Long promoter sequences form higher-order G-quadruplexes: an integrative structural biology study of c-Myc, k-Ras and c-Kit promoter sequences.

Monsen RC, DeLeeuw LW, Dean WL, Gray RD, Chakravarthy S, Hopkins JB, Chaires JB, Trent JO
Nucleic Acids Res (2022 Mar 23)

PMID: 35325198 doi: 10.1093/nar/gkac182

Submitted to SASBDB: 2021 Oct 5 Published in SASBDB: 2022 Mar 25

SASDMJ6 – cMyc-8 Sample: CMyc promoter 8-tract G-quadruplex monomer, 11 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Feb 19 RgGuinier 1.4 nm Dmax 4.6 nm VolumePorod 13 nm3

SASDMM6 – cMyc-12 Sample: CMyc promoter 12-tract G-quadruplex monomer, 23 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 22 RgGuinier 2.3 nm Dmax 8.4 nm VolumePorod 29 nm3

SASDM36 – c-Myc12 DnaseI Treated G-quadruplex Sample: C-Myc 12-tract G-quadruplex monomer Dnase I treated monomer, 22 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Sep 29 RgGuinier 2.0 nm Dmax 6.7 nm VolumePorod 25 nm3

SASDMK6 – cKit-8 Sample: CKit promoter 8-tract G-quadruplex monomer, 12 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Feb 19 RgGuinier 1.5 nm Dmax 4.7 nm VolumePorod 15 nm3

SASDMN6 – cKit-12 Sample: CKit promoter 12-tract G-quadruplex monomer, 20 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Mar 22 RgGuinier 2.5 nm Dmax 9.0 nm VolumePorod 26 nm3

SASDM46 – c-Kit12 DNase I Digest Sample: C-Kit 12-tract G-quadruplex monomer Dnase I treated monomer, 20 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Sep 29 RgGuinier 1.6 nm Dmax 5.7 nm VolumePorod 16 nm3

SASDML6 – kRas-8 Sample: KRas promoter 8-tract G-quadruplex monomer, 14 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Feb 19 RgGuinier 1.7 nm Dmax 5.6 nm VolumePorod 16 nm3

SASDM56 – 2KZD Sample: TERT promoter G-quadruplex antiparallel monomer, 6 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Aug 13 RgGuinier 1.2 nm Dmax 3.6 nm VolumePorod 7 nm3

SASDM76 – 201D Sample: DNA oligonucleotide G4(T4G4)3 monomer, 9 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Aug 12 RgGuinier 1.3 nm Dmax 4.1 nm VolumePorod 10 nm3

SASDM86 – 6GH0 Sample: CKIT 2-tetrad promoter GQ antiparallel monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 21 RgGuinier 1.0 nm Dmax 3.1 nm VolumePorod 8 nm3

SASDM96 – 2GKU Sample: Human telomere 24mer hybrid-1 monomer, 8 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Aug 11 RgGuinier 1.2 nm Dmax 3.8 nm VolumePorod 8 nm3

SASDMA6 – 5I2V Sample: KRas promoter GQ hybrid monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 20 RgGuinier 1.3 nm Dmax 4.9 nm VolumePorod 10 nm3

SASDMB6 – 6L92 Sample: WNT promoter GQ hybrid form monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 21 RgGuinier 1.2 nm Dmax 3.9 nm VolumePorod 8 nm3

SASDMC6 – 2KQG Sample: CKit promoter GQ parallel monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 20 RgGuinier 1.6 nm Dmax 3.2 nm VolumePorod 14 nm3

SASDMD6 – 2LBY Sample: CMyc promoter GQ parallel monomer, 6 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 20 RgGuinier 1.2 nm Dmax 3.9 nm VolumePorod 7 nm3

SASDME6 – 6NEB Sample: CMyc promoter GQ 1:6:1 loop parallel monomer, 9 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 20 RgGuinier 1.4 nm Dmax 4.5 nm VolumePorod 10 nm3

SASDMF6 – 1XAV Sample: CMyc promoter modified GQ parallel monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Aug 11 RgGuinier 1.3 nm Dmax 4.1 nm VolumePorod 9 nm3

SASDM66 – 2KZE Sample: TERT promoter G-quadruplex parallel monomer, 6 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2021 Aug 11 RgGuinier 1.3 nm Dmax 4.2 nm VolumePorod 8 nm3

SASDMG6 – 5CMX Sample: Two-tetrad antiparallel GQ with duplex junction monomer, 10 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Oct 3 RgGuinier 1.5 nm Dmax 5.2 nm VolumePorod 12 nm3

SASDMH6 – 2M27 Sample: VEGF promoter GQ parallel monomer, 7 kDa synthetic construct DNA Buffer: 6 mM Na2HPO4, 2 mM NaH2PO4, 1 mM Na2EDTA, 185 mM KCl, pH: 7.2 Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2020 Nov 20 RgGuinier 1.3 nm Dmax 3.8 nm VolumePorod 8 nm3