unusual behavior exhibited by multistranded guanine-rich dna complexes

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Karen Poon Robert B. Macgregor, Jr. Unusual Behavior Exhibited Department of Pharmaceutical Sciences, by Multistranded Faculty of Pharmacy, University of Toronto, Guanine-Rich DNA Toronto, Ontario, Canada Complexes Received 14 August 1997; accepted 31 October 1997 Abstract: The structural properties of oligonucleotides containing two different types of G- rich sequences at the 3 *-ends were compared. It is shown that oligonucleotides with uninter- rupted runs of guanine residues at the 3 *-end, e.g., d ( T 15 G 12 ) , form multistranded structures stabilized by guanine – guanine interactions. The chemical and physical properties of these complexes differ from those of the complexes formed by oligonucleotides with telomere-like sequences, e.g., d ( T 15 G 4 T 2 G 4 ) . In methylation protection and methylation interference experi- ments, we found all the guanines in complexes formed by d ( T 15 G 15 ) and d ( T 15 G 12 ) to be accessible to methylation. Furthermore, the methylated monomers retain the ability to polymer- ize. This contrasts with the inaccessibility of the guanines in d ( T 15 G 4 T 2 G 4 ) to methylation and the inability of the methylated monomer to form supramolecular structures. The stoichiometry of the complexes arising from the two types of oligonucleotides also differs. The complexes formed by d ( T 15 G 15 ) consist of consecutive integer numbers of DNA strands, whereas complexes formed by telomere-like oligonucleotides contain 1, 2, 4, or multiples of four strands. Magne- sium ions favor formation of high molecular weight complexes by d ( T 15 G 15 ) and d ( T 15 G 12 ), but not by d ( T 15 G 4 T 2 G 4 ). The d ( T 15 G 15 ) and d ( T 15 G 12 ) complexes have very high thermal stability compared with telomeric complexes. However, at low temperatures, the thymine bases within the telomeric motif, TTGGGGTTGGGG, appear to allow for the formation of stable high-molecular weight species with a longer nonguanine portion. q 1998 John Wiley & Sons, Inc. Biopoly 45: 427–434, 1998 Keywords: DNA methylation; telomere; tetraplex; DNA stability; electrophoresis mers. 4–7 Various guanine – quartet structures exist, INTRODUCTION the major ones being G2 *-DNA, bimolecular anti- Guanosine forms self-complementary structures in parallel tetraplexes, 8 G4 *-DNA, unimolecular anti- solution through hydrogen bonding to yield gua- parallel tetraplexes, 9 and G4-DNA tetramolecular nine – guanine base pairs 1,2 and guanine quartets 3 as parallel tetraplexes. 4,5 The formation of these differ- shown in Figure 1. These interactions are assumed ent structures by specific sequences and their stabil- to be responsible for the stabilization of the intramo- ity depend on the temperature, DNA concentration, and most importantly, different cations and their lecular structure formed by telomere-like oligo- Correspondence to: Robert B. Macgregor, Jr., Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2 Canada Contract grant sponsor: Glaxo Wellcome Canada, Inc. K. Poon was supported by an Ontario Graduate Scholarship Biopolymers, Vol. 45, 427–434 (1998) q 1998 John Wiley & Sons, Inc. CCC 0006-3525/98 / 060427-08 427 5560 / 8K45$$5560 02-24-98 10:43:37 bpa W: Biopolymers

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Karen PoonRobert B. Macgregor, Jr. Unusual Behavior ExhibitedDepartment of Pharmaceutical

Sciences, by MultistrandedFaculty of Pharmacy,University of Toronto, Guanine-Rich DNA

Toronto, Ontario, Canada ComplexesReceived 14 August 1997;accepted 31 October 1997

