A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards

Biochemistry. 2008 Jul 8;47(27):7147-57. doi: 10.1021/bi800375m. Epub 2008 Jun 13.

Abstract

Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Pairing / drug effects*
  • Base Sequence
  • Calorimetry
  • Cations
  • Cross-Linking Reagents / pharmacology*
  • Crystallization
  • DNA / chemistry*
  • DNA / genetics
  • Deoxyguanine Nucleotides / chemistry
  • Deoxyguanine Nucleotides / pharmacology
  • Deoxyuridine / analogs & derivatives*
  • Deoxyuridine / metabolism
  • Molecular Sequence Data
  • Nitrogen Mustard Compounds / pharmacology*
  • Nucleic Acid Conformation / drug effects*
  • Nucleic Acid Heteroduplexes / metabolism
  • Static Electricity
  • Thermodynamics
  • Transition Temperature / drug effects
  • Water / chemistry*

Substances

  • Cations
  • Cross-Linking Reagents
  • Deoxyguanine Nucleotides
  • Nitrogen Mustard Compounds
  • Nucleic Acid Heteroduplexes
  • Water
  • 2'-deoxy-7-deazaguanosine triphosphate
  • 5-(3-aminopropyl)-2'-deoxyuridine
  • DNA
  • Deoxyuridine

Associated data

  • PDB/2QEF
  • PDB/2QEG