Self‐Assembly of DNA–Peptide Supermolecules: Coiled‐Coil Peptide Structures Templated by d‐DNA and l‐DNA Triplexes Exhibit Chirality‐Independent but Orientation‐Dependent Stabilizing Cooperativity

Abstract

DNA nanostructures have been designed and used in many differenta pplications.H owever,t he use of nucleic acid scaffolds to promote the self-assembly of artificial protein mimicsi so nly starting to emerge. Herein five coiledcoil peptide structures were templatedb yt he hybridization of a d-DNA triplex or its mirror-image counterpart, an l-DNA triplex.T he self-assembly of the desiredt rimeric structures in solutionw as confirmed by gel electrophoresis and smallangle X-ray scattering,a nd the stabilizing synergyb etween the two domains was found to be chirality-independent but orientation-dependent. This is the first example of using a nucleic acid scaffold of l-DNA to template the formation of artificial protein mimics. The results may advance the emerging POC-basedn anotechnology field by adding two extra dimensions, that is, chirality and polarity,t op rovide innovative molecular tools forr ational design and bottom-up construction of artificial protein mimics, programmable materials and responsive nanodevices.[a] Dr.[a] Thermal denaturation and annealing temperatures (T m and T a values) of POC and ON-reference triple helixes measured at pH 5.5 as an average of three independent melting temperature determinations shownw ith the corresponding standard deviations. The values in brackets are T m and T a values measured for the corresponding underlying duplexes. The experiments werer ecorded at 275 nm in 10 mm acetate buffer( NaOAc/HOAc)c ontaining1 00 mm NaCl. The concentration of the individual duplex components was 1.0 mm while the TFO component was used in 1.5 mm concentration. The peptide moiety is marked in yellowa nd red (l-peptidea sr ight-handed helix, d-peptidea sl eft-handedh elix), the TFO moiety in dark blue (d-nucleotide) or light blue (l-nucleotide),a nd the DNA duplexm oiety in crimson (d-nucleotide) or in orange (l-nucleotide).

Chirality transmission in macromolecular domains

“…Design and synthesis of POC. DNA helices were chosen as the first set of macromolecular helical domain, while two mirrorimaged coiled-coil peptide tertiary structures 30 were employed as another set of macromolecular helical domains derived from coil-V a L d 33 . A series of linker lengths were introduced between the oligonucleotide triplex and the peptide tertiary structures, including 16 bonds, 21 bonds, 24-25 bonds, 30-31 bonds, 35-36 bonds and 44-45 bonds, each counting as the shortest path from 5′-/3′-position (5′-NH/3′-NH or 5′-O/3′-O) of the oligonucleotide (ON) triplex to the N-termini (NH of Tyr) of the peptide (Fig.…”

“…The two peptides, L-azidopeptide and D-azidopeptide , were synthesized through solid-phase peptide synthesis 30 . For the ON triplex, automated DNA synthesis were carried out for eighteen ONs (see Supplementary Discussion ).…”

“…The reduced mechanical stability was interpreted as a minority of DNA duplex formation being perturbed as the result of the TFO injection. In the next experiment, we replaced the DNA triplex template with three POC strands to assemble the chimeric POC triplex where the formation of the DNA triple helix, and the trimeric peptide coiled-coil were cooperative 30 . This chimeric supramolecular complex D,D-POC(1 + 2 + 3) showed much stronger mechanical stability (23.2 pN, Fig.…”

“…Overall, we observed facile binding of the third POC strand to the POC duplex system, likely due to the templated binding effect in which conjugated peptide-oligonucleotide geometry significantly increased the effective concentration of either peptide or oligonucleotide. The sandwiched triple-stranded linker region (24–25 bonds) was previously found to be packed tightly for both L-peptide/D-DNA and D-peptide/L-DNA triple helices 30 , giving rise to a torsionally constrained intersection between two macromolecular domains. In analogy to the helical sense mismatch in the B-Z DNA junctions, when the two torsionally constrained, covalently conjugated macromolecular domains adopt opposite inter-strand helical senses, they may result in a less stable macromolecular state (Fig.…”

“…1). The DNA triplex, composed of a triplex-forming oligonucleotide (TFO) binding to the major groove of a duplex DNA, has shown to facilitate peptide coiled-coil self-assembly [30][31][32] . To achieve this templating effect, each peptide strand was conjugated with a DNA strand, resulting in a peptide-oligonucleotide-conjugate (POC) in which the length of the interdomain linker can be varied.…”