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D M Lilley

Publications and source records attributed to D M Lilley.

At least 109 records · Page 6Linked to original sources
PubMed1994

Uranyl photoprobing of a four-way DNA junction: evidence for specific metal ion binding.

Metal ions are very important in mediating the folding of nucleic acids, as exemplified by the folding of the four-way DNA junction into the stacked X-conformation. Uranyl ion-mediated photocleavage provides a method for the localization of high-affinity ion binding sites in nucleic acids, and we have applied this to the four-way DNA junction. We have made the following observations. (i) Uranyl ions (UO2(2+)) suppressed the reactivity of junction thymine bases against attack by osmium tetroxide, indicating that the uranyl ion induces folding of the junction into a stacked conformation. (ii) DNA located immediately at the point of strand exchange on the two exchanging strands was hypersensitive to uranyl photocleavage. The relative hypersensitivity was considerably accentuated when the photocleavage was carried out in the presence of citrate ions. This suggests the presence of a tight binding site for the uranyl ion in the junction. (iii) The same positions were significantly protected from uranyl cleavage by the presence of hexamminecobalt (III) or spermidine. These ions are known to induce the folded conformation of the four-way junction with high efficiency, suggesting a direct competition between the ions. By contrast, magnesium ions failed to generate a similar protection against photocleavage. These results suggest that the uranyl, hexamminecobalt (III) and spermidine ions compete for the same high affinity binding site on the junction. This site is located at the centre of the junction, at the point where the exchanging strands pass between the stacked helices. We believe that we have observed the first known example of a metal ion 'footprint' on a folded nucleic acid structure.

Base Sequence↗
PubMed1994

Tetraplex folding of telomere sequences and the inclusion of adenine bases.

Telomeres are required for eukaryotic chromosome stability. They consist of regularly repeating guanine-rich sequences, with a single-stranded 3' terminus. Such sequences have been demonstrated to have the propensity to adopt four-stranded structures based on a tetrad of guanine bases. The formation of an intramolecular foldback tetraplex is associated with markedly increased mobility in polyacrylamide. Most telomeric sequences are based either on a repeat of d(TnGGGG) or d(TnAGGG) sequences. We have used a combination 7-deazaguanine or 7-deaza-adenine substitution, chemical modification and gel electrophoresis to address the following aspects of intramolecular tetraplex formation. (i) Intramolecular tetraplex formation by d(TTTTGGGG)4 sequences is prevented by very low levels of 7-deazaguanine substitution. This confirms the important role of guanine N7 in the formation of the tetraplex. (ii) The sequences d(TTAGGG)4 and d(TTTTAGGG)4 fold into tetraplexes. By contrast, the electrophoretic behaviour of d(TTTTGGGA)4, d(TTTTAGAG)4 and d(TTTTGAGA)4 does not indicate formation of stable intramolecular tetraplexes under available conditions. (iii) Selective 7-deazaguanine and 7-deaza-adenine substitutions in d(TTTTAGGG)4 give results consistent with tetraplex folding by the formation of three G4 tetrads, with the adenine bases formally part of the single-stranded loops, where they probably interact with thymine bases. These results demonstrate that eukaryotic cells appear to have selected just those sequences that can adopt the tetraplex conformation for their telomeres, while those that cannot have been avoided. This suggests that the conformation may be significant in the function of the telomere, such as attachment to nuclear structures.

Adenine↗
PubMed1994

Mutational analysis of the DNA binding domain A of chromosomal protein HMG1.

We have mutated several residues of the first of the two HMG-boxes of mammalian HMG1. Some mutants cannot be produced in Escherichia coli, suggesting that the peptide fold is grossly disrupted. A few others can be produced efficiently and have normal DNA binding affinity and specificity; however, they are more sensitive towards heating and chaotropic agents than the wild type polypeptide. Significantly, the mutation of the single most conserved residue in the rather diverged HMG-box family falls in this 'in vitro temperature-sensitive' category, rather than in the non-folded category. Finally, two other mutants have reduced DNA binding affinity but unchanged binding specificity. Overall, it appears that whenever the HMG-box can fold, it will interact specifically with kinked DNA.

Amino Acid Sequence↗
PubMed1994

Molecular recognition of DNA structure by proteins that mediate genetic recombination.

