Tiny telomere DNA

G-quadruplex DNA: A Longer Story

G-quadruplexes (G4s) are distinctive four-stranded DNA or RNA structures found within cells that are thought to play functional roles in gene regulation and transcription, translation, recombination, and DNA damage/repair. While G4 structures can be uni-, bi-, or tetramolecular with respect to strands, folded unimolecular conformations are most significant in vivo. Unimolecular G4 can potentially form in sequences with runs of guanines interspersed with what will become loops in the folded structure: 5'G_xL_yG_xL_yG_xL_yG_x, where x is typically 2-4 and y is highly variable. Such sequences are highly conserved and specifically located in genomes. In the folded structure, guanines from each run combine to form planar tetrads with four hydrogen-bonded guanine bases; these tetrads stack on one another to produce four strand segments aligned in specific parallel or antiparallel orientations, connected by the loop sequences. Three types of loops (lateral, diagonal, or "propeller") have been identified. The stacked tetrads form a central cavity that features strong coordination sites for monovalent cations that stabilize the G4 structure, with potassium or sodium preferred. A single monomeric G4 typically forms from a sequence containing roughly 20-30 nucleotides. Such short sequences have been the primary focus of X-ray crystallographic or NMR studies that have produced high-resolution structures of a variety of monomeric G4 conformations. These structures are often used as the basis for drug design efforts to modulate G4 function.We believe that the focus on monomeric G4 structures formed by such short sequences is perhaps myopic. Such short sequences for structural studies are often arbitrarily selected and removed from their native genomic sequence context, and then are often changed from their native sequences by base substitutions or deletions intended to optimize the formation of a homogeneous G4 conformation. We believe instead that G-quadruplexes prefer company and that in a longer natural sequence context multiple adjacent G4 units can form to combine into more complex multimeric G4 structures with richer topographies than simple monomeric forms. Bioinformatic searches of the human genome show that longer sequences with the potential for forming multiple G4 units are common. Telomeric DNA, for example, has a single-stranded overhang of hundreds of nucleotides with the requisite repetitive sequence with the potential for formation of multiple G4s. Numerous extended promoter sequences have similar potentials for multimeric G4 formation. X-ray crystallography and NMR methods are challenged by these longer sequences (>30 nt), so other tools are needed to explore the possible multimeric G4 landscape. We have implemented an integrated structural biology approach to address this challenge. This approach integrates experimental biophysical results with atomic-level molecular modeling and molecular dynamics simulations that provide quantitatively testable model structures. In every long sequence we have studied so far, we found that multimeric G4 structures readily form, with a surprising diversity of structures dependent on the exact native sequence used. In some cases, stable hairpin duplexes form along with G4 units to provide an even richer landscape. This Account provides an overview of our approach and recent progress and provides a new perspective on the G-quadruplex folding landscape.

Thermally Induced Transitions of d(G4T4G3) Quadruplexes Can Be Described as Kinetically Driven Processes

DNA sequences that are rich in guanines and can form four-stranded structures are called G-quadruplexes. Due to the growing evidence that they may play an important role in several key biological processes, the G-quadruplexes have captured the interest of several researchers. G-quadruplexes may form in the presence of different metal cations as polymorphic structures formed in kinetically governed processes. Here we investigate a complex polymorphism of d(G4T4G3) quadruplexes at different K+ concentrations. We show that population size of different d(G4T4G3) quadruplex conformations can be manipulated by cooling rate and/or K+ concentration. We use a kinetic model to describe data obtained from DSC, CD and UV spectroscopy and PAGE experiments. Our model is able to describe the observed thermally induced conformational transitions of d(G4T4G3) quadruplexes at different K+ concentrations.

Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy

In addition to the canonical double helix form, DNA is known to be extrapolated into several other secondary structural patterns involving themselves in inter- and intramolecular type hydrogen bonding. The secondary structures of nucleic acids go through several stages of multiple, complex, and interconvertible heterogeneous conformations. The journey of DNA through these conformers has significant importance and has been monitored thoroughly to establish qualitative and quantitative information about the transition between the unfolded, folded, misfolded, and partially folded states. During this structural interconversion, there always exist specific populations of intermediates, which are short-lived or sometimes even do not accumulate within a heterogeneous population and are challenging to characterize using conventional ensemble techniques. The single-molecule FRET(sm-FRET) microspectroscopic method has the advantages to overcome these limitations and monitors biological phenomena transpiring at a measurable high rate and balanced stochastically over time. Thus, tracing the time trajectory of a particular molecule enables direct measurement of the rate constant of each transition step, including the intermediates that are hidden in the ensemble level due to their low concentrations. This review is focused on the advantages of the employment of single-molecule Forster's resonance energy transfer (sm-FRET), which is worthwhile to access the dynamic architecture and structural transition of various secondary structures that DNA adopts, without letting the donor of one molecule to cross-talk with the acceptor of any other. We have emphasized the studies performed to explore the states of folding and unfolding of several nucleic acid secondary structures, for example, the DNA hairpin, Holliday junction, G-quadruplex, and i-motif.

Novel Insight into Proximal DNA Domain Interactions from Temperature-Controlled Electrospray Ionization Mass Spectrometry

Quadruplexes are non-canonical nucleic acid structures essential for many cellular processes. Hybrid quadruplex-duplex oligonucleotide assemblies comprised of multiple domains are challenging to study with conventional biophysical methods due to their structural complexity. Here, we introduce a novel method based on native mass spectrometry (MS) coupled with a custom-built temperature-controlled nanoelectrospray ionization (TCnESI) source designed to investigate interactions between proximal DNA domains. Thermal denaturation experiments were aimed to study unfolding of multi-stranded oligonucleotide constructs derived from biologically relevant structures and to identify unfolding intermediates. Using the TCnESI MS, we observed changes in Tm and thermodynamic characteristics of proximal DNA domains depending on the number of domains, their position, and order in a single experiment.

Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands

By substitution of natural nucleotides by their abasic analogs (i.e., 1',2'-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson-Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.

Stability of the Na+ Form of the Human Telomeric G-Quadruplex: Role of Adenines in Stabilizing G-Quadruplex Structure

G-quadruplexes are higher order DNA structures that play significant roles in gene transcription and telomeric maintenance. The formation and stability of the G-quadruplex structures are under thermodynamic control and may be of biological significance for regulatory function of cellular processes. Here, we report the structural influence and energetic contributions of the adenine bases in the loop sequences that flank G-repeats in human telomeric DNA sequence. Spectroscopic and calorimetric techniques are used to measure the thermal stability and thermodynamic contributions to the stability of human telomeric G-quadruplexes that have been designed with systematic changes of A to T throughout the telomeric sequence. These studies demonstrate that the thermal stability of the G-quadruplex structure is directly related to the number and position of the adenines that are present in the telomeric sequence. The melting temperature (T_m) was reduced from 59 °C for the wild-type sequence to 47 °C for the sequence where all four adenines were replaced with thymines (0123TTT). Furthermore, the enthalpy required for transitioning from the folded to unfolded G-quadruplex structure was reduced by 15 kcal/mol when the adenines were replaced with thymines (37 kcal/mol for the wild-type telomeric sequence reduced to 22 kcal/mol for the sequence where all four adenines were replaced with thymines (0123TTT)). The circular dichroism melting studies for G-quadruplex sequences having a single A to T change showed significantly sloping pretransition baselines and their differential scanning calorimetry (DSC) thermograms revealed biphasic melting profiles. In contrast, the deoxyoligonucleotides having sequences with two or more A to T changes did not exhibit sloping baselines or biphasic DSC thermograms. We attribute the biphasic unfolding profile and reduction in the enthalpy of unfolding to the energetic contributions of adenine hydrogen bonding within the loops as well as the adenine stacking to the G-tetrads of the G-quadruplex structure.