Abstract: The structural properties of oligonucleotides containing two different types of G-rich sequences at the 3 *-ends were compared. It is shown that oligonucleotides with uninter-rupted runs of guanine residues at the 3 *-end, e.g., d(T15G12) , form multistranded structuresstabilized by guanine–guanine interactions. The chemical and physical properties of thesecomplexes differ from those of the complexes formed by oligonucleotides with telomere-likesequences, e.g., d(T15G4T2G4) . In methylation protection and methylation interference experi-ments, we found all the guanines in complexes formed by d(T15G15) and d(T15G12) to beaccessible to methylation. Furthermore, the methylated monomers retain the ability to polymer-ize. This contrasts with the inaccessibility of the guanines in d(T15G4T2G4) to methylation andthe inability of the methylated monomer to form supramolecular structures. The stoichiometryof the complexes arising from the two types of oligonucleotides also differs. The complexesformed by d(T15G15) consist of consecutive integer numbers of DNA strands, whereas complexesformed by telomere-like oligonucleotides contain 1, 2, 4, or multiples of four strands. Magne-sium ions favor formation of high molecular weight complexes by d(T15G15) and d(T15G12) ,but not by d(T15G4T2G4) . The d(T15G15) and d(T15G12) complexes have very high thermalstability compared with telomeric complexes. However, at low temperatures, the thymine baseswithin the telomeric motif, TTGGGGTTGGGG, appear to allow for the formation of stablehigh-molecular weight species with a longer nonguanine portion. q 1998 John Wiley &Sons, Inc. Biopoly 45: 427–434, 1998

Keywords: DNA methylation; telomere; tetraplex; DNA stability; electrophoresis

mers.4–7 Various guanine–quartet structures exist,INTRODUCTIONthe major ones being G2*-DNA, bimolecular anti-

Guanosine forms self-complementary structures in parallel tetraplexes,8 G4 *-DNA, unimolecular anti-solution through hydrogen bonding to yield gua- parallel tetraplexes,9 and G4-DNA tetramolecularnine–guanine base pairs1,2 and guanine quartets3 as parallel tetraplexes.4,5 The formation of these differ-shown in Figure 1. These interactions are assumed ent structures by specific sequences and their stabil-to be responsible for the stabilization of the intramo- ity depend on the temperature, DNA concentration,

and most importantly, different cations and theirlecular structure formed by telomere-like oligo-

Correspondence to: Robert B. Macgregor, Jr., Department ofPharmaceutical Sciences, Faculty of Pharmacy, University ofToronto, 19 Russell Street, Toronto, Ontario M5S 2S2 Canada

Contract grant sponsor: Glaxo Wellcome Canada, Inc.K. Poon was supported by an Ontario Graduate Scholarship

Biopolymers, Vol. 45, 427–434 (1998)q 1998 John Wiley & Sons, Inc. CCC 0006-3525/98/060427-08

427

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428 Poon and Macgregor

tween the 3*-guanine residues, which were initiallyassumed to be in a tetrad conformation. However, aswe show here, the aggregated structures formed byoligonucleotides such as d(T15G12) are stabilized byinteractions that differ in several ways from those ofstandard guanine quartets. The differential behaviorsexhibited by these two types of G-rich sequences mayhave significant implications for the properties of te-lomeres with altered sequences. Loss of nonguaninebases in a telomeric sequence through deletion or mu-tation to guanines could result in tracts of DNA withseveral consecutive guanine residues. We propose thatsuch a change might alter the function of the telomerebecause of the unusual physical properties of DNAwith many consecutive guanines.

MATERIALS AND METHODSFIGURE 1 Structure of a guanine quartet showing theinterior (N1-HrrrO|C6) and exterior (N2-HrrrN7)hydrogen bonds. DNA Preparation

The deprotected, desalted, and cartridge purified oligonu-cleotides used in these experiments were purchased from

concentrations.6,10 Structural details revealed by x- the HSC Biotechnology Service Center, Toronto. Theywere used without further purification.ray crystallography show that guanines within a tet-

rad exhibit a high degree of planarity and have adistinctive stacking architecture.11

High-Order Structure FormationRecent interest in self-complementary guaninecomplexes has been motivated by the observation Lyophilized oligomers were dissolved in 89 mM Tris, 89that telomeric sequences, guanine-rich sequences mM boric acid, 2 mM EDTA, pH 8.0 (TBE). The DNAfound at the ends of eukaryotic chromosomes, also oligomers were labeled with 32P using [g-32P]ATP andform guanine-quartets, or tetrads, in intra- and inter- T4 polynucleotide kinase. Labeled oligonucleotides weremolecular structures in vitro.4,12 The structures desalted and unincorporated radiolabel was removed us-

