic acid

We have studied by Raman and ir spectroscopy the metastable complex formed by the self-association of polyinosinic acid in aqueous solution. The complex is easily prepared by quickly cooling to ca. 0 degrees C a warm solution of the polyribonucleotide to which a small amount of rubidium salt has been added. Upon heating, this metastable form melts cooperatively near 13 degrees C, well below the dissociation temperature of a stable four-stranded complex, which occurs at 47 degrees C in the same conditions. The presence of several components in the stretching-mode region of the carbonyl groups in the vibrational spectra of the metastable complex suggests that it also has a parallel four-stranded structure. The difference in structure between the two forms is believed to be caused by the presence of fewer metal ions in the central channel of the metastable complex, in agreement with conclusions reached in previous investigations. The Raman spectra further show that the ribose units in the metastable form have a C3'-endo conformation, in contrast with the stable form, for which we have previously suggested a mixed C2'-endo/C3'-endo conformation.

Hypericin site specific interactions within polynucleotides used as DNA model compounds

Interactions of the antiretroviral hypericin molecule with polynucleotides, i.e. poly(dG-dC), poly(dA-dT), poly(rG) and poly(rC), have been studied in aqueous solutions by resonance Raman spectroscopy, using an UV excitation wavelength which induces a specific resonance enhancement of spectral band intensities corresponding to proper nucleic base modes of vibration. It is shown that: i) hypericin selectively interacts with the N7 sites of purines, ii) the strength of interaction depends on the polymer structure, and: iii) interaction with guanine is stronger than with adenine molecules.

Acid-facilitated supramolecular assembly of G-quadruplexes in d(CGG)4

Molar [K+] induces aggregate formation in d(CGG)4, as evidenced by absorbance, circular dichroic (CD), and gel measurements. The kinetics of this transformation are extremely slow at pH 8 but are found to be greatly facilitated in acidic conditions. Kinetic profiles via absorbance or CD monitoring at single wavelength resemble those of autocatalytic reacting systems with characteristic induction periods. More than 0.8 M KCl is needed to observe the onset of aggregation at 20 degrees C and pH 5.4 within the time span of 1 day. Time-dependent CD spectral characteristics indicate the formation of parallel G-tetraplexes prior to the onset of aggregation. Despite the evidence of K(+)-induced parallel G-quadruplex and higher molecular weight complex formation, both d(TGG)4 and d(CGG)4T fail to exhibit the observed phenomenon, thus strongly implicating the crucial roles played by the terminal G and base protonation of cytosines. A plausible mechanism for the formation of a novel self-assembled structure is speculated. Aided by the C+.C base pair formation, parallel quadruplexes are initially formed and subsequently converted to quadruplexes with contiguous G-tetrads and looped-out cytosines due to high [K+]. These quadruplexes then vertically stack as well as horizontally expand via interquadruplex C+.C base pairing to result in dendrimer-type self-assembled super structures.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG3) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Structure and dynamics of interstrand guanine association in quadruplex telomeric DNA