2'-Fluoroarabinonucleic acid modification traps G-quadruplex and i-motif structures in human telomeric DNA

Human telomeres and promoter regions of genes fulfill a significant role in cellular aging and cancer. These regions comprise of guanine and cytosine-rich repeats, which under certain conditions can fold into G-quadruplex (G4) and i-motif structures, respectively. Herein, we use UV, circular dichroism and NMR spectroscopy to study several human telomeric sequences and demonstrate that G4/i-motif-duplex interconversion kinetics are slowed down dramatically by 2'-β-fluorination and the presence of G4/i-motif-duplex junctions. NMR-monitored kinetic experiments on 1:1 mixtures of native and modified C- and G-rich human telomeric sequences reveal that strand hybridization kinetics are controlled by G4 or i-motif unfolding. Furthermore, we provide NMR evidence for the formation of a hybrid complex containing G4 and i-motif structures proximal to a duplex DNA segment at neutral pH. While the presence of i-motif and G4 folds may be mutually exclusive in promoter genome sequences, our results suggest that they may co-exist transiently as intermediates in telomeric sequences.

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K⁺ and Na⁺, which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations. However, the non-polarizable force fields are very approximate, while QC calculations lack the necessary sampling. Thus, ultimate description of GQ systems would require long-enough simulations using advanced polarizable molecular mechanics (MM). However, to perform such calculations, it is first mandatory to evaluate the method's accuracy using benchmark QC. We report such an evaluation for SIBFA polarizable MM, bearing on the channeling (movement) of an alkali cation (Li⁺, Na⁺, K⁺, or Rb⁺) along the axis of two stacked G quartets interacting with either one or two ions. The QC energy profiles display markedly different features depending upon the cation but can be retrieved in the majority of cases by the SIBFA profiles. An appropriate balance of first-order (electrostatic and short-range repulsion) and second-order (polarization, charge-transfer, and dispersion) contributions within ΔE is mandatory. With two cations in the channel, the relative weights of the second-order contributions increase steadily upon increasing the ion size. In the G8 complexes with two K⁺ or two Rb⁺ cations, the sum of polarization and charge-transfer exceeds the first order terms for all ion positions.

The Truncated Human Telomeric Sequence forms a Hybrid-Type Intramolecular Mixed Parallel/antiparallel G-quadruplex Structure in K(+) Solution

In 80-90% tumor cells, telomerase becomes active and stabilizes the length of telomeres. The formation and stabilization of G-quadruplexes formed from human telomeric sequences have been proved able to inhibit the activity of telomerase, thus human telomeric G-quadruplex structure has become a potential target for the development of cancer therapy. Hence, structure of G-quadruplex formed in K(+) solution has been an attractive hotspot for further studies. However, the exact structure of human telomeric G-quadruplex in K(+) is extremely controversial, this study provides information for the understanding of different G-quadruplexes. Here, we report that 22nt and 24nt human telomeric sequences form unimolecular hybrid-type mixed parallel/antiparallel G-quadruplex in K(+) solution elucidated utilizing Circular Dichroism, Differential Scanning Calorimetry, and gel electrophoresis. Moreover, individual configuration of these two sequences was speculated in this study. The detailed structure information of the G-quadruplex formed under physiologically relevant condition is necessary for structure-based rational drug design.

Targeting human telomeric G-quadruplex DNA with curcumin and its synthesized analogues under molecular crowding conditions

The formation of telomeric G-quadruplexes has been shown to inhibit telomerase activity.

Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding

Mixed duplex/quadruplex oligonucleotides have attracted great interest as therapeutic targets as well as effective biomedical aptamers. In the case of thrombin-binding aptamer (TBA), the addition of a duplex motif to the G-quadruplex module improves the aptamer resistance to biodegradation and the affinity for thrombin. In particular, the mixed oligonucleotide RE31 is significantly more effective than TBA in anticoagulation experiments and shows a slower disappearance rate in human plasma and blood. In the crystal structure of the complex with thrombin, RE31 adopts an elongated structure in which the duplex and quadruplex regions are perfectly stacked on top of each other, firmly connected by a well-structured junction. The lock-and-key shape complementarity between the TT loops of the G-quadruplex and the protein exosite I gives rise to the basic interaction that stabilizes the complex. However, our data suggest that the duplex motif may have an active role in determining the greater anti-thrombin activity in biological fluids with respect to TBA. This work gives new information on mixed oligonucleotides and highlights the importance of structural data on duplex/quadruplex junctions, which appear to be varied, unpredictable, and fundamental in determining the aptamer functional properties.