ing P-6 Bio-Spin Chromatography columns (Bio-Rad,adopted by telomeric DNA and the complexes theyInc.) . Stock solutions of labeled oligonucleotides wereform with telomere binding proteins are believed tomaintained in TBE at about 5 nM strands. 32P-labeledprotect the terminal DNA from nuclease digestion.13

oligomers were incubated with either 1M KCl or 1MThese complexes are also important for the spatialMgCl2 at 907C for 5 min. The samples were subjectedstructure of telomeres and chromosome segregation.to electrophoresis in a 15% polyacrylamide gel underIt has been shown that mutated telomeric DNAdenaturing conditions (7M urea, 557C) with TBE as the

caused by an altered RNA template sequence can running buffer or in a 10% polyacrylamide gel underseverely delay or block the cell division in anaphase native conditions at 47C with TBE or TB (89 mM Tris, 89by inhibiting chromosome separation.14,15

mM boric acid, pH 8.0) as the running buffer. FollowingIn these experiments we compare the properties of electrophoresis, the gels were dried and analyzed with an

two types of oligonucleotides with G-rich 3*-ends, Ambis Model 4000 radioanalytic imager (Ambis, Inc.) .oligonucleotides with telomere-like sequences, e.g.,d(T15G4T2G4), and oligonucleotides with several

Stoichiometryconsecutive guanine residues at the 3*-end, e.g.,d(T15G12). Both types of oligonucleotide can aggre-

The stoichiometry of d(T15G15) complexes was investi-gate to form high molecular weight structures. Our gated by studying the number of hybrids formed withinitial interest in the behavior of oligonucleotides like d(T10G15) . The shorter oligonucleotide forms complexesd(T15G12) arose from the observation that the aggre- similar to those of d(T15G15) , but with different molecu-gated structures formed by oligonucleotides with simi- lar weights and hence different electrophoretic mobilities.lar sequences exhibit extreme thermal stability.16 The Hybrid structures were formed by mixing d(T10G15) and

d(T15G15) in TB containing 10 mM MgCl2.origin of this stability arises from the interactions be-

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Behavior by Multistranded G-Rich DNA 429

Methylation Protection RESULTS

The standard Maxam-Gilbert sequencing procedure for Formation of High-Order Structurestrand cleavage at guanine bases was employed.17 All by d (T15G15 )chemicals were purchased from Sigma, Inc. In a typical

It has been reported that d(A15G15) aggregates toreaction, a 10 mL solution of DNA oligomer complexesform high molecular weight species that arise(50 mM strands) was prepared in 1M MgCl2 or 1M KCl.

Next, 200 mL of dimethyl sulfate (DMS) reaction buffer through interactions between the 15 guanosine resi-(50 mM sodium cacodylate, pH 8.0; 1 mM EDTA) was dues.16 The adenosines remain single stranded. Notadded followed by 1 mL DMS. After incubating at room surprisingly, on account of its sequence similarity,temperature for 4 min, 50 mL of a DMS stop buffer (1.5M d(T15G15) behaves in the same manner. The aggre-sodium acetate, pH 7.0, 1.0M b-mercaptoethanol) and gation of d(T15G15) is apparently identical to that750 mL ethanol (100%, 0207C) were added to stop the

of d(A15G15) ; however, because this is not thereaction. The samples were then immersed in a dry ice/

object of this report, we will only summarize theethanol bath for 5 min. The DNA was precipitated bydata relevant to d(T15G15) aggregation. In casescentrifuging 5 min at 15,0001 g ; the pellets were rinsedwhere the data are not given here, the behavior oftwice with 70% ethanol. The methylated samples wered(T15G15) can be directly compared to that ofseparated on a nondenaturing polyacrylamide gel. Withd(A15G15) in the original publication.16reference to the 32P signal measured by the portable Gei-

ger counter and the position of the blue bromophenol In the absence of added cations, greater than 80%marker in the gel, two samples were excised from the of d(T15G15) exists as an unassociated monomer ingels. One corresponded to the high molecular weight spe- aqueous solution; however, upon addition of metalcies and the other to the monomer. These samples were ions to the buffer, d(T15G15) aggregates to form aeluted from the gel fragments in separate microcentrifuge distribution of high molecular weight species. Thetubes containing 0.25 mL of elution buffer (0.5M ammo-

progress of polymerization can be easily monitorednium acetate, 1 mM EDTA, pH 8.0) with shaking over-

