Monovalent cation-induced structure of telomeric DNA: the G-quartet model

Conformational polymorphism in telomeric structures: loop orientation and interloop pairing in d(G4TnG4)

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways--i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides--to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G4TnG4), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure.

Tandemly repeated pentanucleotides in DNA sequences of eucaryotes

Genetic sequence data banks were scanned in order to retrieve tandemly repeated pentanucleotides (pnts). It was found that among 102 (=(1024-4)/2/5) possible distinct pnts roughly each fourth is involved in tandem repeats. It is shown that tandemly repeated pnts are composed of frequently occurring di- and trinucleotides and that those pnts which occur frequently in the form of mono- or di-pnts form also tandem repeats either in the form of satellites or in the form of shorter tandem repeats. Human satellite III is taken as a specific example. It is shown that the first guanine within GG-AAT pnt exhibits the highest mutability. Sequential distribution of base changes gives evidence that the mutations do not occur at random positions but in a correlated fashion so that long stretches of original pnts remain intact. It is found that pnts related to the satellite III are present in introns and flanking regions of some structural genes, but are not preserved between orthologous genes of related species. The results corroborate the most plausible mechanism of their evolution--rapid amplification followed by successive divergence of repeat units by various mutational processes.

Promotion of parallel DNA quadruplexes by a yeast telomere binding protein: a circular dichroism study

Repressor-activator protein 1 (RAP1) has an essential role in the maintenance of yeast telomeres. Yeast telomeric DNA consists of simple repeated G-rich sequences that are bound by RAP1. We have found that RAP1, in addition to its known binding activity for double-stranded DNA, interacts with the G-rich strand containing guanine base (G)-tetrads. We show here using circular dichroism spectroscopy that RAP1 promotes the formation of one particular type of DNA quadruplex, parallel G4-DNA. Furthermore, RAP1 is able to bind to both preformed parallel and antiparallel DNA quadruplexes. These results have implications for the possible use of DNA quadruplexes in telomere-telomere association in vivo.

The high-resolution crystal structure of a parallel-stranded guanine tetraplex

Repeat tracts of guanine bases found in DNA and RNA can form tetraplex structures in the presence of a variety of monovalent cations. Evidence suggests that guanine tetraplexes assume important functions within chromosomal telomeres, immunoglobulin switch regions, and the human immunodeficiency virus genome. The structure of a parallel-stranded tetraplex formed by the hexanucleotide d(TG4T) and stabilized by sodium cations was determined by x-ray crystallography to 1.2 angstroms resolution. Sharply resolved sodium cations were found between and within planes of hydrogen-bonded guanine quartets, and an ordered groove hydration was observed. Distinct intra- and intermolecular stacking arrangements were adopted by the guanine quartets. Thymine bases were exclusively involved in making extensive lattice contacts.

Tertiary structure motif of Oxytricha telomere DNA

The tertiary structure of a single-stranded DNA containing the sequence of Oxytricha telomere DNA has been determined. This DNA adopts a compact tertiary structure that consists of four base-paired tetrads of guanine residues which are connected by three loops. The tetrads show significant deviations from planarity, and two of the loops exhibit significant loop-loop interactions. The structure of this telomere contains syn-thymine residues, which are in the loops, as well as an intraloop pyrimidine-pyrimidine base pair between residues that are separated by a single residue. The tertiary structure of the telomere DNA is consistent with prior results that showed that two thymines distant in sequence could be photo-cross-linked. The overall folding pattern of this telomere DNA is similar to that previously determined for a DNA aptamer, which binds to and inhibits thrombin, though the details of the two structures are quite distinct.

The DNA of ciliated protozoa

Ciliates contain two types of nuclei: a micronucleus and a macronucleus. The micronucleus serves as the germ line nucleus but does not express its genes. The macronucleus provides the nuclear RNA for vegetative growth. Mating cells exchange haploid micronuclei, and a new macronucleus develops from a new diploid micronucleus. The old macronucleus is destroyed. This conversion consists of amplification, elimination, fragmentation, and splicing of DNA sequences on a massive scale. Fragmentation produces subchromosomal molecules in Tetrahymena and Paramecium cells and much smaller, gene-sized molecules in hypotrichous ciliates to which telomere sequences are added. These molecules are then amplified, some to higher copy numbers than others. rDNA is differentially amplified to thousands of copies per macronucleus. Eliminated sequences include transposonlike elements and sequences called internal eliminated sequences that interrupt gene coding regions in the micronuclear genome. Some, perhaps all, of these are excised as circular molecules and destroyed. In at least some hypotrichs, segments of some micronuclear genes are scrambled in a nonfunctional order and are recorded during macronuclear development. Vegetatively growing ciliates appear to possess a mechanism for adjusting copy numbers of individual genes, which corrects gene imbalances resulting from random distribution of DNA molecules during amitosis of the macronucleus. Other distinctive features of ciliate DNA include an altered use of the conventional stop codons.