Dinuclear nickel(II) triple-stranded supramolecular cylinders: syntheses, characterization and G-quadruplexes binding properties

Three dinuclear nickel triple-stranded supramolecular cylinders [Ni2(L1)3][ClO4]4 (1), [Ni2(L2)3][ClO4]4 (2) and [Ni2(L3)3][ClO4]4 (3) with bis(pyridylimine) Schiff base containing triphenyl groups in the spacers as ligands were synthesized and characterized. The human telomeric G-quadruplexes binding properties of cylinders 1-3 were evaluated by means of UV-Vis spectroscopy, circular dichroism (CD) spectroscopy and fluorescence resonance energy transfer (FRET) melting assay. UV-Vis studies revealed that the supramolecular cylinders 1-3 could bind to G-quadruplex DNA with high binding constants (Kb values ranging from 0.11-2.2×10(6) M(-1)). FRET melting studies indicated that the cylinders 1-3 had much stronger stabilizing effect on G-quadruplex DNA (ΔTm up to 24.5°C) than the traditional cylinder Ni2L3(4+) just containing diphenylmethane spacers (ΔTm=10.6 °C). Meanwhile, cylinders 1-3 were found to have a modest degree of selectivity for the quadruplex DNA versus duplex DNA in competition FRET assays. Moreover, CD spectroscopy revealed that complex 1 could induce G-quadruplex formation in the absence of metal ions solution and convert antiparallel G-quadruplex into hybrid structure in Na(+) solution. These results provided a new insight into the development of supramolecular cylinders as potential anticancer drugs targeting G-quadruplex DNA.

Folding and unfolding pathways of the human telomeric G-quadruplex

Sequence analogs of human telomeric DNA such as d[AGGG(TTAGGG)3] (Tel22) fold into monomeric quadruplex structures in the presence of a suitable cation. To investigate the pathway for unimolecular quadruplex formation, we monitored the kinetics of K(+)-induced folding of Tel22 by circular dichroism (CD), intrinsic 2-aminopurine fluorescence, and fluorescence resonance energy transfer (FRET). The results are consistent with a four-step pathway U ↔ I1 ↔ I2 ↔ I3 ↔ F where U and F represent unfolded and folded conformational ensembles and I1, I2, and I3 are intermediates. Previous kinetic studies have shown that I1 is formed in a rapid pre-equilibrium and may consist of an ensemble of "prefolded" hairpin structures brought about by cation-induced electrostatic collapse of the DNA. The current study shows that I1 converts to I2 with a relaxation time τ1=0.1s at 25 °C in 25 mM KCl. The CD spectrum of I2 is characteristic of an antiparallel quadruplex that could form as a result of intramolecular fold-over of the I1 hairpins. I3 is relatively slowly formed (τ2≈3700s) and has CD and FRET properties consistent with those expected of a triplex structure as previously observed in equilibrium melting studies. I3 converts to F with τ3≈750s. Identical pathways with different kinetic constants involving a rapidly formed antiparallel intermediate were observed with oligonucleotides forming mixed parallel/antiparallel hybrid-1 and hybrid-2 topologies {e.g. d[TTGGG(TTAGGG)3A] and d[TAGGG(TTAGGG)3TT]}. Aspects of the kinetics of unfolding were also monitored by the spectroscopic methods listed above and by time-resolved fluorescence lifetime measurements using a complementary strand trap assay. These experiments reveal a slow, rate-limiting step along the unfolding pathway.

