Thermodynamics of melting of the circular dumbbell d<pCGC-TT-GCG-TT>

Extracellular DNA secreted in yeast cultures is metabolism-specific and inhibits cell proliferation

Extracellular DNA (exDNA) can be actively released by living cells and different putative functions have been attributed to it. Further, homologous exDNA has been reported to exert species-specific inhibitory effects on several organisms. Here, we demonstrate by different experimental evidence, including 1H-NMR metabolomic fingerprint, that the growth rate decline in Saccharomyces cerevisiae fed-batch cultures is determined by the accumulation of exDNA in the medium. Sequencing of such secreted exDNA represents a portion of the entire genome, showing a great similarity with extrachromosomal circular DNA (eccDNA) already reported inside yeast cells. The recovered DNA molecules were mostly single strands and specifically associated to the yeast metabolism displayed during cell growth. Flow cytometric analysis showed that the observed growth inhibition by exDNA corresponded to an arrest in the S phase of the cell cycle. These unprecedented findings open a new scenario on the functional role of exDNA produced by living cells.

High-Resolution Structures of DNA Minidumbbells Comprising Type II Tetraloops with a Purine Minor Groove Residue

Minidumbbell (MDB) is a newly discovered DNA structure formed by native sequences, which serves as a possible structural intermediate causing repeat expansion mutations in the genome and also a functional structural motif in constructing DNA-based molecular switches. Until now, all the reported MDBs containing two adjacent type II tetraloops were formed by pyrimidine-rich sequences 5'-YYYR YYYR-3' (Y and R represent pyrimidine and purine, respectively), wherein the second and sixth residues folded into the minor groove and interacted with each other. In this study, we have conducted a high-resolution nuclear magnetic resonance (NMR) spectroscopic investigation on alternative MDB-forming sequences and discovered that an MDB could also be formed stably with a purine in the minor groove, which has never been observed in any previously reported DNA type II tetraloops. Our refined NMR solution structures of the two MDBs formed by 5'-CTTG CATG-3' and 5'-CTTG CGTG-3' reveal that the sixth purine residue was driven into the minor groove via base-base stacking with the second thymine residue and adenine stacked better than guanine. The results of our present research work expand the sequence criteria for the formation of MDBs and shed light to explore the significance of MDBs.

An Extraordinarily Stable DNA Minidumbbell

The minidumbbell (MDB) is a new type of native DNA structure. At neutral pH, two TTTA or CCTG repeats can fold into the highly compact MDB with a melting temperature of ∼22 °C. Owing to the relatively low thermodynamic stability, MDBs have been proposed to be the structural intermediates that lead to efficient DNA repair escape and thus repeat expansions. In this study, we reveal that two CCTG repeats can also form an extraordinarily stable MDB with a melting temperature of ∼46 °C at pH 5.0. This unusual stability predominantly results from the formation of a three hydrogen bond C⁺·C mispair between the two minor groove cytosine residues. Due to the drastic stability change, the CCTG MDB, when combined with its complementary sequence, shows instant and complete structural conversions when the pH switches between 5.0 and 7.0, making the system serve as a simple and efficient pH-controlled molecular switch.

The competing mini-dumbbell mechanism: new insights into CCTG repeat expansion

CCTG repeat expansions in intron 1 of the cellular nucleic acid-binding protein gene are associated with myotonic dystrophy type 2. Recently, we have reported a novel mini-dumbbell (MDB) structure formed by two CCTG or TTTA repeats, which potentially has a critical role in repeat expansions. Here we present a mechanism, called the competing MDB mechanism, to explain how the formation of MDB can lead to efficient mismatch repair (MMR) escape and thus CCTG repeat expansions during DNA replication. In a long tract of CCTG repeats, two competing MDBs can be formed in any segment of three repeats. Fast exchange between these MDBs will make the commonly occupied repeat behave like a mini-loop. Further participations of the 5'- or 3'-flanking repeat in forming competing MDBs will make the mini-loop shift in the 5'- or 3'-direction, thereby providing a pathway for the mini-loop to escape from MMR. To avoid the complications due to the formation of hairpin conformers in longer CCTG repeats, we made use of TTTA repeats as model sequences to demonstrate the formation of competing MDBs and shifting of mini-loop in a long tract of repeating sequence.