following addition of cations to the solution. Asnight at 377C. The eluted DNA samples were then ethanolexpected, the extent of aggregation also depends onprecipitated and the pellet rinsed twice with 70% ethanol.the total concentration of d(T15G15) ; the fraction ofThe purified and lyophilized samples were then reactedhigh order structure formation increases as the ini-with 70 mL of a solution of 10% piperidine in water attial oligonucleotide concentration is raised from 2.5907C for 30 min, after which the piperidine was removed

by drying under vacuum. Traces of piperidine were re- nM to 250 mM (data not shown).moved by resuspending the samples in 20 mL of water Electrophoresis of d(T15G15) complexes underand then vacuum drying. This process was repeated two denaturing conditions, 15% polyacrylamide, 7Mtimes. The samples were analyzed in a denaturing gel. urea, TBE running buffer, 557C (Figure 2), gener-Methylation protection experiments were repeated using ated not only the anticipated band due to the single-different methylation times (30 s or 3 h) and a longer

stranded DNA oligomer, but also six additionalreaction time (1 h) in 10% piperidine. The latter proce-

bands with lower mobilities, demonstrating thedure was performed to ensure the complete digestion ofextreme thermal stability of the aggregates ofthe methylated samples, although 30 min is sufficientd(T15G15) . A similar pattern of bands was also ob-under normal circumstances.served after electrophoresis under nondenaturing(native) conditions (data not shown). Plotting thelogarithm of the relative mobility of each band un-der denaturing and native conditions against the cor-Methylation Interferenceresponding band number yields straight lines (re-sults not shown). This indicates that the bands rep-We also carried out methylation interference experimentsresent complexes of similar molecular structure butin which the samples (5 nM strands) , methylated as de-

scribed, were incubated with 1M MgCl2 or 1M KCl at of different molecular weight. Similar results were907C for 5 min to determine whether the methylated oli- found for complexes formed by d(T15G12) (data notgonucleotides would form complexes as observed for the shown).nonmethylated oligonucleotides. The low oligonucleotideconcentration ensured that most of the oligonucleotidesremained in the unassociated monomeric state before Stoichiometry of Complexes Formedthe methylation reaction. After incubation of the meth- by d (T15G15 )ylated oligonucleotides in the presence of a cation, the

To determine the stoichiometry of the aggregatedsamples were analyzed on a native gel with TB bufferat run at 47C. forms of d(T15G15) , we mixed it with d(T10G15) ,

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430 Poon and Macgregor

and conclude that consecutive bands on the gel cor-respond to differences of a single strand of oligonu-cleotide.

d (T15G12 ) vs d (T15G4T2G4 )

d(T15G12) self-associates to form denaturation-re-sistant high molecular weight complexes in a man-ner similar to d(A15G15) , d(T15G15) , and d(T10G15) .We have compared this oligonucleotide withd(T15G4T2G4) , the 3 *-end of which has the samesequence as the Tetrahymena telomere ( i.e.,G4T2G4) . In contrast to the behavior of d(T15G12)and similar oligonucleotides, aggregated forms ofd(T15G4T2G4) are observed only in native poly-acrylamide gels run at 47C after incubation with K/

(Figure 4) and are not observed under denaturingconditions. In the presence of Mg2/ , d(T15G12)formed high molecular weight species while the te-lomere-like sequence did not (Figure 4). Judgingby the relative mobilities of the complexes formedby the two oligonucleotides, it appears thatd(T15G12) forms complexes of higher molecular

FIGURE 2 Banding pattern of 32P-labeled d(T15G15) weight than d(T15G4T2G4) .on a denaturing 15% polyacrylamide gel. Seven bandsare resolved by the gel.

an oligonucleotide that also forms high molecularweight complexes. The complexes formed byd(T10G15) have a lower molecular weight, and thushigher electrophoretic mobility, than those ofd(T15G15) (Figure 3, lane 7). In Figure 3, the high-est mobility band in lanes 1 and 7 represents mono-mer and the second band corresponds to an aggre-gated structure of the oligonucleotides. Differentmolar ratios of the two oligonucleotides were mixedand allowed to form hybrid structures (lanes 2–6).In lanes where the d(T10G15) and d(T15G15) weremixed, the two bands with the highest mobilitiesrepresent the single strands. Three bands corre-sponding to the three possible dimers are observedas indicated in Figure 3. The simplest interpretationof these data is that the three possible dimeric spe-