Thermodynamic characterization of human telomere quadruplex unfolding

The 3'-terminal extensions of eukaryotic chromosomes are unique examples of functional single-stranded DNA. Human telomeres are constructed of the repeated DNA sequence 5'-d(TTAGGG). Four-repeats of human telomeric DNA have been characterized by high-resolution techniques to be capable of forming at least five distinct monomeric conformations. The predominant solution topology is influenced by solution conditions and the presence of 3'- or 5'-flanking residues. This study describes the unfolding mechanisms for human telomeric quadruplexes formed by eight sequence variants that form three unique antiparallel topologies in K(+) solution. Thermal unfolding monitored by circular dichroism is analyzed by singular value decomposition to enumerate the number of significant spectral species required to model the unfolding process. Thermal denaturation of all quadruplexes studied is found to be best modeled by a four-state sequential mechanism with two populated intermediates. The thermal unfolding was also investigated in 50% (v/v) acetonitrile in which a parallel topology is favored. Under these dehydrating conditions, quadruplex thermal denaturation is best modeled by a three-state sequential unfolding mechanism with one populated intermediate. Dehydrated parallel quadruplexes demonstrate increased thermal stability. The spectral properties of the unfolding intermediate suggest that it is most likely a triple-helical structure.

Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions.

Combination of i-motif and G-quadruplex structures within the same strand: formation and application

Peaceful coexistence: A double quadruplex composed of an i-motif and a G-quadruplex was constructed within one oligonucleotide strand (see picture). The defined double-quadruplex structure can serve as a NOTIF logic gate on the basis of the fluorescence of crystal violet.

G-quadruplexes form ultrastable parallel structures in deep eutectic solvent

G-quadruplex DNA is highly polymorphic. Its conformation transition is involved in a series of important life events. These controllable diverse structures also make G-quadruplex DNA a promising candidate as catalyst, biosensor, and DNA-based architecture. So far, G-quadruplex DNA-based applications are restricted done in aqueous media. Since many chemical reactions and devices are required to be performed under strictly anhydrous conditions, even at high temperature, it is challenging and meaningful to conduct G-quadruplex DNA in water-free medium. In this report, we systemically studied 10 representative G-quadruplexes in anhydrous room-temperature deep eutectic solvents (DESs). The results indicate that intramolecular, intermolecular, and even higher-order G-quadruplex structures can be formed in DES. Intriguingly, in DES, parallel structure becomes the G-quadruplex DNA preferred conformation. More importantly, compared to aqueous media, G-quadruplex has ultrastability in DES and, surprisingly, some G-quadruplex DNA can survive even beyond 110 °C. Our work would shed light on the applications of G-quadruplex DNA to chemical reactions and DNA-based devices performed in an anhydrous environment, even at high temperature.

New horizons for diagnostics and therapeutic applications of graphene and graphene oxide

Graphene, a one-atom-thick two-dimensional (2D) layer of sp(2) -bonded carbon, has received worldwide attention owing to its extraordinary physical and chemical properties. Recently, great efforts have been devoted to explore potential applications of graphene and its oxide in life science, especially in disease-related diagnostics, near-Infrared (NIR) phototherapy and imaging. Here we will introduce recent advances and new horizons in this area, and focus on the rising progress on NIR photothermal therapy for cancer and Alzheimer's disease (AD), human telomerase detection, stem cell proliferation and differentiation on graphene substrate, diagnosis of cancer cell and related biomarkers, drug/nucleotide/peptide delivery and cell imaging, which have not been comprehensively reviewed. We hope to provide an outlook to the applications of graphene and its oxide, especially on the new horizons in this field, and inspire broader interests across various disciplines.

G-quadruplex and i-motif are mutually exclusive in ILPR double-stranded DNA

G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5'-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force≥17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.

pH-controlled reversible drug binding and release using a cytosine-rich hairpin DNA

Here we report that a cytosine-rich DNA carrier, that oscillates between a hairpin and an i-motif structure in its response to pH variation, can be used as a drug binding and release device.

