Erin Shammel Baker

G-quadruplex DNA assemblies: loop length, cation identity, and multimer formation.

G-rich DNA sequences are able to fold into structures called G-quadruplexes. To obtain general trends in the influence of loop length on the structure and stability of G-quadruplex structures, we studied oligodeoxynucleotides with random bases in the loops. Sequences studied are dGGGW(i)GGGW(j)GGGW(k)GGG, with W = thymine or adenine with equal probability, and i, j, and k comprised between 1 and 4. All were studied by circular dichroism, native gel electrophoresis, UV-monitored thermal denaturation, and electrospray mass spectrometry, in the presence of 150 mM potassium, sodium, or ammonium cations. Parallel conformations are favored by sequences with short loops, but we also found that sequences with short loops form very stable multimeric quadruplexes, even at low strand concentration. Mass spectrometry reveals the formation of dimers and trimers. When the loop length increases, preferred quadruplex conformations tend to be more intramolecular and antiparallel. The nature of the cation also has an influence on the adopted structures, with K(+) inducing more parallel multimers than NH4(+) and Na(+). Structural possibilities are discussed for the new quadruplex higher-order assemblies.

DNA hairpin, pseudoknot, and cruciform stability in a solvent-free environment.

The secondary structures of DNA hairpins, pseudoknots and cruciforms are of great interest because of their possible role in materials applications and biological functions such as regulating transcription. To determine the stability of these structures, DNA sequences capable of forming each were analyzed with mass spectrometry, ion mobility, and molecular dynamics calculations. Nano-ESI mass spectra indicated that stoichiometries compatible with hairpin, pseudoknot, and cruciform structures were present. Ion mobility spectrometry (IMS) was utilized to obtain experimental collision cross sections for all complexes. These cross sections were compared with structures from molecular dynamics, and in all cases, the lowest-charge states could be matched with a structure for an intact hairpin, pseudoknot, or cruciform. However, as the charge states of the single-stranded hairpins and pseudoknots increased, their structures elongated, and all Watson-Crick pairs were broken.

3-Dimensional structural characterization of cationized polyhedral oligomeric silsesquioxanes (POSS) with styryl and phenylethyl capping agents

Abstract The 3-dimensional gas-phase conformations of polyhedral oligomeric silsesquioxanes (POSS), R 8 Si 8 O 12 , capped with styryl and phenylethyl substituents (R) and cationized by sodium were examined. MALDI was used to generate sodiated styryl–POSS (Na + Sty 8 T 8 ) and phenylethyl–POSS (Na + PhEt 8 T 8 ) ions and their collision cross-sections in helium were measured using ion mobility-based methods. Five distinct conformers with different collision cross-sections were experimentally observed for Na + Sty 8 T 8 while only one conformer was detected for Na + PhEt 8 T 8 . Theoretical modeling of Na + Sty 8 T 8 , using molecular mechanics/dynamics calculations, predicts three low-energy conformations. In each conformer, the Na + ion binds to four oxygens on one side of the SiO cage and the styryl groups extend away from the cage. However, different numbers of styryl groups “pair” together (forming 2, 3 or 4 pairs), yielding three different conformations. The calculated cross-sections of these conformers match the largest three cross-sections obtained from the ion mobility experiments (∼2% error). If, however, one or two of the styryl groups are rotated so that the phenyl groups are “ cis ” with respect to the Si atom on the cage (i.e., the SiCCC dihedral angle changes from 180 to 0°) two smaller conformers are predicted by theory whose cross-sections match the smallest two values obtained from the ion mobility experiments (1–2% error). Theoretical modeling of Na + PhEt 8 T 8 yields one low-energy conformation in which the Na + ion binds to one oxygen on the SiO cage and is sandwiched between two phenyl groups. The remaining phenylethyl groups fold toward the SiO cage, yielding a significantly more compact structure than Na + Sty 8 T 8 (∼20% smaller cross-section). The calculated cross-section of the predicted Na + PhEt 8 T 8 structure agrees very well with the experimental cross-section obtained from the ion mobility experiments (∼1% error).

Sodium stabilization of dinucleotide multiplexes in the gas phase

The aggregation and conformations of sodiated dinucleotides were studied in the gas phase. MALDI was used to generate [M − (n − 1)H + nNa]+ ions, yielding single-strand ions having n = 1–3, duplex ions with n = 1–7 and triplex ions with n = 3–10. Collision cross-sections of each sodiated complex were measured in helium using ion mobility based methods and compared to calculated cross-sections of theoretical structures generated by molecular mechanics/dynamics calculations. Three distinct single-strand conformers were observed: one with the nucleobases stacked, one with the planes oriented perpendicular to each other and one with the bases coplanar to each other. One conformer is observed for all of the duplexes except dTG·dTG, dGT·dGT and dTT·dTT (in which two conformers are observed depending on whether the guanine or thymine bases stack). For low values of n, the Na+ ions cluster around the two deprotonated phosphates. However, as n increases, the Na+ ions become more dispersed along the duplex. One conformer is also observed for all of the triplexes. For n = 3–6, three Na+ ions and the three phosphates form a quasi-planar ring with the additional Na+ ions resting above, below and in the middle of the ring. Cytosine and thymine also coordinate to the Na+ ions but adenine and guanine prefer to stack and do not coordinate to the Na+ ions in the ring. The addition of the seventh to tenth Na+ ions breaks the sodium-phosphate ring and the Na+ ions become scattered around the triplex. Differences between experimental and theoretical cross-sections (averaged over the lowest 5 kcal mol−1 structures) of each sodiated complex fell between 1–2%.