The fragile X syndrome d(CGG)n nucleotide repeats form a stable tetrahelical structure

The fragile X mental retardation syndrome is associated with the expansion of trinucleotide 5'-d(CGG)-3' repeats within the FMR1 gene and with hypermethylation of the cytosine residues of these repeats. The expansion and hypermethylation may account for the suppression of the transcription of the FMR1 gene and for the delay of its replication during the cell cycle. Here we show that d(CGG)n oligomers can form a stable Hoogsteen-bonded structure that exhibits properties consistent with those of tetraplex DNA. Oligomers, d(mCGG)n, (n = 4, 5, or 7), at pH 8.0 and in the presence of an alkali metal ion form stable species exhibiting a reduced electrophoretic mobility in nondenaturing polyacrylamide gels. These species are denatured by heating at 90 degrees C for 10 min. With a short d(mCGG)5 oligomer, the slowly migrating species is formed only when the cytosine residue is 5-methylated, whereas with the longer d(CGG)7 it is generated whether or not cytosine is 5-methylated. By contrast, complementary cytosine-rich oligomers do not form analogous complexes. The second-order association kinetics of the formation of the slowly migrating species of d(mCGG)5 suggests that it is an interstrand complex. Formation of intermediate-size complexes between d(mCGG)5 and d(mCGG)7 indicates that the stoichiometry of the slowly migrating structures is tetramolecular. Protection of the complex from methylation by dimethyl sulfate indicates the involvement of the N-7 positions of the guanine residues in Hoogsteen hydrogen bonding, a characteristic of quadruplex structures. If formed in vivo along the expanded and hypermethylated d(mCGG)n stretch, this tetraplex structure could suppress transcription and replication of the FMR1 gene in the fragile X syndrome cells.

Formation of a hairpin structure by telomere 3' overhang

The telomeres of most eukaryotes contain tandemly-repeated DNA sequences, with a cluster of G residues on one strand. Recent studies showed that the Oxytricha telomeric DNA oligonucleotide, d(G4T4G4), dimerizes to form a quadruplex in the presence of Na+ or K+. We have observed that the oligonucleotide d(G4T4G4) does not dimerize in the presence of Li+ ion at low sample concentrations. In the monomeric state, this molecule forms a simple foldback hairpin structure containing G x G reverse Hoogsteen basepairs in the stem region. This hairpin structure has a thermal stability which is well reconciled with telomere functions in vivo.

Mammalian telomere dynamics: healing, fragmentation shortening and stabilization

Telomeres are essential for stable chromosome maintenance. The simple G-rich sequence motif d(TTAGGG)n is all that is required in cis for telomere function in mammalian cells, as in other eukaryotes. Using this fact, telomeres have been used to specifically fragment mammalian chromosomes to dissect their structure and function. Telomere length maintenance is altered in cancer cells. Trans-acting factors, such as telomerase and telomere-binding proteins, may determine telomere function in both normal and cancer cells. Current experiments are aimed at understanding the role of telomerase and telomere-binding proteins in cellular senescence and immortalization.

Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5'-->3' digestion of the transcript

The first step in the decay of some eukaryotic mRNAs is the shortening of the poly(A) tail. To examine how the transcript body was degraded after deadenylation, we followed the decay of a pulse of newly synthesized MFA2 transcripts while utilizing two strategies to trap intermediates in the degradation pathway. First, we inserted strong RNA secondary structures, which can slow exonucleolytic digestion and thereby trap decay intermediates, into the MFA2 5' UTR. Following deadenylation, fragments of the MFA2 mRNA trimmed from the 5' end to the site of secondary structure accumulated as full-length mRNA levels decreased. In addition, in cells deleted for the XRN1 gene, which encodes a major 5' to 3' exonuclease in yeast, the MFA2 transcript is deadenylated normally but persists as a full-length mRNA lacking the 5' cap structure. These results define a mRNA decay pathway in which deadenylation leads to decapping of the mRNA followed by 5'-->3' exonucleolytic degradation of the transcript body. Because the poly(A) tail and the cap structure are found on essentially all mRNAs, this pathway could be a general mechanism for the decay of many eukaryotic transcripts.

Refined solution structure of the dimeric quadruplex formed from the Oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG)

BACKGROUND

Telomeres, the structures at the ends of linear eukaryotic chromosomes, are essential for chromosome replication and stability. The telomeres of the unicellular ciliate Oxytricha contain a 3' single strand overhang composed of two repeats of the telomere repeat sequence d(TTTTGGGG). It has been proposed that oligonucleotides containing this repeat can form DNA quadruplexes via hydrogen bonding of the guanines into quartets. Such structures may be relevant to the biological function of the telomere, and in G-rich sequences elsewhere in the genome.

RESULTS

We have previously determined from solution NMR data that the Oxy-1.5 Oxytricha repeat oligonucleotide d(GGGGTTTTGGGG) dimerizes to form an intermolecular quadruplex composed of four guanine quartets and with the thymines in loops across the diagonal at opposite ends of the quadruplex. We report here the refined solution structure of Oxy-1.5. This structure is compared with the previously published crystal structure of the same oligonucleotide.