A label-free, quadruplex-based functional molecular beacon (LFG4-MB) for fluorescence turn-on detection of DNA and nuclease

We demonstrate a novel concept for the construction of a label-free, quadruplex-based functional molecular beacon (LFG4-MB) by using G-quadruplex motif as a substitute for Watson-Crick base pairing in the MB stem and a specific G-quadruplex binder, N-methyl mesoporphyrin IX (NMM) as a reporter. It shows high sensitivity in assays for UDG activity/inhibition and detection of DNA sequence based on the unique fluorescence increase that occurs as a result of the strong interaction between NMM and the folded quadruplex upon removal of uracil by UDG or displacement of block sequence by target DNA. The LFG4-MB is simple in design, fast in operation and could be easily transposed to other biological relevant target analysis by simply changing the recognition portion. The LFG4-MB does not require any chemical modification for DNA, which offers the advantages of simplicity and cost efficiency and obviates the possible interference with the affinity and specificity of the MB as well as the kinetic behavior of the catalysts caused by the bulky fluorescent groups. More importantly, the LFG4-MB offers great extent of freedom to tune the experimental conditions for the general applicability in bioanalysis.

Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions

It has been generally recognized that understanding the molecular basis of some important cellular processes is hampered by the lack of knowledge of forces that drive spontaneous formation/disruption of G-quadruplex structures in guanine-rich DNA sequences. According to numerous biophysical and structural studies G-quadruplexes may occur in the presence of K(+) and Na(+) ions as polymorphic structures formed in kinetically governed processes. The reported kinetic models suggested to describe this polymorphism should be considered inappropriate since, as a rule, they include bimolecular single-step associations characterized by negative activation energies. In contrast, our approach in studying polymorphic behavior of G-quadruplexes is based on model mechanisms that involve only elementary folding/unfolding transitions and structural conversion steps that are characterized by positive activation energies. Here, we are investigating a complex polymorphism of d(G(4)T(4)G(3)) quadruplexes in K(+) solutions. On the basis of DSC, circular dichroism and UV spectroscopy and polyacrylamide gel electrophoresis experiments we propose a kinetic model that successfully describes the observed thermally induced conformational transitions of d(G(4)T(4)G(3)) quadruplexes in terms of single-step reactions that involve besides single strands also one tetramolecular and three bimolecular quadruplex structures.

Folding equilibrium constants of telomere G-quadruplexes in free state or associated with proteins determined by isothermal differential hybridization

Guanine rich (G-rich) nucleic acids form G-quadruplex structures that are implicated in many biological processes, pharmaceutical applications, and molecular machinery. The folding equilibrium constant (K(F)) of the G-quadruplex not only determines its stability and competition against duplex formation in genomic DNA but also defines its recognition by proteins and drugs and technical specifications. The K(F) is most conveniently derived from thermal melting analysis that has so far yielded extremely diversified results for the human telomere G-quadruplex. Melting analysis cannot be used for nucleic acids associated with proteins, thus has difficulty to study how protein association affects the folding equilibrium of G-quadruplex structure. In this work, we established an isothermal differential hybridization (IDH) method that is able to determine the K(F) of G-quadruplex, either alone or associated with proteins. Using this method, we studied the folding equilibrium of the core sequence G(3)(T(2)AG(3))(3) from vertebrate telomere in K(+) and Na(+) solutions and how it is affected by proteins associated at its adjacent regions. Our results show that the K(F) obtained for the free G-quadruplex is within 1 order of magnitude of most of those obtained by melting analysis and protein binding beside a G-quadruplex can dramatically destabilize the G-quadruplex.

