ABSTRACT
DNA from Space ...................................................................................................... 7 1.3 Desorption Techniques ......................................................................................................... 8
1.3.1 MALDI-TOF-MS Technique .................................................................................... 8 1.3.1.1 MALDI-TOF-MS Characterization of Nucleosides .................................. 8 1.3.1.2 MALDI-TOF-MS Characterization of Nucleotides ................................... 9 1.3.1.3 Characterization of Oligonucleotides ...................................................... 10 1.3.1.4 MALDI-TOF-MS Characterization of RNA-Protein Complexes ........... 24 1.3.1.5 Atmospheric Pressure MALDI-FT-ICR-MS
Characterization of RNA-Protein Complexes ......................................... 24 1.3.1.6 MALDI-TOF-MS Characterization of DNA Adducts ............................. 25
1.3.2 Surface-Enhanced Laser Desorption/Ionization (SELDI)-TOF-MS ...................... 25 1.3.3 MS/MS Analysis of Oligonucleotides .................................................................... 26
1.3.3.1 AP-MALDI-FT-ICR-MSn of Normal and Chemically Modi ed RNA ......................................................................................... 27
1.3.3.2 RNA Fragmentation in MALDI-TOF-TOF-MS/MS Studied by H/D Exchange ........................................................................ 28
1.3.4 Secondary Ion Mass Spectrometry ......................................................................... 29 1.3.5 Liquid Secondary Ion Mass Spectrometry ............................................................. 30
1.4 Spray Ionization Techniques ............................................................................................... 31 1.4.1 Electrospray Ionization ........................................................................................... 31
1.4.1.1 ESI-MS Characterization of Nucleosides ................................................ 32 1.4.2 ESI-MS Characterization of Nucleotides ............................................................... 33
1.4.2.1 Analysis of Nucleotides in Champagne ................................................... 33 1.4.2.2 Determination of Nucleotides in Biomimicking
Prebiotic Synthesis ................................................................................... 33
1.4.2.3 Determination of Nucleotides on PressureAssisted Capillary Electrophoresis .......................................................... 34
1.4.2.4 HPLC-ESI-MS Quanti cation of Nucleotides ......................................... 34 1.4.3 ESI-MS Characterization of DNA Adducts ........................................................... 35
1.4.3.1 Enediyne-DNA Adducts .......................................................................... 35 1.4.3.2 Etheno-DNA Adducts .............................................................................. 36 1.4.3.3 Base-Alkylated Adducts .......................................................................... 36 1.4.3.4 LC-MS Analysis of Oxidized Damaged
Bases on Nucleotides ............................................................................... 36 1.4.4 ESI-MS Genotyping of SNPs ................................................................................. 37 1.4.5 ESI-MS Characterization of Oligonucleotides ....................................................... 39
1.4.5.1 Practical Aspects of Oligonucleotides Analysis ...................................... 39 1.4.5.2 ESI-MS Analysis of Synthetic Oligonucleotides ..................................... 41 1.4.5.3 ESI-MS Oligonucleotides Sequencing ..................................................... 41 1.4.5.4 Combined ESI-MS Analyses of DNA
Oligonucleotides and DNA Adducts ........................................................ 41 1.4.6 ESI-MS Characterization of PCR Products ........................................................... 42 1.4.7 ESI-MS Characterization of Covalent or Noncovalent DNA and
RNA Complexes ..................................................................................................... 42 1.4.7.1 ESI-MS Characterization of Covalent DNA Complexes ......................... 42 1.4.7.2 ESI-MS Characterization of Noncovalent DNA Complexes ................... 44 1.4.7.3 ESI-MS Characterization of Noncovalent Complexes of
Peptides and Double-Stranded DNA ....................................................... 45 1.4.7.4 ESI-MS Characterization of Complexes of
Actinomycin D and Oligonucleotides ...................................................... 46 1.4.7.5 ESI-MS Characterization of Complexes of
Ribonuclease A and Cytidylic Acid Ligands ........................................... 46 1.4.7.6 ESI-MS Characterization of Complexes of
Platinum(II) and Nucleobases .................................................................. 46 1.4.7.7 ESI-MS Characterization of DNA Triplexes ........................................... 47 1.4.7.8 ESI-MS Characterization of RNA Noncovalent Interactions .................. 47 1.4.7.9 ESI-MS Characterization of RNA Duplexes ........................................... 49 1.4.7.10 Interaction of Cisplatin with DNA ........................................................... 50
1.4.8 Charge Detection ESI-MS ...................................................................................... 50 1.4.9 Atmospheric Pressure Photoionization MS ............................................................ 50
1.5 Tandem Mass Spectrometry ............................................................................................... 51 1.5.1 FAB-MS/MS ........................................................................................................... 51
1.5.1.1 FAB-MS/MS Characterization of Nucleosides ....................................... 51 1.5.1.2 FAB-MS/MS Characterization of Nucleotides ........................................ 52
1.5.2 ESI-MS/MS ............................................................................................................ 53 1.5.2.1 MS/MS Characterization of Nucleosides ................................................ 53 1.5.2.2 MS/MS Characterization of Ribonucleosides ......................................... 58 1.5.2.3 MS/MS Characterization of Geometric
Deoxynucleoside Adducts ........................................................................ 58 1.5.2.4 MS/MS Characterization of Nucleotides ................................................. 59 1.5.2.5 CID-MS/MS Sequencing of Small Oligonucleotides .............................. 60 1.5.2.6 MS/MS Characterization of DNA Complexes ........................................ 62 1.5.2.7 MS/MS Characterization of DNA Adducts ............................................. 63
1.5.3 ESI-FT-ICR-MSn Mapping Noncovalent Ligand Binding to Stemloop Domains of the HIV-1 Packaging Signal ............................................... 66
1.6 Novel Mass Analyzers ........................................................................................................ 66
1.6.1 Characterization of DNA Noncovalent Complexes Using LTQ-Orbitrap Hybrid Mass Spectrometer ............................................................. 67
1.6.2 Ion Mobility Spectrometry ..................................................................................... 67 1.6.2.1 Matrix-Assisted Laser-Desorption Ionization Followed
by Ion Mobility Separation and Time-of-Flight Mass Analysis (MALDI-IM-TOF-MS) ................................................... 68
1.7 Summary ............................................................................................................................ 68 References .................................................................................................................................... 68
Nucleic acids and their components play an important role in a variety of fundamental biological processes.1 The elucidation of the molecular structure of DNA in 1953 by Watson and Crick led to the so-called central dogma of molecular biology.2 This dogma proclaims that DNA is transcribed to form a messenger RNA (mRNA) of a complementary sequence that directs its own replication, and the sequence of nucleobases in the RNA is then translated to the corresponding sequence of amino acids to form a protein.2 In addition to mRNA, two other RNA species, transfer RNA (tRNA) and ribosomal RNA (rRNA), are required for this translation process. Nucleic acid research has consequently had a most profound impact on molecular biology, initiating an avalanche of new disciplines. The eld of genomics has evolved over the last few years, culminating in the sequencing and characterization of the entire human genome.3 Current challenges include the unraveling of the relationship between the genome and the proteome. The genome can be used to predict the total potential proteome, including all of the modi cations that can be carried out after the initial translation from mRNA to protein. Mass spectrometry (MS) has had a major role in elucidating the regulatory mechanism involved in the progression from gene to functional protein.4
