Kinetic studies on the formation of DNA triplexes containing the nucleoside analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine

We have examined the kinetics of triple helix formation of oligonucleotides that contain the nucleotide analogue 2'-O-(2-aminoethyl)-5-(3-amino-1-propynyl)uridine (bis-amino-U, BAU), which forms very stable base triplets with AT. Triplex stability is determined by both the number and location of the modifications. BAU-containing oligonucleotides generate triplexes with extremely slow kinetics, as evidenced by 14 degrees C hysteresis between annealing and melting profiles even when heated at a rate as slow as 0.2 degrees C min(-1). The association kinetics were measured by analysis of the hysteresis profiles, temperature-jump relaxation and DNase I footprinting. We find that the slow kinetics are largely due to the decreased rate of dissociation; BAU modification has little effect on the association reaction. The sequence selectivity is also due to the slower dissociation of BAU from AT than other base pairs.

Preferred binding sites for the bifunctional intercalator TANDEM determined using DNA fragments that contain every symmetrical hexanucleotide sequence

We have prepared novel DNA footprinting substrates that contain all 64 symmetrical hexanucleotide sequences. These were contained in two restriction fragments that were cloned into the pUC19 polylinker site; each fragment was also obtained in both orientations. These fragments were used to assess the sequence binding preferences of the synthetic quinoxaline antibiotic TANDEM. We found that, although the ligand binds to most TpA steps, the affinity is affected by the flanking sequences. The best binding sites contain the tetranucleotide sequence ATAT, although YATATR is a better site than RATATY. TTAA always is a poor binding site, especially TTTAAA. The binding to GTAC is strongly dependent on the flanking bases, with good binding to GGTACC but none at all to CGTACG.

Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands

Footprinting is a simple method for assessing the sequence selectivity of DNA-binding ligands. The method is based on the ability of the ligand to protect DNA from cleavage at its binding site. This review describes the use of DNase I and hydroxyl radicals, the most commonly used footprinting probes, in footprinting experiments. The success of a footprinting experiment depends on using an appropriate DNA substrate and we describe how these can best be chosen or designed. Although footprinting was originally developed for assessing a ligand's sequence selectivity, it can also be employed to estimate the binding strength (quantitative footprinting) and to assess the association and dissociation rate constants for slow binding reactions.

Intramolecular DNA quadruplexes with different arrangements of short and long loops

We have examined the folding, stability and kinetics of intramolecular quadruplexes formed by DNA sequences containing four G₃ tracts separated by either single T or T₄ loops. All these sequences fold to form intramolecular quadruplexes and 1D-NMR spectra suggest that they each adopt unique structures (with the exception of the sequence with all three loops containing T₄, which is polymorphic). The stability increases with the number of single T loops, though the arrangement of different length loops has little effect. In the presence of potassium ions, the oligonucleotides that contain at least one single T loop exhibit similar CD spectra, which are indicative of a parallel topology. In contrast, when all three loops are substituted with T₄ the CD spectrum is typical of an antiparallel arrangement. In the presence of sodium ions, the sequences with two and three single T loops also adopt a parallel folded structure. Kinetic studies on the complexes with one or two T₄ loops in the presence of potassium ions reveal that sequences with longer loops display slower folding rates.

Directing quadruplex-stabilizing drugs to the telomere: synthesis and properties of acridine-oligonucleotide conjugates

Conjugates containing quadruplex-stabilizing acridines linked to oligonucleotides that are complementary to the G-rich human telomere sequence were synthesized. Acylation of 3,6-diaminoacridine followed by two Michael reactions provided derivatives suitable for conjugation, which were coupled to resin-linked amine-modified oligonucleotides by activating the carboxyl group with pentafluorophenyl 4-nitrobenzenesulfonate. After deprotection with aqueous ammonia at room temperature, conjugates incorporating different acridines, linkers, and oligonucleotide sequences were obtained. These were tested for their ability to stabilize intramolecular DNA quadruplexes that are based on the human telomeric repeat sequence (GGGTTA)(n).