Context dependence of trinucleotide repeat structures

Long repeated sequences of DNA and their associated secondary structure govern the development and severity of a significant class of neurological diseases. Utilizing the effect of base stacking on fluorescence quantum yield, 2-aminopurine substitutions for adenine previously demonstrated sequestered bases in the stem and exposed bases in the loop for an isolated (CAG)(8) sequence. This study evaluates (CAG)(8) that is incorporated into a duplex, as this three-way junction is a relevant model for intermediates that lead to repeat expansion during DNA replication and repair. From an energetic perspective, thermally induced denaturation indicates that the duplex arms dictate stability and that the secondary structure of the repeated sequence is disrupted. Substitutions with 2-aminopurine probe base exposure throughout this structure, and two conclusions about secondary structure are derived. First, the central region of (CAG)(8) is more solvent-exposed than single-stranded DNA, which suggests that hairpin formation in the repeated sequence is disrupted. Second, base stacking becomes compromised in the transition from the duplex to (CAG)(8), resulting in bases that are most similar to single-stranded DNA at the junction. Thus, an open (CAG)(8) loop and exposed bases in the arms indicate that the strand junction profoundly influences repeated sequences within three-way junctions.

Human telomeric G-quadruplex: thermodynamic and kinetic studies of telomeric quadruplex stability

Thermodynamic and kinetic studies complement high-resolution structures of G-quadruplexes. Such studies are essential for a thorough understanding of the mechanisms that govern quadruplex folding and conformational changes in quadruplexes. This perspective article reviews representative thermodynamic and kinetic studies of the folding of human telomeric quadruplex structures. Published thermodynamic data vary widely and are inconsistent; possible reasons for these inconsistencies are discussed. The key issue of whether such folding reactions are a simple two-state process is examined. A tentative energy balance for the folding of telomeric quadruplexes in Na(+) and K(+) solution, and for the conformational transition between these forms is presented.

Small-molecule selectively recognizes human telomeric G-quadruplex DNA and regulates its conformational switch

Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na(+) or K(+) solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions. These results may stimulate the design of new quadruplex binders that would be capable of discriminating different G-quadruplex structures as well as controlling biological phenomena, functional molecules, and nanomaterials.

Stability and kinetics of G-quadruplex structures

In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function. The unifying theme in this review is energetics. The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides. We provide an overview of the principles of stability and where available the experimental data that report on these principles. Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes. Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations. Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium. The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence.

Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA

Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

Single-walled carbon nanotubes binding to human telomeric i-motif DNA under molecular-crowding conditions: more water molecules released

The natural occurrence of the human telomeric G-quadruplex or i-motif in vivo has not been demonstrated and the biological effects of the induction of these structures need to be clarified. Intracellular environments are highly crowded with various biomolecules and in vitro studies under molecular-crowding conditions will provide important information on how biomolecules behave in cells. Here we report that cell-mimic crowding can increase i-motif stability at acid pH and cause dehydration. However, crowding can not induce i-motif formation at physiological pH. Intriguingly, single-walled carbon nanotubes (SWNTs) can drive i-motif formation under cell-mimic crowding conditions and cause more water to be released. To our knowledge, there is no report to show how SWNTs can influence DNA under cell-mimic crowding conditions. Our results indicate that SWNTs may have the potential to modulate the structure of human telomeric DNA in vivo, like DNA B-A transitions and B-Z changes on SWNTs in live cells, which demonstrates potential for drug design and cancer therapy.

Targeting human telomeric G-quadruplex DNA with oxazole-containing macrocyclic compounds

Oxazole-containing macrocycles, which include the natural product telomestatin, represent a promising class of anticancer agents that target G-quadruplex DNA. Two synthetic hexaoxazole-containing macrocyclic compounds (HXDV and HXLV-AC) have been characterized with regard to their cytotoxic activities versus human cancer cells, as well as the mode, thermodynamics, and specificity with which they bind to the intramolecular (3+1) G-quadruplex structural motif formed in the presence of K+ ions by human telomeric DNA. Both compounds exhibit cytotoxic activities versus human lymphoblast (RPMI 8402) and oral carcinoma (KB3-1) cells, with associated IC50 values ranging from 0.4 to 0.9microM. The compounds bind solely to the quadruplex nucleic acid form, but not to the duplex or triplex form. Binding to the quadruplex is associated with a stoichiometry of two ligand molecules per DNA molecule, with one ligand molecule binding to each end of the host quadruplex via a nonintercalative "terminal capping" mode of interaction. For both compounds, quadruplex binding is primarily entropy driven, while also being associated with a negative change in heat capacity. These thermodynamic properties reflect contributions from favorable ligand-induced alterations in the loop configurational entropies of the quadruplex, but not from changes in net hydration. The stoichiometry and mode of binding revealed by our studies have profound implications with regard to the number of ligand molecules that can potentially bind the 3-overhang region of human telomeric DNA.