FIGURE 3 Determination of the stoichiometry of thecies are formed, namely d(T10G15)rd(T10G15) ,complexes form by d(T15G15) . d(T15G15) was mixedd(T10G15)rd(T15G15) , and d(T15G15)rd(T15G15) .with d(T10G15) in various proportions and the bandingThus, in lanes containing a single oligonucleotide,pattern of the hybrid structures was monitored. (1) 2.5

the highest mobility band represent the monomer nM 32P-d(T15G15) ; (2) 2.5 nM 32P-d(T10G15) / 2.5 nMoligonucleotides and the second highest mobility 32P-d(T15G15) ; (3) 2.5 nM 32P-d(T10G15) / 10 mMband corresponds to a dimer. Based on the linearity 32P-d(T15G15) ; (4) 10 mM 32P-d(T10G15) / 2.5 nMof plots of the logarithm of the relative mobility vs 32P-d(T15G15) ; (5) 2.5 nM 32P-d(T10G15) / 10 mM unla-band number, we can extrapolate this result to the beled d(T15G15) ; (6) 10 mM unlabeled d(T10G15) and 2.5

nM 32P-d(T15G15) ; (7) 10 mM 32P-d(T10G15) .other lower mobility bands observed on the gels

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Behavior by Multistranded G-Rich DNA 431

these two possibilities we exposed the complexesto methylation for times ranging from 30 s to 3 h.The reaction with DMS was followed by digestionof the methylated product with piperidine. If thecomplexes are reasonably homogeneous structuresin which the guanines are uniformly accessible tomethylation, then we would expect the molecularweight of the piperidine digestion products to shiftprogressively to lower molecular weights. Con-versely, if the guanine accessibility arises from het-erogeneously aggregated structures, then the DMSwill react with the exposed N7s and the others willremain unreacted. In this case, increasing the timethat the complexes are exposed to DMS should notlead to significant changes in the reaction products.

FIGURE 4 Influence of cations on the ability of Examination of the effect of different methylationd(T15G4T2G4) and d(T15G12) to form high molecular times shows that there is a shift of the digestedweight aggregated structures. Native 10% gel at 47C species to lower molecular weights (Figure 6). Thisshowing banding pattern of oligomers after polymeriza- suggests that all the guanines in d(T15G12) com-tion in aqueous solution containing different cations. (1)

plexes are accessible to methylation.d(T15G4T2G4) in 1M MgCl2; (2) d(T15G4T2G4) in 1MKCl; (3) d(T15G12) in 1M MgCl2; (4) d(T15G12) in 1MKCl. Methylation Interference

We next assessed the ability of methylated oligonu-cleotides to form aggregated complexes using prod-Methylation Protectionucts from the methylation reaction not subjected to

The single-stranded oligonucleotides d(T15G4T2G4), cleavage with piperidine. After methylation, single-d(T15G12) , d(T15G15) , and their complexes were stranded d(T15G12) retained its ability to polymerizereacted with the guanosine N7 methylating reagentdimethylsulfate (DMS). High molecular weightstructures not destabilized by the methylation reac-tion were isolated on a native gel at 47C, elutedfrom the gel, and then analyzed in a denaturinggel. The complexes formed by d(T15G4T2G4) in thepresence of K/ protected all the guanine bases frommethylation (Figure 5). In contrast, all twelve gua-nines in the high molecular weight complexes ofd(T15G12) were susceptible to methylation. We ob-served the same result independent of whether K/

or Mg2/ was employed as the cation (Figure 5).Similar results were observed for d(T15G15) (resultsnot shown).