The latter half of genetic recombination is mediated by proteins that recognise the structure of the four-way DNA junction, and manipulate this structure. In solution the four-way junction adopts a stacked X-structure in the presence of metal ions. The folding is brought about by the pairwise coaxial stacking of helices in a right-handed antiparallel X-shaped structure. The four-way junction is cleaved by structure-selective resolving enzymes that have been isolated from a wide variety of sources, from eubacteria and their phages through to mammals. In addition, another class of proteins accelerate the branch migration of the junction. These proteins all appear to be divisible into a component that recognises structure and another that carries out a reaction on the junction. Thus the ability of structure-selective binding to the four-way DNA junction is a key feature of enzymes important in genetic recombination.

Animals↗
PubMed1994

The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis.

The four-way DNA (Holliday) junction is an important postulated intermediate in the process of genetic recombination. Earlier studies have suggested that the junction exists in two alternative conformations, depending upon the salt concentration present. At high salt concentrations the junction folds into a stacked X structure, while at low salt concentrations the data indicate an extended unstacked conformation. The stereochemical conformation of the four-way DNA junction at low salt (low alkali ion concentration and no alkaline earth ions) was established by comparing the efficiency of fluorescence resonance energy transfer (FRET) between donor and acceptor molecules attached pairwise in three permutations to the 5' termini of the duplex arms. A new variation of FRET was implemented based upon a systematic variation of the fraction of donor labeled single strands. The FRET results indicate that the structure of the four-way DNA junction at low salt exists as an unstacked, extended, square arrangement of the four duplex arms. The donor titration measurements made in the presence of magnesium ions clearly show the folding of the junction into the X stacked structure. In addition, the FRET efficiency can be measured. The fluorescence anisotropy of the acceptor in the presence of Mg2+ during donor titrations was also measured; the FRET efficiency can be calculated from the anisotropy data and the results are consistent with the folded, stacked X structure.

Base Composition↗
PubMed1994

Topological promoter coupling in Escherichia coli: delta topA-dependent activation of the leu-500 promoter on a plasmid.

The leu-500 promoter of Salmonella typhimurium is activated in topA mutants. We have previously shown that this promoter can be activated on circular plasmids in a manner that depends on transcription and translation of the tetracycline resistance gene tetA and insertion of its product into the cell membrane. We have suggested that in the absence of enzymatic relaxation by topoisomerase I, the local domain of transcription-induced DNA supercoiling reaches a steady-state level that leads to the activation of the leu-500 promoter. In the present paper, we have shown that the leu-500 promoter may also be activated in Escherichia coli. Comparison of the closely related pair of E. coli strains DM800 (delta topA) and SD108 (topA+) shows that the activation is dependent on the presence of a null mutation in topA. We have also shown that activation of the plasmid-borne leu-500 promoter depends, as in S. typhimurium, on the function of an adjacent tetA gene, suggesting that membrane anchorage of the TetA peptide prevents dissipation of transcription-induced supercoiling by superhelical diffusion. The activity of the leu-500 promoter is boosted by placing a divergent tac promoter on the side opposite to tetA. The topoisomer distributions of these plasmids extracted from the cell have been analyzed. We find that when the parent plasmid pLEU500Tc, containing the leu-500 promoter upstream of the complete tetA gene, is extracted from E. coli DM800 (delta topA), the distribution of linking numbers is bimodal. There is a fraction with a lower level of supercoiling (mean linking difference approximately -0.05) that is constant for all plasmids extracted from either delta topA or topA+ cells. In addition, we observe a second fraction with highly negatively supercoiled DNA (mean linking difference approximately -0.09) only in DNA extracted from delta topA cells. The proportion of the oversupercoiled fraction correlates with the activity of the leu-500 promoter: it is strongly reduced when the tetA promoter is deleted or when translation of TetA is prematurely terminated, while it is increased when the strong tac promoter is present in cis. We suggest that this oversupercoiled fraction represents the proportion of plasmid molecules active in tetA transcription and that it is this supercoiling that activates the leu-500 promoter.

Antiporters↗
PubMed1993

Activation of the leu-500 promoter: a topological domain generated by divergent transcription in a plasmid.