Differential scanning calorimetry

Differential scanning calorimetry (DSC) has emerged as a powerful experimental technique for determining thermodynamic properties of biomacromolecules. The ability to monitor unfolding or phase transitions in proteins, polynucleotides, and lipid assemblies has not only provided data on thermodynamic stability for these important molecules, but also made it possible to examine the details of unfolding processes and to analyze the characteristics of intermediate states involved in the melting of biopolymers. The recent improvements in DSC instrumentation and software have generated new opportunities for the study of the effects of structure and changes in environment on the behavior of proteins, nucleic acids, and lipids. This review presents some of the details of application of DSC to the examination of the unfolding of biomolecules. After a brief introduction to DSC instrumentation used for the study of thermal transitions, the methods for obtaining basic thermodynamic information from the DSC curve are presented. Then, using DNA unfolding as an example, methods for the analysis of the melting transition are presented that allow deconvolution of the DSC curves to determine more subtle characteristics of the intermediate states involved in unfolding. Two types of transitions are presented for analysis, the first example being the unfolding of two large synthetic polynucleotides, which display high cooperativity in the melting process. The second example shows the application of DSC for the study of the unfolding of a simple hairpin oligonucleotide. Details of the data analysis are presented in a simple spreadsheet format.

Energetic aspects of locked nucleic acids quadruplex association and dissociation

The design of modified nucleic acid aptamers is improved by considering thermodynamics and kinetics of their association/dissociation processes. Locked Nucleic Acids (LNA) is a promising class of nucleic acid analogs. In this work the thermodynamic and kinetic properties of a LNA quadruplex formed by the TGGGT sequence, containing only conformationally restricted LNA residues, are reported and compared to those of 2'-OMe-RNA (O-RNA) and DNA quadruplexes. The thermodynamic analysis indicates that the sugar-modified quadruplexes (LNA and O-RNA) are stabilized by entropic effects. The kinetic analysis shows that LNA and O-RNA quadruplexes are characterized by a slower dissociation and a faster association with respect to DNA quadruplex. Interestingly, the LNA quadruplex formation process shows a second-order kinetics with respect to single strand concentration and has a negative activation energy. To explain these data, a mechanism for tetramer formation with two intermediate states was proposed.

Defining the mode, energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric G-quadruplex DNA

Oxazole-containing macrocycles represent a promising class of anticancer agents that target G-quadruplex DNA. We report the results of spectroscopic studies aimed at defining the mode, energetics and specificity with which a hexaoxazole-containing macrocycle (HXDV) binds to the intramolecular quadruplex formed by the human telomeric DNA model oligonucleotide d(T2AG3)4 in the presence of potassium ions. HXDV binds solely to the quadruplex nucleic acid form, but not to the duplex or triplex form. HXDV binds d(T2AG3)4 with a stoichiometry of two drug molecules per quadruplex, with these binding reactions being coupled to the destacking of adenine residues from the terminal G-tetrads. HXDV binding to d(T2AG3)4 does not alter the length of the quadruplex. These collective observations are indicative of a nonintercalative 'terminal capping' mode of interaction in which one HXDV molecule binds to each end of the quadruplex. The binding of HXDV to d(T2AG3)4 is entropy driven, with this entropic driving force reflecting contributions from favorable drug-induced alterations in the configurational entropy of the host quadruplex as well as in net hydration. The 'terminal capping' mode of binding revealed by our studies may prove to be a general feature of the interactions between oxazole-containing macrocyclic ligands (including telomestatin) and intramolecular DNA quadruplexes.