Structures and stabilities of small DNA dumbbells with Watson-Crick and Hoogsteen base pairs

The structures and stabilities of cyclic DNA octamers of different sequences have been studied by NMR and CD spectroscopy and by restrained molecular dynamics. At low oligonucleotide concentrations, some of these molecules form stable monomeric structures consisting of a short stem of two base pairs connected by two mini-loops of two residues. To our knowledge, these dumbbell-like structures are the smallest observed to date. The relative stabilities of these cyclic dumbbells have been established by studying their melting transitions. Dumbbells made up purely of GC stems are more stable than those consisting purely of AT base pairs. The order of the base pairs closing the loops also has an important effect on the stabilities of these structures. The NMR data indicate that there are significant differences between the solution structures of dumbbells with G-C base pairs in the stem compared to those with A-T base pairs. In the case of dumbbells with G-C base pairs, the residues in the stem form a short segment of a BDNA helix stabilized by two Watson-Crick base pairs. In contrast, in the case of d<pCATTCATT>, the stem is formed by two A-T base pairs with the glycosidic angles of the adenine bases in a syn conformation, most probably forming Hoogsteen base pairs. Although the conformations of the loop residues are not very well defined, the thymine residues at the first position of the loop are observed to fold back into the minor groove of the stem.

Solution structure of a DNA three-way junction containing two unpaired thymidine bases. Identification of sequence features that decide conformer selection

The solution structure of a DNA three-way junction (3H) containing two unpaired thymidine bases at the branch site (3HT2), was determined by NMR. Arms A and B of the 3HT2 form a quasi-continuous stacked helix, which is underwound at the junction and has an increased helical rise. The unstacked arm C forms an acute angle of approximately 55 degrees with the unique arm A. The stacking of the unpaired thymidine bases on arm C resembles the folding of hairpin loops. From this data, combined with the reported stacking behavior of 23 other 3HS2 s, two rules are derived that together correctly reproduce their stacking preference. These rules predict, from the sequence of any 3HS2, its stacking preference. The structure also suggests a plausible mechanism for structure-specific recognition of branched nucleic acids by proteins.

Efficient synthesis of DNA dumbbells using template-induced chemical ligation in double-stranded polynucleotides closed by minihairpin fragments

The chemical ligation of 17 50-54-membered nicked DNA dumbbells with different closing fragments, nick positions, and nucleotides facing the nick were investigated. T4, T5, GTA4C, GCGA2GC, and GCGA3GC sequences were chosen as the closing fragments. The nicks were placed in the center of the duplex stem or were adjacent to the closing fragments. N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide and cyanogen bromide were used as the condensing agents. We showed that the ligation efficiency is 10%-90% depending on the sequence of the closing fragments, nick position, and nucleotides facing the nick. Coupling yields of 80%-90% were observed when the nick was situated in the middle of the molecule between two T residues or was adjacent to GCGA2GC or GCGA3GC minihairpins. In the last case, the reacting 3'-phosphate and 5'-hydroxy groups were brought close together by only two base pair minihairpins. The coupling yields did not depend on the nature of the condensing agent. On the basis of the results obtained, we believe a rational design of nicked DNA dumbbells has been developed for efficient chemical synthesis of closed dumbbells.

Anti-Syn conformational range of pyrimidines with deoxyribofuranose

The ability of pyrimidine bases to adopt the syn conformation in DNA has been investigated. The distances between atoms on the sugar and base and the resulting steric energies have been calculated as a function of glycosidic torsion angle for the principal sugar puckers of the deoxyribose of cytosine. The results indicate that pyrimidines can assume both the anti and syn conformations for the 3E, 4E, 1E, 2E, 3E sugar puckers and syn for the 2E sugar pucker. For these sugar puckers the difference between the minimum energies of the anti and syn conformations is in the range of 0.1-2.0 kcal/mole, with the minimum syn energy being lower in the case of the 4E, 1E and 2E sugar puckers. It is particularly significant that cytosine can assume the syn conformation for the 3E sugar pucker commonly observed for the syn nucleotides in Z-DNA with both alternating pyrimidine/purine (APP) and non-APP sequences. The results of this investigation confirm that steric interactions resulting from putting a pyrimidine nucleotide in the syn conformation are not a major factor in the preference for APP base sequences in Z-DNA.

Three-way and four-way junctions in DNA: a conformational viewpoint

DNA junctions are potential intermediates in various important genetic processes, including mutagenesis and recombination. The quantity of research carried out in this area is rapidly increasing. Examples of three-way and four-way junctions are now relatively well characterized and a few common properties have been recognized, of which the most important is the tendency of junctions to fold into one or more coaxially stacked helical conformations or cross-over structures.