Sequence effects of single base loops in intramolecular quadruplex DNA

We have examined the properties of intramolecular G-quadruplexes in which the G3 tracts are separated by single base loops. The most stable complex contained 1',2'-dideoxyribose in all three loops, while loops containing T and C were slightly less stable (by about 2 degrees C). Quadruplexes containing loops with single A residues were less stable by 8 degrees C for each T to A substitution. These folded sequences display similar CD spectra, which are consistent with the formation of parallel stranded complexes with double-chain reversal loops. These results demonstrate that loop sequence, and not just length, affects quadruplex stability.

Effect of G-tract length on the topology and stability of intramolecular DNA quadruplexes

G-Rich sequences are known to form four-stranded structures that are based on stacks of G-quartets, and sequences with the potential to adopt these structures are common in eukaryotic genomes. However, there are few rules for predicting the relative stability of folded complexes that are adopted by sequences with different-length G-tracts or variable-length linkers between them. We have used thermal melting, circular dichroism, and gel electrophoresis to examine the topology and stability of intramolecular G-quadruplexes that are formed by sequences of the type d(GnT)4 and d(GnT2)4 (n = 3-7) in the presence of varying concentrations of sodium and potassium. In the presence of potassium or sodium, d(GnT)4 sequences form intramolecular parallel complexes with the following order of stability: n = 3 > n = 7 > n = 6 > n = 5 > n = 4. d(G3T)4 is anomalously stable. In contrast, the stability of d(GnT2)4 increases with the length of the G-tract (n = 7 > n = 6 > n = 5 > n = 4 > n = 3). The CD spectra for d(GnT)4 in the presence of potassium exhibit positive peaks around 260 nm, consistent with the formation of parallel topologies. These peaks are retained in sodium-containing buffers, but when n = 4, 5, or 6, CD maxima are observed around 290 nm, suggesting that these sequences [especially d(G5T)4] have some antiparallel characteristics. d(G3T2)4 adopts a parallel conformation in the presence of both sodium and potassium, while all the other d(GnT2)4 complexes exhibit predominantly antiparallel features. The properties of these complexes are also affected by the rate of annealing, and faster rates favor parallel complexes.

Triplex staples: DNA double-strand cross-linking at internal and terminal sites using psoralen-containing triplex-forming oligonucleotides

A method has been developed to attach 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen to the 5 position of thymine bases during solid-phase oligonucleotide synthesis. UV irradiation of triplex-forming oligonucleotides (TFOs) containing internally attached psoralens produces photoadducts at TpA steps within target duplexes, thus relaxing the constraints on selection of psoralen target sequences. Photoreaction of TFOs containing two psoralens, located at the 5'- and 3'-ends, has been used to create double-strand cross-links (triplex staples) at both termini of the TFO. Such complexes have no free single-stranded ends. TFOs containing 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen, 3-methyl-2-aminopyridine, and 5-(3-aminoprop-2-ynyl)deoxyuridine formed photoadducts with target duplexes under near-physiological conditions.

Feasibility of an exercise rehabilitation programme for cancer patients

A growing body of evidence indicates the benefits of exercise as a rehabilitation intervention for cancer patients. However, few hospitals offer exercise-based rehabilitation programmes to patients. This study evaluated the feasibility and acceptability of a group-based exercise programme for cancer patients attending a local oncology centre. The intervention consisted of a weekly instructor-led circuit training class supplemented by home-based activity 4 days/week for 10 weeks. From 28 eligible patients, 12 were recruited (43%), of whom nine completed the intervention (75%). The three withdrawals were due to worsening of disease. Adherence (mean of 7.5 classes attended and 4 days/week of home activity performed) and tolerability (no adverse events) were good. Positive features of the programme identified in interviews with participants included the variety and scope of the exercises, and the empathetic but positive approach of the instructors. The small group format was highly valued with participants receiving social support and inspiration from each other. Perceived outcomes included improved fitness, reduced fatigue, enjoyment, enhanced mood and a sense of achievement. Several participants felt that the intervention represented a stepping stone to becoming habitual exercisers. Results suggested that the programme was feasible and acceptable to patients, but uptake was low, indicating a need for more effective recruitment strategies in order for a cost-effective service to be implemented.