Exchanges of the amino and imino protons in guanine quartets of telomeric DNA have been time-resolved by laser Raman spectroscopy. The Raman dynamic probe has been applied to parallel and antiparallel quadruplexes formed by the telomeric repeat of Oxytricha nova, d(T4G4)4, and to the highly thermostable parallel quadruplex formed by d(G12). Time-dependent Raman spectra of the d(G12) quadruplex reveal two characteristic exchange reactions for guanine N2 amino groups. At 10 degrees C, the pseudo-first-order exchange rates are kN2H(10 degrees C) = 5.7 x 10(-3) and k'N2H'(10 degrees C) = 1.2 x 10(-2) min-1, assignable to Hoogsteen-hydrogen-bonded and non-hydrogen-bonded N2 protons, respectively. These measurements provide the first quantitative determination of two kinetically distinct N2 amino proton exchange reactions in the guanine quartet and demonstrate that amino group rotation about the C2-N2 bond is highly restricted in the quadruplex. No exchange of guanine N1 imino sites occurs in d(G12) at 10 degrees C, and N1 exchange remains slow even at 95 degrees C [kN1H(95 degrees C) = 2.7 x 10(-2) min-1], indicating severe suppression of imino exchange in guanine quartets. For both parallel and antiparallel quadruplexes of d(T4G4)4, proton exchange rates decrease in the order thymine N3 imino > guanine N2 amino > guanine N1 imino. The rapid exchange of thymine N3 imino sites indicates that thymine quartets are not stabilized in Oxytricha quadruplexes. The protium-->deuterium exchange experiments also establish new guanine Raman band assignments. Importantly, the 1603 cm-1 band is due to in-plane bending of N1-H, while the 1644 cm-1 band involves scissoring of the N2 amino group. Accordingly, the 1603 and 1644 cm-1 bands are potentially valuable markers of hydrogen-bonding interactions specific to guanine imino and amino sites, respectively. The present findings also show that guanine hydrogen bonding and exchange dynamics are not interrelated in a simple manner. Despite extraordinary retardation of N1 imino proton exchange, Raman markers suggest that Hoogsteen-type guanine-guanine hydrogen bonding (N1-H...O=C6) is comparable in strength to hydrogen bonding of N1-H with water and, surprisingly, much weaker than hydrogen bonding between N1-H and the cytosine N3 acceptor of Watson-Crick B DNA.

Telomere structure and function

Telomeres, the termini of linear eukaryotic chromosomes, contain specific DNA sequences that are widely conserved. These sequences not only recruit telomere-specific proteins, but also give telomeric DNA the ability to fold into four-stranded DNA structures. Recent structural studies have shown that the repertoire of quadruplexes formed by the G-rich strand is larger than had been envisaged. Even more surprising is a novel four-stranded structure formed by the C-rich strand, called the i-tetraplex. Genetic and biochemical analyses have been used to identify proteins involved in telomeric DNA packaging and organization. The possibility that four-stranded structures may play a role in telomere function has been strengthened by the discovery that telomeric proteins can bind to and promote the formation of G-quadruplexes.

Duplex to quadruplex equilibrium of the self-complementary oligonucleotide d(GGGGCCCC)

The structure of the deoxyoligonucleotide d(GGGGCCCC) has been monitored by 1H and 31P NMR, and by gel electrophoresis. In low-salt solution, this oligonucleotide forms a stable duplex structure. Upon titration with KCl, an equilibrium is established between duplex and quadruplex forms. The quadruplex form is the dominant one at physiological KCl concentrations, despite the fact that fewer hydrogen bonds are formed per strand in the quadruplex than in the duplex.

The thermodynamics of DNA structures that contain lesions or guanine tetrads

It is becoming increasingly apparent that energetic as well as structural information is required to develop a complete appreciation of the critical interrelationships between structure, energetics, and biological function. Motivated by this recognition, we have reviewed in this article the current state of the thermodynamic databases associated with lesion-containing DNA duplexes and DNA quadruplexes, while highlighting important considerations concerning the methods used to obtain the requisite data.

A phase diagram for sodium and potassium ion control of polymorphism in telomeric DNA

Switching between antiparallel and parallel quadruplex structures of telomeric DNA under the control of intracellular Na+ and K+ has been implicated in the pairing of chromosomes during meiosis. Using Raman spectroscopy, we have determined the dependence of the interquadruplex equilibrium of the telomeric repeat of Oxytricha nova, upon solution concentrations of Na+ and K+. Both alkali cations facilitate the formation of an antiparallel foldback quadruplex at low concentration, and a parallel extended quadruplex at higher concentration. However, K+ is more effective than Na+ in inducing the parallel association. We propose a phase diagram relating d(T4G4)4 polymorphism to intracellular [Na+]/[K+] ratios. The phase diagram indicates that the interquadruplex equilibrium is highly sensitive to changes in the mole fraction of either cation when the total concentration falls within the interval 65 to 225 mM, a range which encompasses total of the Na+ and K+ concentrations occurring in a typical mammalian cell. These results support a role for the guanine-rich overhang of eukaryotic DNA in promoting chromosome association during meiotic synapsis.