The accessibility of all of the guanines ind(T15G12) complexes toward methylation could bedue to heterogeneously aggregated structures—forexample, through the formation of unpaired G-loopsrandomly along the G-quartet tract. In heteroge-neous structures, DMS would react with whichever

FIGURE 5 Accessibility of guanines to methylation.guanine was exposed to the solvent and it would Banding pattern of oligonucleotides following guanineappear as if all the guanines were uniformly accessi- methylation and electrophoresis in a denaturing 20% gel.ble. A second possible origin of the uniform accessi- (1) d(T15G4T2G4) monomer; (2) d(T15G4T2G4) com-bility of guanines is that they are associated in a plexes with 1M KCl; (3) d(T15G12) monomer; (4)conformation in which the N7 groups are exposed d(T15G12) complexes with 1M MgCl2; (5) d(T15G12)

monomer; (6) d(T15G12) complexes with 1M KCl.to the solvent. In an attempt to distinguish among

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432 Poon and Macgregor

FIGURE 6 The accessibility of guanines to methylation as a function of time of exposureto the methylating agent, DMS. Banding pattern and corresponding histogram of d(T15G12)complexes with 1M MgCl2 following different guanine methylation time and electrophoresisin a denaturing 20% gel. (1) 30 s; (2) 3 h.

in solutions containing either K/ or Mg2/ (Figure pears to be similar to that observed with the unmeth-ylated oligonucleotides at 5 nM strand concentra-7) . This was not true for d(T15G4T2G4) ; aggregated

species were not observed following methylation of tion; however, we did not quantitate the amount ofDNA after methylation. These results mirror thosethe single-stranded oligonucleotide (Figure 7). The

relative amount of aggregation after methylation ap- in methylation protection study.

DISCUSSION

As shown in Figure 2, d(T15G15) self-associates toform thermally stable high molecular weight spe-cies, a behavior similar to that recently reported ford(A15G15) .16 Replacing the 15 adenines with thy-mines does not qualitatively affect the polymeriza-tion. Addition of an oligonucleotide complementaryto the nonguanine portion, i.e., d(A15) , to thed(T15G15) complexes, resulted in binding to thehigh order structures of d(T15G15) without signifi-cant destabilization of the high molecular weightstructures (results not shown). This further con-firms that the guanines play the determining role in

FIGURE 7 Ability of methylated oligonucleotides to the self-assembly processes.form high molecular weight structures. Native 10% poly-

The formation of high molecular weight struc-acrylamide gel run at 47C showing the banding patterntures by oligonucleotides with several consecutiveof the methylated oligomers polymerized with differentguanines, such as d(A15G15) and d(T15G12) (NxGysalt solutions. (1) methylated d(T15G4T2G4) , 1M KCl;oligonucleotides) , is influenced by the temperature,(2) methylated d(T15G12) , 1M KCl; (3) methylatedinitial DNA concentration, as well as cations andd(T15G4T2G4) , 1M MgCl2; (4) methylated d(T15G12) ,

1M MgCl2. their concentrations. Guanine-rich telomeric se-

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Behavior by Multistranded G-Rich DNA 433

quences exhibit similar behavior.6,10 However, these these two molecules to form stabile complexes.These results imply that the two pairs of thyminestwo classes of oligonucleotides exhibit a marked

difference in the cation dependence of the com- at the 3 *-end play a role in the stabilization andformation processes, possibly by reducing the stericplexes they form. In the present study, comparing

the effect of either Mg2/ or K/ alone, we have clash between the tetraplex and single or double-stranded N29 regions.8,20 Based upon their data itshown that d(T15G12) forms high molecular weight

complexes in the presence of either cation at 907C, appears that telomeric sequences can accommodatelonger nonguanine portions in stable structures, per-whereas only K/ leads to the formation of com-

plexes by the telomere sequence of d(T15G4T2G4) . haps due to a greater conformational heterogeneity.Our laboratory has begun a systematic investigationHowever, Henderson and co-workers18 found that

high molecular aggregates of d(G4T2G4) form in of the role of the guanine and nonguanine bases inthe stabilization of high molecular weight aggre-the presence of K/ or Mg2/ . Comparison of the role

of these two ions in the stabilization of aggregated gates.The complexes formed by telomere-like oligonu-structures formed by d(T15G4T2G4) appears to un-

derscore the importance of the nonguanine bases at cleotides, however, are less thermally stable thanthose formed by contiguous guanine sequences:the 5 *-end. Previous studies have shown that K/ ,

because of its ionic radius, should be better than Complexes made from NxGy oligonucleotides re-main stabile under denaturing gel conditionsother cations such as Na/ or Mg2/ in terms of

stabilizing the tetraplex.19 However, we found that whereas complexes made from oligonucleotidescontaining telomere-like sequences do not. TheMg2/ offered the greatest enhancement of higher

order structure formation for NxGy oligonucleotides, work of Henderson et al. using telomeric sequencesfrom several organisms corroborates this finding.12especially at 377C (results not shown).

