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

Minidumbbell: A New Form of Native DNA Structure

The non-B DNA structures formed by short tandem repeats on the nascent strand during DNA replication have been proposed to be the structural intermediates that lead to repeat expansion mutations. Tetranucleotide TTTA and CCTG repeat expansions have been known to cause reduction in biofilm formation in <i>Staphylococcus aureus</i> and myotonic dystrophy type 2 in human, respectively. In this study, we report the first three-dimensional minidumbbell (MDB) structure formed by natural DNA sequences containing two TTTA or CCTG repeats. The formation of MDB provides possible pathways for strand slippage to occur, which ultimately leads to repair escape and thus expansion mutations. Our result here shows that MDB is a highly compact structure composed of two type II loops. In addition to the typical stabilizing interactions in type II loops, MDB shows extensive stabilizing forces between the two loops, including two distinctive modes of interactions between the minor groove residues. The formation of MDB enriches the structural diversity of natural DNA sequences, reveals the importance of loop–loop interactions in unusual DNA structures, and provides insights into novel mechanistic pathways of DNA repeat expansion mutations

Formation of a DNA Mini-Dumbbell with a Quasi-Type II Loop

Quasi-loops, wherein the backbone has a discontinuous site in the loop, have been found to provide structural flexibility in the formation of DNA three-way junctions. Recently, a highly compact mini-dumbbell (MDB) structure composed of two adjacent CCTG or TTTA type II loops has been reported. Yet, it remains elusive if the presence of a quasi-loop will also facilitate the formation of an MDB. In this study, the possibility of whether an MDB can be formed containing a quasi-type II loop has been investigated. We first demonstrate that two adjacent CTTG type II loops can also form an MDB, which is thermodynamically more stable than those formed by CCTG and TTTA loops. Then, we systematically introduce quasi-type II loops with their discontinuous sites at different backbone positions in the CTTG MDB. Our results show that an MDB can be formed with a quasi-type II loop, in which there is a discontinuous site between the third thymine and the fourth guanine loop residues. The possible inclusion of a quasi-loop in MDBs expands the sequence criteria for the formation of MDBs by natural DNA sequences

Close view of different projections of antennal sensory pathways in the brain, gnathal ganglion, and prothoracic ganglion.

<p>(A) Three-dimensional reconstruction model showing the antennal sensory pathway (indicated by arrows) in the brain, GNG, and proTG in a ventral view. (B) Three-dimensional reconstruction model showing antennal sensory pathways (indicated by arrows) in the brain, GNG, and proTG in a lateral view. (C) Three-dimensional reconstruction model showing different tracts of antennal sensory pathway in the brain, GNG, and proTG in a ventral view. (D) Three-dimensional reconstruction model showing different tracts of antennal sensory pathways in the brain, GNG, and proTG in a lateral view. (E-I) Confocal image of the GNG and proTG with different tracts of antennal sensory pathway at different depths. (E) 12 μm. (F) 21 μm. (G) 30 μm. (H) 39 μm. (I) 48 μm. GNG, gnathal ganglion; proTG, prothoracic ganglion. Directions: a, anterior; d, dorsal; l, lateral; p, posterior, v, ventral. Scale bars: 100 μm.</p

Confocal images of the antennal lobe with staining of antennal sensory neurons.

<p>(A) Confocal image of the AL showing the innervation of antennal sensory neurons throughtout the AL. (B-E) Confocal images of the AL with staining of antennal sensory neurons at different depths. (B) 18 μm. (C) 33 μm. (D) 45 μm. (E) 57 μm. AN, antennal nerve; AL, antennal lobe; AMMC, antennal mechanosensory and motor center; ES, esophagus. Directions: a, anterior; m, medial. Scale bars: 100 μm.</p

The central nervous system of <i>A</i>.<i>lucorum</i>.

<p>(A) Diagram of the body of <i>A</i>. <i>lucorum</i> showing the location and composition of the central nervous system (CNS). (B) Confocal image of the section showing the location and composition of the CNS in the body of <i>A</i>. <i>lucorum</i>. (C) Dissected CNS with all ganglia. AN, antennal nerve; AL, antennal lobe; Br, brain; CNS, central nervous system; Con, connective; ES, esophagus; GNG: gnathal ganglion; OL, optic lobe; PG, posterior ganglion; proTG, prothoracic ganglion. Directions: a, anterior; d, dorsal; l, lateral; p, posterior, v, ventral. Scale bars: 1 mm in A, 100 μm in B and C.</p

Close view of projections of antennal sensory pathway in posterior ganglion.

<p>(A) Three-dimensional reconstruction of the PG with axons of antennal sensory neurons (ventral view). (B) Three-dimensional reconstruction model of the posterior ganglion with axons of antennal sensory neurons (lateral view). (C) Confocal image of the PG at the depth of 45 μm showing axons of antennal sensory neurons (indicated by arrows) in the mesoTG and metaTG. (D) Confocal image of the PG at the depth of 51 μm showing axons of antennal sensory neurons (indicated by an arrow) in the AG. AG, abdominal ganglion; mesoTG, mesothoracic ganglion; metaTG, metathroacic ganglion. Directions: a, anterior; d, dorsal; l, lateral; p, posterior, v, ventral. Scale bars: 100 μm.</p

Confocal images and three-dimensional reconstructions of the antennal lobe glomeruli.

<p>(A-F) Confocal images of AL sections at different depths. (A) 14 μm. (B) 22 μm. (C) 32 μm. (D) 40 μm. (E) 48 μm. (F) 56 μm. (G-L) Three-dimensional reconstructions of the AL in different views. (G) anterior view. (H) posterior view. (I) dorsal view. (J) ventral view. (K) lateral view. (L) medial view. ALG, antennal lobe glomerulus; AN, antennal nerve; cb, cell body cluster. Stars indicate AL hub. Directions: a, anterior; d, dorsal; l, lateral; m, medial; p, posterior; v, ventral. Scale bars = 50 μm.</p

Three-dimensional reconstructions including antennal sensory pathways in the central nervous system.

<p>(A) Three-dimensional reconstruction model of the CNS in a ventral view. (B) Three-dimensional reconstruction model of the CNS in a lateral view. (C) Confocal image showing the antennal sensory pathway in the CNS. (D) Three-dimensional reconstruction model showing the antennal sensory pathway (indicated by arrows) in the CNS in a ventral view. (E) Three-dimensional reconstruction model showing the antennal pathway in the CNS in a lateral view. (F) Three-dimensional reconstruction of tracts of antennal sensory neurons in a ventral view. (G) Three-dimensional reconstruction of tracts of antennal sensory neurons in a lateral view. AG, abdominal ganglion; AN, antennal nerve; AL, antennal lobe; AMMC, antennal mechanosensory and motor center; Con, connective; ES, esophagus; GNG: gnathal ganglion; mesoTG, mesothoracic ganglion; metaTG, metathoracic ganglion; OL, optic lobe; PE, protocerebrum; PG, posterior ganglion; proTG, prothoracic ganglion; TR, tritocerebrum. Directions: a, anterior; d, dorsal; l, lateral; p, posterior, v, ventral. Scale bars: 100 μm.</p

Additional file 1 of Comparative physiological and coexpression network analyses reveal the potential drought tolerance mechanism of peanut

Additional file 1