The Salmonella typhimurium leu-500 promoter is active only in topA strains. In an earlier study (Chen, D., Bowater, R., Dorman, C., & Lilley, D. M. J. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 8784-8788), we showed that the activity of this promoter on a circular plasmid is a function of the transcription and translation of an adjacent tetA gene, and we suggested that the effect arises because of increased local negative superhelix density due to transcription (Liu, L. F., & Wang, J. C. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 7024-7027) initiated at the tetA promoter. In this study we show that translation of the 5' (N-terminal) section of tetA is required for activity of the leu-500 promoter, consistent with a requirement for membrane association of TetA. We have also shown the importance of a second transcription unit, the ampicillin resistance gene bla, in the activation of the leu-500 promoter. Thus the activity of the leu-500 promoter was reduced by partial deletion or premature termination of bla and was increased when the transcription of bla was boosted by the insertion of the stronger tac promoter. However, even in the latter situation the role of the tetA gene is dominant, and deletion of the tetA gene reduced activity of the leu-500 promoter to very low levels. These results suggest the existence of a topological domain defined by the divergent bla and tetA transcription units. Membrane insertion at tetA is essential to provide an anchorage point.(ABSTRACT TRUNCATED AT 250 WORDS)

Antiporters↗
PubMed1993

Structures of bulged three-way DNA junctions.

We have studied a series of three-way DNA junctions containing unpaired bases on one strand at the branch-point of the junctions. The global conformation of the arms of the junctions has been analysed by means of polyacrylamide gel electrophoresis, as a function of conditions. We find that in the absence of added metal ions, all the results for all the junctions can be accounted for by extended structures, with the largest angle being that between the arms defined by the strand containing the extra bases. Upon addition of magnesium (II) or hexamine cobalt (III) ions, the electrophoretic patterns change markedly, indicative of ion-dependent folding transitions for some of the junctions. For the junction lacking the unpaired bases, the three inter-arm angles appear to be quite similar, suggesting an extended structure. However, the addition of unpaired bases permits the three-way junction to adopt a significantly different structure, in which one angle becomes smaller than the other two. These species also exhibit marked protection against osmium addition to thymine bases at the point of strand exchange. These results are consistent with a model in which two of the helical arms undergo coaxial stacking in the presence of magnesium ions, with the third arm defining an angle that depends upon the number of unpaired bases.

Base Sequence↗
PubMed1993

T4 endonuclease VII cleaves DNA containing a cisplatin adduct.

T4 endonuclease VII is an enzyme that cleaves four-way junctions and other branched DNA structures. We now show that a DNA duplex containing a single cis-diammineplatinum (II) adduct at either GpG or ApG sequences is a good substrate for precise cleavage by this enzyme. The GpG platinated DNA was cleaved more efficiently than the equivalent ApG platinated DNA. A duplex containing a trans-diammineplatinum (II) adduct at a GpTpG sequence was refractory to cleavage. We suggest that local kinking of the helix due to the chemical modification by cis-dichlorodiammineplatinum (II) could be responsible for the sensitivity of the DNA to attack by endonuclease VII, in common with the structures of many other substrates for this enzyme. These results are in keeping with a general role for T4 endonuclease VII in the repair of DNA structure, and a mechanism of substrate recognition that is based on sensitivity to axial inclination.

Base Sequence↗
PubMed1993

Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer.

The efficiency of fluorescence resonance energy transfer (FRET) between fluorescein and rhodamine covalently attached to both 5' termini of a series of double-stranded DNA species (ranging from 8 to 20 bp) was measured. FRET efficiency varied with a dependence compatible with dye-to-dye distances (R) calculated on the basis of double-stranded B-DNA structure; the helical geometry of double-stranded DNA in solution is clearly evident. The experimental data were consistent with a 1/[1 + (R/R0)6] dependence of FRET efficiency characteristic for the Förster dipole-dipole mechanism. The thermal dissociation of the strands of the duplex DNA species can be followed by using FRET, and from these data we have been able to obtain enthalpies of duplex formation in good agreement with earlier measurements using alternative techniques. FRET measurements at very different salt concentrations can be accurately compared. We conclude that FRET is a reliable and valuable method for studying structure and conformational transitions in nucleic acids.

Base Sequence↗
PubMed1993

Conformational junctions between left-handed DNA in (dA-dT)16 and contiguous B-DNA in a supercoiled plasmid contain chemically reactive bases.