Although the nonguanine portion is not the de- Oligonucleotides consisting of repeats of the Tetra-hymena telomeric sequence, (T2G4)4 , displayed atermining factor in complex formation, it is im-

portant in the stability of the complexes. Sundquist well-defined reversible transition at about 407C. Wewould not expect complexes formed by these se-and Klug demonstrated this previously in experi-

ments using d(N29G12) ; the twelve consecutive gua- quences to be stable under the conditions of denatur-ing polyacrylamide gels (557C, 7M urea) . Althoughnines of this oligonucleotide do not favor formation

of stable high molecular weight structures.8 We there is a larger number of guanines involved in thestabilization of the high molecular weight structureshave found that decreasing the length of the nongua-

nine portion resulted in the formation of stabile formed by d(T2G4)4 , compared to d(T15G12) , thecomplexes formed by telomere-like oligonucleotidecomplexes by d(T15G12) . Thus, in light of Sund-

quist and Klug’s data it appears that the stability of are less stabile. Thus, the removal of thymineswithin the telomeric sequences significantly in-self-associated structures represents a balance be-

tween the favorable free energy of the guanine– creases the thermal stability of the high order com-plexes. Despite the implication of guanine quartetsguanine interactions and the unfavorable contribu-

tion of bases not involved in these interactions. It as a stabilization force in several different struc-tures, 1–9 there does not appear to be a direct correla-was previously reported that the high molecular

weight complexes formed by d(A15G15) were desta- tion between the fraction of guanine–guanine inter-actions and the stability of the complexes in thebilized through interactions with the partial comple-

mentary strand, d(C11T15) .16 The destabilization is present study.The goal of the methylation protection/interfer-likely due to the imbalance between favorable free

energy of the guanine–guanine interactions by the ence experiments was to investigate the conforma-tion of the guanines in the aggregates of NxGy oligos.four guanine bases at the 3*-end and the unfavorable

contribution of the remaining 26 bases engaged in If the complexes formed by NxGy oligonucleotidesarose through the formation of guanine quartets,complementary base pairing at the 5* extension.

Sundquist and Klug studied d(N29T2G4T2G4) and Hoogsteen hydrogen bonding between adjacentguanines within a tetrad should protect the N7 site ofd(N29G12) with the N29 region single stranded and

bound to a complementary oligonucleotide.8 The the guanine base from methylation.4 Such protectionhas been shown in various studies.4–6 However, we3 *-end of d(N29T2G4T2G4) is the sequence of the

Tetrahymena telomere. They showed that this oligo- found that all the guanines in complexes formed bythese oligonucleotides are accessible to methylationnucleotide forms high molecular weight aggregates

whereas d(N29G12) does not. Thus, the exchange of (Figures 5 and 6). Furthermore, methylated mono-mers retain their ability to aggregate (Figure 7),guanines and thymines modulates the ability of

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434 Poon and Macgregor

offering further evidence that the guanines in these tution or loss of nonguanine spacers within the te-lomeric region of a chromosome could significantlycomplexes do not adopt a standard guanine quartet

conformation. alter the behavior of the telomere. Such changesmight affect the binding to the telomeric bindingThe complexes formed by the two types of oligo-

nucleotides also differ in their molecularity. Oligo- proteins, as well as physically modify the self-as-sembly behavior of the telomeric DNA. This couldnucleotides with many consecutive guanines from

various complexes consisting of consecutive num- influence the biological function of the telomericregion of a chromosome.bers of strands, e.g., [d(T15G12)]x , x Å 1, 2, 3, 4,

rrrThe aggregated complexes of some telomericsequences, e.g., [d(NnT2G4T2G4)]x form complexes

REFERENCESconsisting of only 1, 2, and 4 strands (x Å 1, 2,4) , 6,8,20,21 while the complexes of other telomeric

1. Gellert, M., Lipsett, M. N. & Davies, D. R. (1962)sequences contain multiples of four strands.5,7 ThisProc. Natl. Acad. Sci. USA 48, 2013–2018.is further indication that the high molecular weight

2. Panyutin, I. G., Kovalsky, O. I. & Budowsky, E. I.structures arising from NxGy oligonucleotides adopt(1989) Nucleic Acids Res. 17, 8257–8271.

a conformation differentiating them from the com- 3. Lu, M., Guo, Q. & Kallenbach, N. R. (1993) Bio-plexes formed by telomere-like oligomers. chemistry 32, 598–601.