CONCLUSIONS

Oxy-1.5 forms a well-defined, symmetrical structure with ordered thymine loops. Both the solution and crystal structures of Oxy-1.5 are quadruplexes with alternating syn and anti glycosyl conformation of guanines along each strand of the helix and have thymine loops at opposite ends. However, the topology of the two structures is fundamentally different, leading to significant structural differences. A topological pathway for the formation and interconversion of the two structures is proposed.

Human telomeric C-strand tetraplexes

Telomeric C-strand sequences form non-Watson-Crick base-paired structures in supercoiled plasmids and in oligonucleotides at low pH. Here we examine oligonucleotides composed of 2 or 4 repeats of the human telomeric C-strand sequence d(CCCTAA)n. At low pH, the 2-repeat molecule forms a dimer which exhibits H1'-H1' nuclear Overhauser effects (NOEs) between stacked CC+ base pairs. These NOEs are characteristic of the i-motif, which is a tetraplex composed of two intercalated CC+ duplexes. The 4-repeat molecule forms an intramolecular monomeric structure at low pH, suggesting that four contiguous cytosine tracts fold into a CC+ intercalated tetraplex. These unusual structures may be relevant to the formation of guanine tetraplexes by complementary G-rich sequences. They may also provide a general mechanism for self-recognition by nucleic acids.

Telomeric DNA sequence and structure following de novo telomere synthesis in Euplotes crassus

To learn more about the mechanism of de novo telomere synthesis, we have characterized the sequence and structure of newly synthesized telomeres from Euplotes crassus. E. crassus is a particularly useful organism for studying telomere synthesis because millions of telomeres are made in each cell at a well-defined time during the sexual stage of the life cycle. These newly synthesized telomeres are approximately 50 bp longer than mature macronuclear telomeres. We have investigated the structure of the newly synthesized telomeres and have found that they are much more heterogeneous in length than mature telomeres. Most of the heterogeneity is present on the G-rich strand, indicating that the length of this strand is rather loosely controlled. In contrast, the length of the C-rich strand is much less variable, suggesting that synthesis of this strand is the more precisely regulated step in telomere addition. The G-rich strand exhibits variability both in the total number of G4T4 repeats and in the identity of the terminal nucleotide. In most cases, the G-rich strnd extends beyond the C-rich strand to leave a 3' overhang. While the size of this overhang is variable, the median length is 10 nucleotides. This research provides the first detailed picture of a newly synthesized telomere and has allowed us to formulate a model to describe the various steps involved in de novo telomere synthesis.

Telomeric DNA sequence and structure following de novo telomere synthesis in Euplotes crassus

To learn more about the mechanism of de novo telomere synthesis, we have characterized the sequence and structure of newly synthesized telomeres from Euplotes crassus. E. crassus is a particularly useful organism for studying telomere synthesis because millions of telomeres are made in each cell at a well-defined time during the sexual stage of the life cycle. These newly synthesized telomeres are approximately 50 bp longer than mature macronuclear telomeres. We have investigated the structure of the newly synthesized telomeres and have found that they are much more heterogeneous in length than mature telomeres. Most of the heterogeneity is present on the G-rich strand, indicating that the length of this strand is rather loosely controlled. In contrast, the length of the C-rich strand is much less variable, suggesting that synthesis of this strand is the more precisely regulated step in telomere addition. The G-rich strand exhibits variability both in the total number of G4T4 repeats and in the identity of the terminal nucleotide. In most cases, the G-rich strnd extends beyond the C-rich strand to leave a 3' overhang. While the size of this overhang is variable, the median length is 10 nucleotides. This research provides the first detailed picture of a newly synthesized telomere and has allowed us to formulate a model to describe the various steps involved in de novo telomere synthesis.

DNA comes in many forms

Forty years ago, we learned of the major double helical structure adopted by DNA. It combined both elegance and simplicity in its design. Since then we have learned that DNA can also adopt other conformations. We now know that it can exist in a variety of triple-stranded and quadruple-stranded forms, as well as forms that are left-handed. The list of alternative conformations that can be adopted by this molecule is still growing. These conformations represent a major biological challenge to understand their role in biological systems. This type of work represents an active frontier in molecular biology today.

Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex

BACKGROUND

Repeats of Gn sequences are detected as single strand overhangs at the ends of eukaryotic chromosomes together with associated binding proteins. Such telomere sequences have been implicated in the replication and maintenance of chromosomal termini. They may also mediate chromosomal organization and association during meiosis and mitosis.

RESULTS

We have determined the three-dimensional solution structure of the human telomere sequence, d[AG3(T2AG3)3] in Na(+)-containing solution using a combined NMR, distance geometry and molecular dynamics approach (including relaxation matrix refinement). The sequence, which contains four AG3 repeats, folds intramolecularly into a G-tetraplex stabilized by three stacked G-tetrads which are connected by two lateral loops and a central diagonal loop. Of the four grooves that are formed, one is wide, two are of medium width and one is narrow. The alignment of adjacent G-G-G segments in parallel generates the two grooves of medium width whilst the antiparallel arrangement results in one wide and one narrow groove. Three of the four adenines stack on top of adjacent G-tetrads while the majority of the thymines sample multiple conformations.

