From solution to a solvent-free environment: Probing the structures of noncovalently bound DNA and RNA complexes

Although DNA and RNA noncovalently bound complexes have been investigated with mass spectrometry for over ten years, a prevailing question is whether any solution phase structural features are retained once the solvent is removed. To address this question, a variety of different DNA and RNA noncovalently bound complexes were studied with mass spectrometry, ion mobility and theoretical calculations. Ions for each complex were formed by either nano-ESI or MALDI and their collision cross sections were measured using ion mobility methods. Conformational information was obtained by generating theoretical structures with molecular mechanics/dynamics calculations and comparing the theoretical cross sections to the experimental values.; A variety of DNA secondary structures, such as duplexes, G-quadruplexes, hairpins, cruciforms and pseudoknots, are discussed in this dissertation. Double-stranded DNA is prevalent in vivo, so DNA duplexes were analyzed first. To begin understanding the Watson-Crick pairing of a duplex, dinucleotides were studied with a series of metal cations. Watson-Crick pairing was observed in the dinucleotide duplexes with certain metal cations, so DNA duplexes from 4 to 30 base pairs (bp) in length were examined. In the solution phase, a majority of DNA duplexes are organized into B-form helices. However, in solvent-free conditions the duplexes from 4 to 18 bp converted to A-form helices, while sequences longer than 18 bp retain their B-DNA conformations.; Although DNA helices are the most abundant form of DNA secondary structures, a wide variety of conformations such as G-quadruplexes, hairpins, pseudoknots and cruciforms have been implicated in the regulation of transcription, aging and cancer. DNA G-rich telomeric and promoter region sequences were examined with and without salt and found to form stable G-quadruplexes in both conditions. DNA hairpin, pseudoknot and cruciform structures were also analyzed and found to exist in the solvent-free environment. While hairpins and cruciforms are only a small percentage of DNA conformations, they are a large percentage of RNA secondary structures, so RNA hairpins and cruciforms were studied. Stable RNA hairpin and cruciform complexes were observed without solvent. Aminoglycoside antibiotics were then added to the RNA complexes to understand the conformational changes observed upon their binding.