Although the work of Miura and Thomas22 using 4. Sen, D. & Gilbert, W. (1988) Nature 334, 364–366.Raman spectroscopy showed that the structures 5. Sen, D. & Gilbert, W. (1992a) Biochemistry 31, 65–formed by d(G12) were similar to that formed by a 70.

6. Sen, D. & Gilbert, W. (1990) Nature 344, 410–414.telomere-like oligomer, they also observed differ-7. Venczel, E. A. & Sen, D. (1993) Biochemistry 32,ences between these two types of G-rich sequences.

6220–6228.The d(G12) complexes exhibited a significant sup-8. Sundquist, W. I. & Klug, A. (1989) Nature 342,pression of imino exchange at N1-H in the interior

825–829.hydrogen bond of guanine quartet ( i.e., virtually9. Panyutin, I. G., Kovalsky, O. I., Budowsky, E. I.,complete protection from hydrogen/deuterium ex-

Dickerson, R. E., Rikhirev, M. E. & Lipanov, A. A.change). In their interpretation of these results, Mi- (1990) Biochemistry 87, 867–870.ura and Thomas proposed the existence of the tet- 10. Sen, D. & Gilbert, W. (1992b) Methods Enzymol.raplex in extraordinarily rigid structure that differs 211, 191–199.from the G-quartet observed in telomeric se- 11. Laughlan, G., Murchie, A. I. H., Norman, D. G.,quences.22 In our present study, the single-stranded Moore, M. H., Moody, P. C. E., Lilley, D. M. J. &

Luisi, B. (1994) Science 265, 520–524.thymines are added to the G-rich complexes formed12. Henderson, E., Hardin, C. C., Walk, S. K., Tinoco,by d(T15G12) and d(T15G15) , the unexpected prop-

I., Jr. & Blackburn, E. H. (1987) Cell 51, 899–908.erties for N7 sites not required in hydrogen bonding13. Gottschling, D. & Zakian, V. A. (1986) Cell 47,are likely due to structural changes arising from the

195–205.presence of the 5* nonguanine extensions.14. Kirk, K. E., Harmon, B. P., Reichardt, I. K., Sedat,The data we have presented suggest the existence

J. W. & Blackburn, E. H. (1997) Science 275, 1441–of a multistranded DNA structure with guanine in- 1443.teractions that differ from those of the guanine tet- 15. Hawley, R. S. (1997) Science 275, 1478–1481.raplex. Among the distinguishing properties of these 16. Protozanova, E. & Macgregor, R. B., Jr. (1996) Bio-structures are the stabilization by magnesium ions, chemistry 35, 16638–16645.the extreme thermal stability, the stoichiometry, the 17. Maxam, A., & Gilbert, W. (1980) Methods Enzymol.

65, 499–560.methylation protection pattern, and the ability of18. Marsh, T. C., Vesenka, J., & Henderson, E. (1995)methylated oligonucleotides to form complexes. We

Nucleic Acids Res. 23, 696–700.have not directly investigated the minimum number19. Hardin, C. C., Watson, T., Corregan, M. & Bailey,of consecutive guanines necessary to stabilize these

C. (1992) Biochemistry 31, 833–841.structures; however, 12 are sufficient. Alternative20. Hardin, C. C., Henderson, E., Watson, T. & Prosser,models, other than tetraplex formation, for the self-

J. K. (1991) Biochemistry 30, 4460–4472.interaction of guanines has been proposed.23 How- 21. Wang, Y. & Patel, D. J. (1992) Biochemistry 31,ever, we are still in the process of collecting more 8112–8119.evidence for the nature of these structures before 22. Miura, T. & Thomas, G. J., Jr. (1995) Biochemistryproposing a more-detailed model. 34, 9645–9654.

The extreme stability of these complexes may 23. Suda, T., Mashima, Y., Asakura, H. & Kominami,R. (1995) Nucleic Acids. Res. 23, 3771–3777.have biological implications insofar as base substi-

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