Crossvalidation of anthropometry against magnetic resonance imaging for the assessment of visceral and subcutaneous adipose tissue in children

BACKGROUND

The study of the relationship between anthropometry and visceral adipose tissue (VAT) is of great interest because VAT is associated with many risk factors for noncommunicable diseases and anthropometry is easy to perform in clinical practice. The studies hitherto available for children have, however, been performed on small sample sizes.

DESIGN

Pooling of the data of studies published from 1992 to 2004 as indexed on Medline.

AIMS

To assess the relationship between anthropometry and VAT and subcutaneous adipose tissue (SAT) as measured by magnetic resonance imaging (MRI) in children and to analyze the effect of age, gender, pubertal status and ethnicity.

SUBJECTS AND METHODS

Eligible subjects were 7-16 year-old, with availability of VAT and SAT, gender, ethnicity, body mass index (BMI) and waist circumference (WC). A total of 497 subjects were collected from seven different investigators and 407 of them (178 Caucasians and 229 Hispanics) were analyzed.

RESULTS

Despite ethnic differences in MRI data, BMI, WC and age, no difference in VAT was found between Caucasians and Hispanics after correction for SAT and BMI. Univariate regression analysis identified WC as the best single predictor of VAT (64.8% of variance) and BMI of SAT (88.9% of variance). The contribution of ethnicity and gender to the unexplained variance of the VAT-WC relationship was low (< or =3%) but significant (P < or =0.002). The different laboratories explained a low (< or =4.8%) but significant (P < 0.0001) portion of the unexplained variance of the VAT-WC and SAT-BMI relationships. Prediction equations for VAT (VAT (cm(2)) = 1.1 x WC (cm)-52.9) and SAT (SAT (cm(2)) = 23.2 x BMI (kg/m(2))-329) were developed on a randomly chosen half of the population and crossvalidated in the remaining half. The pure error of the estimate was 13 cm(2) for VAT and 57 cm(2) for SAT.

CONCLUSIONS

WC can be considered a good predictor of VAT as well as BMI of SAT. The importance of ethnicity and gender on VAT estimation is not negligible.

DNA sequence recognition by an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B)

We have used DNA footprinting and fluorescence melting experiments to study the sequence specific binding of an imidazole-containing isopropyl-substituted thiazole polyamide (thiazotropsin B) to DNA. While the parent compound (thiazotropsin A) binds to the hexanucleotide sequence ACTAGT, changing one of the N-methylpyrrole groups to N-methylimidazole changes the preferred binding sequence to (A/T)CGCG(T/A). Experiments with DNA fragments that contain variants of this sequence suggest that the ligand can also bind, with lower affinity, to sequences which differ from this by 1bp in any position.

Obesity, fitness and health in Taiwanese children and adolescents

OBJECTIVE

To examine the prevalence of childhood and adolescent obesity in Taiwan and investigate the association between excess weight and physical fitness and blood pressure.

DESIGN

Cross-sectional study.

SUBJECTS

A total of 13 935 children and adolescents aged 6-18 years (boys: 7031, girls: 6904) were involved in the 1999 survey and 24 586 (boys: 12 367, girls: 12 219) were available in the 2001 survey.

MEASUREMENTS

Weight, height, systolic and diastolic blood pressures, and health-related fitness tests (bent-leg curl-ups, sit-and-reach test and step test) were measured.

RESULTS

The overall prevalence of obesity (including overweight) in boys was 19.8% in 1999 and 26.8% in 2001. It was lower in girls with 15.2% in 1999 and 16.5% in 2001. The normal weight group performed better (P<0.05) than the overweight/obese group in all fitness tests except in the 2001 sit-and-reach test where there were no differences between the two groups. The risk of hypertension increased nearly two times for the overweight/obese-fit group and nearly three times for the overweight/obese-unfit group compared to the normal weight-fit group (adjusted odds ratio (AOR)=1.93, 95%CI=1.514-2.451 and AOR=2.93, 95%CI=2.493-3.454, respectively).

CONCLUSION

Overall, the findings demonstrated that there is an increasing trend in overweight/obesity prevalence for Taiwanese youth even in a 2-year period. The overweight/obese youngsters tend to have poorer muscular strength and cardiovascular endurance than the normal weight group. The overweight/obese and unfit group had a greater risk of hypertension than other groups. However, this risk was significantly lower if obese/overweight children had a higher than average level of cardiovascular fitness.