CONCLUSIONS

The availability of the d[AG3(T2AG3)3] solution structure containing four AG3 human telomeric repeats should permit the rational design of ligands that recognize and bind with specificity and affinity to the individual grooves of the G-tetraplex, as well as to either end containing the diagonal and lateral loops. Such ligands could modulate the equilibrium between folded G-tetraplex structures and their unfolded extended counterparts.

A single trinucleotide, 5'AGC3'/5'GCT3', of the triplet-repeat disease genes confers metal ion-induced non-B DNA structure

Expansion of (AGC)n repeats has been associated with genetic disorders called triplet-repeat diseases such as Huntington's disease (HD), myotonic muscular dystrophy (DM) and Kennedy's disease. To gain insight into the abnormal behavior of these repeats, we studied their structural properties in supercoiled DNA. Chemical probing revealed that, under physiological salt and pH conditions, Zn2+ or Co2+ ions induce (AGC)n repeats to adopt a novel non-B DNA structure in which all cytosine but none of adenine residues in either strand become unpaired. The minimum size of (AGC)n repeat that could form this structure independently of neighboring sequences is a single unit of double-stranded trinucleotide, 5'AGC3'/5'GCT3'. Other trinucleotide units of the same nucleotide composition, 5'CAG3'/5'CTG3' or 5'GCA3'/5'TGC3', do not form non-B DNA structures. This unusual DNA structural properly adopted by a single 5'AGC3'/5'GCT3' trinucleotide may contribute to expansion of (AGC)n sequences in triplet-repeat diseases.

Monovalent cation effects on intermolecular purine-purine-pyrimidine triple-helix formation

The binding of a 19-mer guanosine-rich oligodeoxyribonucleotide, TG3TG4TG4TG3T (ODN 1), to a complementary polypurine DNA target was investigated by DNase I footprinting and restriction endonuclease protection assays. Monovalent cations inhibited intermolecular purine-purine-pyrimidine triple-helical DNA formation, with K+ and Rb+ being most effective, followed by NH4+ and Na+. Li+ and Cs+ had little to no effect. Similar results were observed with the G/A-rich oligonucleotide AG3AG4AG4AG3AGCT. Kinetic studies indicated that monovalent cations interfered with oligonucleotide-duplex DNA association but did not significantly promote triplex dissociation. The observed order of monovalent cation inhibition of triplex formation is reminiscent of their effect on tetraplex formation with G/T-rich oligonucleotides. However, using electrophoretic mobility shift assays we found that the oligonucleotide ODN 1 did not appear to form a four-stranded species under conditions promoting tetraplex formation. Taken together, our data suggest that processes other than the self-association of oligonucleotides into tetraplexes might be involved in the inhibitory effect of monovalent cations on purine-pyrimidine-purine triplex formation.

Telomere processing in Euplotes

In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudden decrease in telomere length takes place at a specific time during macronuclear development. The decrease in telomere length is not caused by incomplete replication of the most terminal DNA sequences; rather it is the result of an active processing event that occurs independently of DNA replication. The developmentally regulated telomere shortening that takes place in Euplotes is reminiscent of the sudden reductions in telomere length which have been observed in other eukaryotes.

Characterization of a G-quartet formation reaction promoted by the beta-subunit of the Oxytricha telomere-binding protein

Telomeres, the ends of linear chromosomes, typically consists of tandem repeats of a simple guanine-rich sequence. Telomeric DNA is able to form intermolecular G-quartet structures. The beta-subunit of the Oxytricha telomere-binding protein acts as a molecular chaperone to promote the formation of dimers and specific higher order complexes of telomeric DNA stabilized by G-quartets; these reactions occur under physiological conditions in vitro. In the present article, we show that, at saturating protein concentrations (> or = 200 nM), beta-mediated G-quartet formation is a first-order reaction with respect to DNA concentration, with k approximately 1 h-1 at 37 degrees C. In contrast, the protein-independent reaction is a second-order reaction. The beta-subunit enhances the rate of G-quartet formation by 10(5)-10(6)-fold at a telomeric DNA concentration of 20 nM. The beta-mediated higher order complexes are identified as parallel four-stranded tetramers of telomeric DNA (G4-DNA). Poly-L-lysine also promotes formation of the tetramers, but not dimers. These DNA structures were studied by irreversible thermal melting experiments and probed by annealing to different complementary strands. Guanine residues important for structure formation were analyzed by methylation interference experiments. On the basis of these data, models for the beta-mediated structures are proposed, and possible mechanisms for the beta-mediated reaction are discussed. In addition, we found that the beta-subunit promotes the annealing of two complementary strands into a duplex, as do many other basic proteins. However, not all proteins with annealing-promoting activity are active in the formation of G-quartet structures. The activity of the telomere protein in promoting the formation of telomeric DNA structures may enable chromosome-chromosome association or the regulation of telomerase activity in vivo.