Alternating adenine-thymine sequences in supercoiled DNA may undergo a transition to the left-handed Z-conformation in the presence of Ni2+ ions and high Na+ concentrations [(1989) FEBS Lett. 243, 313-317]. In this work we have studied the junctions between B- and Z-conformations in a supercoiled plasmid containing a (dA-dT)16 insert, by means of chemical probing. We observed enhanced reactivity of bases at both ends of the alternating tract to chloro- and bromoacetaldehyde. The degree of chemical reactivity was found to increase with the level of negative supercoiling. Only individual bases were observed to be reactive in the B-Z junctions, consistent with tightly localized interfacial regions.

Acetaldehyde↗
PubMed1993

Nuclear magnetic resonance study of a deoxyoligonucleotide duplex containing a three base bulge.

The three-dimensional structures of a DNA oligonucleotide containing three extra unpaired adenosine residues (dGCCAGGAAATGGAC+dGTCCGACCTGGC) and that of the perfect duplex analogue (dGCCAGGTCGGAC+dGTCCGACCTGGC) have been studied in solution by 1H and 13C nuclear magnetic resonance. All non-exchangeable aromatic and H-1', H-2', H-2" sugar protons were assigned using standard assignment pathways for B-DNA. All cross-peaks within these pathways were present for the perfect duplex molecule as would be expected for a right-handed A or B-form duplex. However, a few cross-peaks which would be expected in the standard case are extremely weak in the nuclear Overhauser enhancement spectroscopy (NOESY) spectrum of the bulged duplex even at long mixing times (250 ms). For example, almost no cross-relaxation is observed between the H-6 proton of C22 and the H-1' of A21, directly across from the three base bulge. Yet the continuity of assignment pathways through the three base bulge argues against any discontinuous "looping out" of one or more of the extra adenosine residues. Double quantum-filtered correlated spectroscopy experiments demonstrate very little deviation from south sugar conformations for residues at or near the bulge. The perfect duplex contains three A.T basepairs as expected, resulting in three very intense T imino-AH2 cross-peaks in the H2O NOESY experiment. In contrast, only two such intense cross-peaks are observed in the same experiment using the bulged duplex sample. Assignments of the two T imino peaks using one-dimensional NOEs are consistent with disruption of the T.A base-pair immediately 3' to the bulge; this is consistent with our earlier observation of chemical reactivity at a T 3' to an An or Tn bulge. We also find evidence of disruption of the G.C base-pair immediately 5' to the bulge.

Base Sequence↗
PubMed1993

The four-way DNA junction: a fluorescence resonance energy transfer study.

Fluorescence resonance energy transfer (FRET) measurements on four-way DNA junctions have been carried out in order to analyze the global structure and its dependence on the concentration of several types of ions. The stereochemical arrangement of the four DNA helices that make up the four-way junction was established by a global comparison of the efficiency of FRET between donor and acceptor molecules attached pairwise in all possible permutations to the 5' termini of the duplex arms of the four-way structure. The results indicate that the four-way junction isomerizes from an unstacked extended square arrangement of the four duplex arms at low ion concentration to an antiparallel stacked X-structure as the salt is added. The ion-related conformational change progresses in a continuous non-cooperative manner as the ionic strength of the solution increases.

DNA, Recombinant↗
PubMed1992

NMR study of parallel-stranded tetraplex formation by the hexadeoxynucleotide d(TG4T).

Multistranded DNA structures based upon guanine association have been proposed to be important in the structure of chromosome telomeres and in immunoglobulin class switching. Nucleic acids containing runs of guanine bases form a number of structures in vitro, including fold-back structures (Fig. 1a) and parallel-stranded quadruplex structures in DNA and RNA. The features of fold-back structures have now been determined at high-resolution. The different structures are probably based on a tetrad of hydrogen-bonded guanine bases (Fig. 1b), with buffer conditions and sequence effects mediating isomerization between the different forms. Here we use NMR spectroscopy to investigate the solution structure of the complex formed by the hexadeoxynucleotide d(TG4T) in the presence of sodium ions. We have observed the formation of a parallel-stranded quadruplex containing hydrogen-bonded tetrads of guanine. The parallel-stranded form differs significantly from the fold-back form, with individual nucleotide conformations being closer to those of B-form DNA.

DNA↗