DNA triple-helix formation at target sites containing duplex mismatches

We have studied the formation of DNA triple helices at target sites that contain mismatches in the duplex target. Fluorescence melting studies were used to examine a series of parallel triple helices that contain all 64 N.XZ triplet combinations at the centre (where N, X and Z are each of the four natural DNA bases in turn). Similar experiments were also performed with N=bis-amino-U (BAU) (for stable recognition of AT base pairs) and N=S (for recognition of TA inversions). We find that the introduction of a duplex mismatch destabilises the C+.GZ, T.AZ and G.TZ triplets. A similar effect is seen with BAU.AZ triplets. In contrast, other base combinations, based on non-standard triplets such as C.AZ, T.TZ, G.CZ and A.CZ are stabilised by the presence of a duplex mismatch. In each case S binds to sites containing duplex mismatches better than the corresponding Watson-Crick base pairs.

An extra dimension in nucleic acid sequence recognition

Watson-Crick base pairing is a natural molecular recognition process that has been exploited in molecular biology and universally adopted in many fields. An additional mode of nucleic acid sequence recognition that could be used in combination with normal base pairing would add an exta dimension to nucleic acid interactions and open up many new applications. In principle the triplex approach could provide this if developed to recognize any DNA sequence. To this end modified nucleosides have been incorporated into triple-helix-forming oligonucleotides (TFOs) and used to recognize mixed sequence DNA with high selectivity and affinity at neutral pH. Continuing developments are directed towards improving TFO affinity at high pH and increasing triplex association kinetics. A number of applications of triplexes are currently being explored.

A polarized-light spectroscopy study of interactions of a hairpin polyamide with DNA

We here study the interactions of a polyamide with large DNA, and compare to those of minor groove binder distamycin (DST), including high ligand/DNA binding ratios. Specific as well as nonspecific binding is probed using polarized-light spectroscopy combined with singular value decomposition analysis. Circular and linear dichroism data confirm binding geometries consistent with minor groove binding for both of the ligands. Interestingly, at high and intermediate ligand/DNA ratios the polyamide exhibits no significant sequence discrimination between mixed-sequence (calf thymus) and AT DNA as compared to DST. Each ligand is concluded to exhibit two different binding modes depending upon ligand/DNA ratio and nucleo-base sequence. At high binding ratios, distinct differences between the ligands are observed: circular dichroism spectra exciton effects provide evidence of bimolecular interactions of the polyamide when bound to AT-DNA, whereas no effects are seen with DST or mixed-sequence DNA. Also linear dichroism indicates that a change in binding geometry occurs at high polyamide/AT ratios, and that the effect occurs only with polyamide in contrast to DST. Since the effect is insignificant with DST, or with calf thymus DNA, it is concluded that it relates to the sizes of the ligands and the minor grooves, becoming critical in the limit of crowding.

Do children from an inner city British school meet the recommended levels of physical activity? Results from a cross sectional survey using objective measurements of physical activity

Questionnaire surveys suggest physical activity levels in children are low, particularly among children from deprived areas. Using accelerometers, it was found that children from a deprived inner city school were active at recommended levels and had similar levels of activity to children in other studies from more affluent populations. However, this finding was dependent on the threshold used to define moderate activity.

A fast algorithm for the construction of universal footprinting templates in DNA

We introduce and give a complete description of a new graph to be used for DNA sequencing questions. This graph has the advantage over the classical de Bruijn graph that it fully accounts for the double stranded nature of DNA, rather than dealing with single strands. Technically, our graph may be thought of as the quotient of the de Bruijn graph under the natural involution of sending a DNA strand to its complementary strand. However, this involution has fixed points, and this complicates the structure of the quotient graph which we have therefore modified herein. As an application and motivating example, we give an efficient algorithm for constructing universal footprinting templates for n-mers. This problem may be formulated as the task of finding a shortest possible segment of DNA which contains every possible sequence of base pairs of some fixed length n. Previous work by Kwan et al has attacked this problem from a numerical point of view and generated minimal length universal footprinting templates for n = 2, 3, 5, 7, together with unsubstantiated candidates for the case n = 4. We show that their candidates for n = 4 are indeed minimal length universal footprinting templates.