Dimethylsulfate methylation of guanine residues in mammalian DNA: inverse correlation between methylation susceptibility and mutagenesis by bromodeoxyuridine and thymidine

We have previously demonstrated that mutagenesis by bromodeoxyuridine (BrdU) and thymidine (dT) in mammalian cells occurs with a high degree of sequence specificity within runs of multiple adjacent guanine residues. To determine whether there is a structural component to this sequence specificity, we have analyzed stereochemical properties of guanine residues in different sequence contexts. Stereochemical differences were assessed by measuring the susceptibility of individual guanine residues to methylation by the agent dimethylsulfate (DMS). The results from this study suggest that there is a strong inverse correlation between susceptibility of various guanine residues to DMS methylation and the susceptibility of those residues to mutagenesis by BrdU and dT. These results suggest that the stereochemical attributes of guanine residues in different sequence contexts affect the susceptibility of those guanine residues to mutagenesis by BrdU and dT.

The multimerization state of retroviral RNA is modulated by ammonium ions and affects HIV-1 full-length cDNA synthesis in vitro

Genomic human immunodeficiency virus type 1 (HIV-1) RNA fragments containing the dimer linkage structure (DLS) can be dimerized and multimerized in the presence of NH4+ and in the absence of any other cation and any viral or cellular protein. This effect strongly supports the notion that dimerization and multimerization of genomic RNA occurs via purine-quartet formation in quadruple helical RNA structures. The efficiency of RNA dimerization and multimerization in the presence of ammonium ions is about 400 fold increased as compared to alkali metal ions such as potassium. Dimerized retroviral RNA representing a pseudodiploid genome could account for genetic recombination within the virion and during reverse transcription. Application of a novel South-Northern-Blotting procedure with biotinylated RNA and digoxigenin-labelled cDNA in vitro reveals that efficient human- and bovine tRNA(Lys3) primed full-length cDNA-synthesis only takes place with a predominantly monomerized RNA template. Dimerization and multimerization of the RNA significantly reduces full-length cDNA-synthesis. This suggests that monomerization of the dimerized RNA, effected by deionization in vitro, is essential for efficient retroviral reverse transcription in vivo.

Telomeres and telomerases

The ends of eukaryotic chromosomes are defined by specialized nucleoprotein complexes called telomeres. Telomeres impart stability to the genome and are of general interest due to their unique structure and unconventional mode of synthesis. Recent work has identified new components of the telomere complex and expanded our understanding of the role of terminal structures in maintaining cell viability.

The beta subunit of Oxytricha telomere-binding protein promotes G-quartet formation by telomeric DNA

Telomeres, the ends of linear chromosomes, typically consist of tandem repeats of simple G-rich sequences. At high concentrations, single-stranded telomeric DNA can form dimers and tetramers involving G-quartets. We show that under physiological conditions, the beta subunit of the Oxytricha telomere-binding protein greatly accelerates G-quartet formation. The reaction occurs with oligonucleotides ending in the Oxytricha (T4G4T4G4) and Tetrahymena (T2G4T2G4) telomeric sequences; the sequence preceding these telomeric repeats can be nontelomeric, single-, or double-stranded. Protein deletion analysis indicates that the carboxy-terminal highly basic domain of the beta subunit, which is dispensible for telomeric complex formation, is sufficient for mediating G-quartet formation. The finding that a telomeric protein acts as a molecular chaperone for G-quartet formation provides a strong argument that such DNA structures exist in vivo at chromosome telomeres.

Telomeric DNA binding proteins

The physical ends of eukaryotic chromosomes form a specialized nucleoprotein complex composed of DNA and DNA binding proteins. This nucleoprotein complex, termed the telomere, is essential for chromosome stability. In most organisms, the DNA portion of the nucleo-protein complex consists of simple tandem DNA repeats with one strand guanine rich. The protein portion of the complex is less well understood. The experiments presented in two recent papers represent different stages in the characterization of the telomeric DNA binding proteins. The first paper presents a structure-function study of the Oxytricha telomeric DNA binding proteins and the second paper shows the identification and initial characterization of a telomeric DNA binding activity from Xenopus laevis. These two reports provided valuable information in understanding the structure and function of telomeres.

A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation

To determine pathways of mRNA turnover in yeast, we have followed the poly(A) tail removal and degradation of a pulse of newly synthesized transcripts from four different genes. Before decay of both stable and unstable mRNAs initiated, there was a temporal lag during which the poly(A) tail was deadenylated to an oligo(A) length. Altering the deadenylation rate of an mRNA led to a corresponding change in the length of this lag. The rate of deadenylation and the stability of the oligo(A) species varied between mRNAs, explaining the differences in mRNA half-lives. To examine how the transcript body was degraded following deadenylation, we used the strategy of inserting strong RNA secondary structures, which can slow exonucleolytic digestion and thereby trap decay intermediates, into the 3' UTR of mRNAs. Fragments lacking the 5' portion of two different mRNAs accumulated after deadenylation as full-length mRNA levels decreased. Therefore, these results define an mRNA decay pathway in which deadenylation leads to either internal cleavage or decapping followed by 5'-->3' exonucleolytic degradation of the mRNA.

