title: Higher-order structure of nucleic acids in the gas phase: top-down analysis of base-pairing interactions.
abstract: Non-ergodic as well as ergodic activation methods are capable of maintaining the integrity of base pairs during the top-down analysis of nucleic acids. Here, we investigate the significance of this characteristic in the investigation of higher-order structures of increasing complexity. We show that cognate fragments produced by typical backbone cleavages may not be always detected as separate sequence ions, but rather as individual products that remain associated through mutual pairing contacts. This effect translates into unintended masking of cleavage events that take place in double-stranded regions, thus leading to the preferential detection of fragments originating from unpaired regions. Such effect is determined by the stability of the weak non-covalent association between complementary stretches, which is affected by base composition, length of the double-stranded structure, and charge of the precursor ion selected for analysis. Although such effect may prevent the achievement of full sequence coverage for primary structure determination, it may provide the key to correctly differentiate double- versus single-stranded regions, in what could be defined as gas-phase footprinting experiments. In light of the critical role played by base pairs in defining the higher-order structure of nucleic acids, these approaches will be expected to support an increased utilization of mass spectrometry for the investigation of nucleic acid structure and dynamics.
authors.affiliation: The RNA Institute, University at Albany.
authors.forename: D
authors.initials: D
authors.lastname: Fabris
authors.forename: K A
authors.initials: KA
authors.lastname: Kellersberger
authors.forename: J A
authors.initials: JA
authors.lastname: Wilhide
keywords: ECD; EDD; IRMPD; Top-down; base-pairing; higher-order structure; nucleic acids
references.citation: J Am Soc Mass Spectrom. 1996 Sep;7(9):923-9
references.pmid: 24203606
references.citation: Anal Bioanal Chem. 2006 Oct;386(3):675-81
references.pmid: 16855815
references.citation: J Am Soc Mass Spectrom. 1992 Sep;3(6):599-614
references.pmid: 24234564
references.citation: J Am Soc Mass Spectrom. 1998 Jul;9(7):683-91
references.pmid: 9879378
references.citation: J Am Soc Mass Spectrom. 2002 Jan;13(1):91-8
references.pmid: 11777205
references.citation: Mass Spectrom Rev. 1996;15(2):67-138
references.pmid: 27082318
references.citation: Biopolymers. 2009 Apr;91(4):283-96
references.pmid: 18946871
references.citation: Rapid Commun Mass Spectrom. 2001;15(1):8-14
references.pmid: 11135418
references.citation: Anal Chem. 2007 Mar 1;79(5):2067-77
references.pmid: 17249688
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9528-33
references.pmid: 15210983
references.citation: J Mol Biol. 2007 Jun 8;369(3):812-28
references.pmid: 17466332
references.citation: Biochemistry. 2009 Jul 28;48(29):6988-97
references.pmid: 19449839
references.citation: J Am Soc Mass Spectrom. 2007 Jun;18(6):984-90
references.pmid: 17383194
references.citation: J Am Soc Mass Spectrom. 2006 Oct;17(10):1402-1411
references.pmid: 16872834
references.citation: J Am Chem Soc. 1998 Sep 23;120(37):9605-13
references.pmid: 16498487
references.citation: Anal Chem. 2005 Mar 15;77(6):1876-82
references.pmid: 15762599
references.citation: J Am Soc Mass Spectrom. 2008 Dec;19(12):1832-40
references.pmid: 18799321
references.citation: J Am Soc Mass Spectrom. 1995 Oct;6(10):972-5
references.pmid: 24214041
references.citation: Nucleic Acids Res. 2008 May;36(8):2799-810
references.pmid: 18400780
references.citation: J Am Soc Mass Spectrom. 2002 Aug;13(8):936-45
references.pmid: 12216734
references.citation: J Mol Biol. 2007 Jan 12;365(2):396-410
references.pmid: 17070549
references.citation: Anal Biochem. 1987 Aug 15;165(1):175-82
references.pmid: 3688431
references.citation: Angew Chem Int Ed Engl. 2003 Oct 20;42(40):4900-4
references.pmid: 14579433
references.citation: J Am Soc Mass Spectrom. 2000 May;11(5):450-7
references.pmid: 10790849
references.citation: Annu Rev Phys Chem. 1999;50:517-36
references.pmid: 10575730
references.citation: J Am Chem Soc. 2001 Oct 10;123(40):9792-9
references.pmid: 11583540
references.citation: J Am Soc Mass Spectrom. 1992 Jan;3(1):60-70
references.pmid: 24242838
references.citation: J Am Soc Mass Spectrom. 2009 Feb;20(2):176-9
references.pmid: 18835725
references.citation: J Mass Spectrom. 2001 Apr;36(4):397-402
references.pmid: 11333443
references.citation: Curr Opin Struct Biol. 2006 Jun;16(3):279-87
references.pmid: 16713707