Combining nucleoside analogues to achieve recognition of oligopurine tracts by triplex-forming oligonucleotides at physiological pH

We have used DNase I footprinting to examine DNA triple helix formation at a 12 base pair oligopurine.oligopyrimidine sequence, using oligonucleotides that contain combinations of 2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine (bis-amino-U, BAU) and 3-methyl-2-aminopyridine (MeP) in place of T and C, respectively. This combination acts cooperatively to enable high affinity triple helix formation at physiological pH. The affinity depends on the number of substitutions and their arrangement; oligonucleotides in which these analogues are evenly distributed throughout the third strand bind much better than those in which they are clustered together.

Efficient Solid-Phase-Based Total Synthesis of the Bisintercalator TANDEM

[reaction: see text] In this article, the first solid-phase-based total synthesis of TANDEM, a synthetic analogue of triostin A, is described. In initial studies, the synthesis incorporated depsipeptide formation, introduction of chromophores, and disulfide bond formation on the solid phase, prior to a final solution-phase macrolactamization, to give the target molecule. Although pure TANDEM was obtained in an overall yield comparable to those for all syntheses to date, the yield of the final cyclization was low (11%). A more efficient approach involved removal from the solid phase prior to disulfide bond formation. The resulting linear peptide underwent macrolactamization under mild conditions and high dilution. Final disulfide bond formation was essentially quantitative and gave the target molecule, TANDEM, in an overall yield of 18%. The final compound was assessed for its ability to bind to 5'-TpA sequences on DNA by DNase I footprinting. This efficient synthesis sets the stage for a study of the structure-activity relationship of TANDEM and the natural product triostin A, with analogues containing "point mutations" at every site within the cyclic compounds.

Inosine substitutions demonstrate that intramolecular DNA quadruplexes adopt different conformations in the presence of sodium and potassium

We have examined the stability of fluorescently-labelled oligonucleotides that are based on the human telomeric repeat [(GGGTTA)(3)GGG], in which one of the guanines in turn is substituted with inosine. We show that the relative stability of the substitutions is different in the presence of sodium and potassium. The data for potassium suggest a parallel arrangement of the strands, while the sodium form is mixed parallel and antiparallel.

Stable recognition of TA interruptions by triplex forming oligonucleotides containing a novel nucleoside

We have prepared the 2'-aminoethoxy derivative of the S nucleoside ((2AE)S) and incorporated it into triplex-forming oligonucleotides for recognition of TA interruptions within a target oligopurine tract. Fluorescence melting, UV melting, and DNase I footprinting experiments show that (2AE)S has greater affinity than G or S for a single TA interruption. Stable triplexes are formed at pH 6.0 at an 18-mer target site containing two TA interruptions, even though this contains eight C(+).GC triplets. Although (2AE)S and S produce stable triplexes at TA interruptions, they also interact with other base pairs, in particular, CG, although the selectivity for TA improves with increased pH.( 2AE)S is the best nucleoside described so far for recognition of TA within a triple-helix target.

Four base recognition by triplex-forming oligonucleotides at physiological pH

We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2'-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, (Me)P (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while (A)PP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, (Me)P and (A)PP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.

Kinetic stability of intermolecular DNA quadruplexes

Fluorescently labeled oligodeoxyribonucleotides containing a single tract of four successive guanines have been used to study the thermodynamic and kinetic properties of short intermolecular DNA quadruplexes. When these assemble to form intermolecular quadruplexes the fluorophores are in close proximity and the fluorescence is quenched. On raising the temperature these complexes dissociate and there is a large increase in fluorescence. These complexes are exceptionally stable in potassium-containing buffers, and possess Tm values that are too high to measure. Tm values were determined in sodium-containing buffers for which the rate of reannealing is extremely slow; the melting profiles are effectively irreversible, and the apparent melting temperatures are dependent on the rates of heating. The dissociation kinetics of these complexes was estimated by rapidly increasing the temperature and following the time-dependent changes in fluorescence. From these data we have estimated the half-lives of these quadruplexes at 37 degrees C. Addition of a T to the unlabeled end of the oligonucleotide increases quadruplex stability. In contrast, addition of a T between the fluorophore and the oligonucleotide leads to a decrease in stability.