Genetic and physical mapping of telomeres and macrosatellites of rice

Telomeres and telomere-associated satellites of rice were genetically and physically analyzed by pulsed-field gel electrophoresis (PFGE) using Arabidopsis telomeric DNA and rice satellite sequences as probes. We demonstrate that Arabidopsis telomeric sequences hybridize to rice telomeres under the conditions of high stringency. Using the Arabidopsis probe, multiple, discrete telomeric fragments could be identified on pulsed-field gel blots of rice DNAs digested with rare-cutting restriction enzymes. Most of the telomeric bands larger than 300 kb are physically linked with satellite bands as revealed by PFGE. Some of the telomeric and satellite bands segregate in a Mendelian fashion and are highly reproducible. Three such telomeric bands have been mapped to the distal ends of RFLP linkage groups: Telsm-1 on chromosome 8, Telsa-1 on chromosome 9 and Telsm-3 on chromosome 11. One segregating satellite band was mapped to an internal region of chromosome 10. Telomeric fragments were shown not only to be genetically linked to but also physically linked (based on PFGE) to the terminal RFLP markers. The physical distance from telomeric sequences to a distal RFLP marker, r45s gene, on chromosome 9, is 200 kb while the distance from telomeric sequences to RG98, a terminal RFLP marker on chromosome 11, is 260 kb. Physical maps of the telomere regions of chromosome 9 and chromosome 11 are presented.

Oxytricha telomere-binding protein: DNA-dependent dimerization of the alpha and beta subunits

A telomere-binding protein consisting of 56-kDa (alpha) and 41-kDa (beta) subunits binds specifically to the single-stranded T4G4T4G4 sequence at the termini of macronuclear DNA molecules in Oxytricha nova. The recent availability of separate alpha and beta polypeptides, expressed in Escherichia coli, allows investigation of the assembly of the telomeric complex ("telosome") from its individual components. By mixing wild-type subunits and electrophoretically distinct variants, we verify that the telosome contains one alpha and one beta subunit. By using telomeric DNAs of two lengths, we find that there is one DNA molecule per telosome. The DNA-protein and subunit-subunit interactions were studied by glycerol gradient sedimentation and chemical cross-linking. The formation of alpha-DNA and beta-DNA cross-links in the telomeric complex indicates that both subunits are in proximity to the DNA. When incubated together, both subunits exist predominantly as monomers in the absence of telomeric DNA. Upon binding to DNA, alpha and beta subunits directly interact with each other to form a heterodimer. We suggest that this DNA-dependent dimerization may allow each subunit to carry out distinct functions as a monomer, in addition to its participation in chromosome capping as part of the heterodimer.

The role of DNA repeats and associated secondary structures in genomic instability and neoplasia

Tumour-associated genetic changes frequently involve DNA translocation or deletion. Many of these events will have arisen from initial genomic damage, induced by either the activity of endogenous metabolic processes or from exposure to environmental genotoxic agents. Although initial genomic damage will have been widely distributed, tumorigenic events are confined to certain DNA target sites. Furthermore, within these target sites there appear to be regions of preferential DNA rearrangement, and examination of these sites implies that the location and extent of such rearrangement may be influenced by DNA primary and secondary structure rather than simply by the point of damage. We selectively review evidence relating to DNA structures that may predispose certain regions of the genome to damage-induced rearrangement, and discuss the possible role of interstitial, inverted telomere-like sequence arrays in promoting chromosomal events of a type known to be associated with some human and animal tumours.

Direct detection of repetitive, whole chromosome paint and telomere DNA probes by immunogold electron microscopy

Biotinylated repetitive, whole chromosome paint and telomere DNA probes were investigated at the electron microscope level after non-isotopic in situ hybridization and direct immunogold detection. The protocol described allowed the visualization of a biotinylated chromosome 1 specific satellite DNA probe in the light microscope without silver intensification. This sensitive method was exploited to analyse factors contributing to signal strength in immunogold chromosome painting. Furthermore, it allowed us to investigate the distribution of (TTAGGG)n telomere repeats in human metaphase chromosomes and interphase nuclei. Telomeric and internal (TTAGGG)n repeats were detected at high spatial resolution in human metaphase chromosomes. In the periphery of lymphocyte interphase nuclei, two types of telomere hybridization signals were observed. They differed remarkably in compactness, indicating two types of chromatin conformation present at the interphase telomeres in situ.

Weiss Lecture. Effects of radiations of different qualities on cells: molecular mechanisms of damage and repair

Studies of ionizing radiations of different quality are discussed with particular emphasis on damage to DNA of mammalian cells. Three related themes are followed. Firstly, inactivation and mutation experiments with ultrasoft X-rays and slow heavy ions, coupled with theoretical analyses of the structures of the radiation tracks, have emphasized the biological importance of localized track features over nanometre dimensions. This led to the suggestion that the critical physical features of the tracks are the stochastic clusterings of ionizations, directly in or very near to DNA, resulting in clustered initial molecular damage including various combinations of breaks, base damages, cross-links, etc. in the DNA. The quantitative hypotheses imply that final cellular effects from high-LET radiations are dominated by their more severe, and therefore less repairable, clustered damage, and that these are qualitatively different from the dominant low-LET damage. Second, relative effectiveness of different types of radiation led to questions on the mechanisms of induction of chromosome exchanges. The high efficiency of ultrasoft X-rays, despite their very short track lengths, suggested that single sites of DNA damage may lead to exchanges by a molecular process involving interaction with undamaged DNA. Also it is shown that a single site-specific DNA break, introduced by restriction enzymes, sometimes leads to a large deletion when misrepaired by cell extracts. These deletions occur between short DNA repeats, and are therefore a form of 'illegitimate' recombination, but clearly do not involve the interaction of two damage sites. Third, it was shown that cells from patients with the radiosensitive disorder ataxia-telangiectasia (AT) lack a post-irradiation recovery process. The sensitivity of AT cells to high LET radiations was found to be reduced relative to that for normal cells, reinforcing the concept that high LET damage is less easy to repair. AT patients are prone to lymphoreticular cancers, and their cells show characteristic chromosomal rearrangements, which may be associated with misrepair at specific genomic sequences. Similarly, studies of radiation-induced leukaemia in the mouse have implicated rearrangement at specific interstitial chromosome sites, which are rich in telomere-like repeat sequences.

A Xenopus egg factor with DNA-binding properties characteristic of terminus-specific telomeric proteins

We have identified a Xenopus laevis protein factor that specifically recognizes vertebrate telomeric repeats at DNA ends. This factor, called Xenopus telomere end factor (XTEF), is detected predominantly in extracts of Xenopus eggs and ovaries, which are estimated to contain sufficient XTEF to bind approximately 3 x 10(7) DNA ends. In contrast, XTEF is much less abundant (approximately 90 per cell) in extracts of somatic cell nuclei. Mobility retardation analysis of the XTEF activity in egg extracts indicates that this factor binds the vertebrate telomeric repeat sequence (TTAGGG)2 when present in a single-stranded 3' overhang. Single-stranded 3' extensions of (TTTGGG)2, (AAAGGG)2, (TTACCC)2, or a nonrepetitive sequence fail to bind XTEF efficiently, whereas changes in the double-stranded sequence 5' to the TTAGGG repeat tail are tolerated. TTAGGG repeats are not recognized at internal position, at a 5' protruding end, or in double-stranded DNA. In addition, the factor does not bind RNA with single-stranded UUAGGG repeats at a 3' end. XTEF-DNA complexes form and are stable in high salt. The DNA-binding properties of XTEF resemble the characteristics of a class of terminus-specific telomere proteins identified previously in hypotrichous ciliates.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus 1 genomic RNA

Retroviruses package two homologous single-stranded RNA genomes within a gag protein-RNA complex. In mature virion particles, the two RNA strands are thought to associate primarily through direct RNA-RNA interactions, although the structural basis for this stable association is unknown. We now report that a 127-nucleotide (nt) HIV-1NL4-3 RNA fragment (positions 732-858) encompassing the 5' end of the gag gene dimerizes spontaneously under high ionic strength conditions in the absence of any protein cofactor. The HIV-1 RNA dimer is dramatically and specifically stabilized by the monovalent cation potassium. Thermal dissociation of the dimer occurs at 80 degrees C in 100 mM K+ (5 mM Mg2+) but at significantly lower temperatures in the presence of either smaller or larger monovalent cations (100 mM Li+, 40 degrees C; 100 mM Na+, 55 degrees C; 100 mM Cs+, 30 degrees C). Deletion analyses of the 3' end of the 127-nt fragment reveal that an HIV-1 RNA fragment as short as 94 nt (732-825) can dimerize spontaneously, but a further 9-base deletion of the purine-rich sequence, GGGGGAGAA from positions 817 through 825, eliminates dimerization. These experimental results support a model in which HIV-1 RNA dimerizes by forming an interstrand quadruple helix stabilized by guanine (and/or purine)-base tetrads in analogy to the well-known dimerization of telomeric DNA. We speculate that this structure may also mediate the association of genomic HIV-1 RNA in vivo, revealing how RNA itself can achieve the self-recognition required for subsequent genetic recombination.

Identification and characterization of a nuclease activity specific for G4 tetrastranded DNA

We have identified a nuclease activity that is specific for G4 tetrastranded DNA. This activity, found in a partially purified fraction for a yeast telomere-binding protein, binds to DNA molecules with G4 tetrastranded structure, regardless of their nucleotide sequences, and cleaves the DNA in a neighboring single-stranded region 5' to the G4 structure. Competition with various G4-DNA molecules inhibits the cleavage reaction, suggesting that this nuclease activity is specific for G4 tetrastranded DNA. The existence of this enzymatic activity that reacts with G4 DNAs but not with single-stranded or Watson-Crick duplex DNAs suggests that tetrastranded DNA may have a distinct biological function in vivo.

Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution

We have used two-dimensional 1H NMR spectroscopy to study the conformation of the thrombin-binding aptamer d(GGTTGGTGTGGTTGG) in solution. This is one of a series of thrombin-binding DNA aptamers with a consensus 15-base sequence that was recently isolated and shown to inhibit thrombin-catalyzed fibrin clot formation in vitro [Bock, L. C., Griffin, L. C., Latham, J. A., Vermaas, E. H. & Toole, J. J. (1992) Nature (London) 355, 564-566]. The oligonucleotide forms a unimolecular DNA quadruplex consisting of two G-quartets connected by two TT loops and one TGT loop. A potential T.T bp is formed between the two TT loops across the diagonal of the top G-quartet. Thus, all of the invariant bases in the consensus sequence are base-paired. This aptamer structure was determined by NMR and illustrates that this molecule forms a specific folded structure. Knowledge of this structure may be used in the further development of oligonucleotide-based thrombin inhibitors.

Spontaneous assembly of a self-complementary oligopeptide to form a stable macroscopic membrane

A 16-residue peptide [(Ala-Glu-Ala-Glu-Ala-Lys-Ala-Lys)2] has a characteristic beta-sheet circular dichroism spectrum in water. Upon the addition of salt, the peptide spontaneously assembles to form a macroscopic membrane. The membrane does not dissolve in heat or in acidic or alkaline solutions, nor does it dissolve upon addition of guanidine hydrochloride, SDS/urea, or a variety of proteolytic enzymes. Scanning EM reveals a network of interwoven filaments approximately 10-20 nm in diameter. An important component of the stability is probably due to formation of complementary ionic bonds between glutamic and lysine side chains. This phenomenon may be a model for studying the insoluble peptides found in certain neurological disorders. It may also have implications for biomaterials and origin-of-life research.

A DNA aptamer which binds to and inhibits thrombin exhibits a new structural motif for DNA

The investigation of the three-dimensional structure of the DNA aptamer d(G1G2T3-T4G5G6T7G8T9G10G11T12T13G14G15) which binds to and inhibits thrombin has been carried out by NMR methods. This DNA exhibits a number of long-range NOEs between residues which are not adjacent in sequence, which allowed the determination of the novel tertiary structure adopted. This DNA adopts a highly compact, highly symmetrical structure which consists of two tetrads of guanosine base pairs and three loops. The residues of the tetrads alternate anti-syn-anti-syn. This novel structural motif for DNA may also be relevant to the structure of telomere DNA.

Direct observation of a DNA quadruplex by electrospray ionization mass spectrometry

In 10 mM sodium phosphate, pH 7.6, containing 0.1 mM ethylenediaminetetraacetic acid, ions correspondings to the non-calent, four-stranded oligonucleotide, d(CGCG4GCG)4, were detected by negative ion electrospray ionization (ESI) mass spectrometry at a low nozzle-skimmer (delta NS) bias (-150 V), but not at a higher delta NS bias (> -250 V). In contrast, when the sample was desalted and analyzed by ESI mass spectrometry at a low delta NS bias only ions for the single-stranded d(CGCG4GCG) species were observed. These data agree with spectroscopic evidence which showed that oligonucleotides with the sequence motif 5'd(CGCGnGCG)3', where n = 2-5, formed stable four-stranded complexes in the presence of monatomic cations, like K+, Ca2+, Na+ and Li+, but not in their absence.

Identification of a nonprocessive telomerase activity from mouse cells

Telomerase activity was identified in extracts from several different mouse cell lines. Addition of telomeric TTAGGG repeats was specific to telomeric oligonucleotide primers and sensitive to pretreatment with RNase A. In contrast to the hundreds of repeats synthesized by the human and Tetrahymena telomerase enzymes in vitro, mouse telomerase synthesized only one or two TTAGGG repeats onto telomeric primers. The products observed after elongation of primers with circularly permuted (TTAGGG)3 sequences and after chain termination with ddATP or ddTTP indicated that mouse telomerase pauses after the addition of the first dG residue in the sequence TTAGGG. The short length of the products synthesized by mouse telomerase was not due to a diffusible inhibitor in the mouse extract, because the human telomerase continued to synthesize long products when mixed with mouse fractions. Primer challenge experiments showed that the human enzyme synthesized long TTAGGG repeats processively in vitro, whereas the mouse telomerase appeared to be much less processive. The identification of short telomerase reaction products in mouse extracts suggests that extracts from other organisms may also generate only short products. This knowledge may aid in the identification of telomerase activity in organisms where activity has not yet been detected.