back calculated data agree with experimental NOESY spectrum
Representative
Model #1
closest to the average
-
Components
#1: DNA chain
5'-D(*GP*TP*GP*CP*GP*(CTG)P*GP*TP*TP*TP*GP*T)-3'
Mass: 3749.425 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain
5'-D(*AP*CP*AP*AP*AP*CP*GP*CP*GP*CP*AP*C)-3'
Mass: 3625.397 Da / Num. of mol.: 1 / Source method: obtained synthetically
-
Experimental details
-
Experiment
Experiment
Method: SOLUTION NMR Details: When base paired with guanine, exchange between Tg isomers cis-5R,6S-TG and trans-5R,6R-TG was not observed. In addition, the TG can pucker so that the CTG CH3 is in an axial or equatorial ...Details: When base paired with guanine, exchange between Tg isomers cis-5R,6S-TG and trans-5R,6R-TG was not observed. In addition, the TG can pucker so that the CTG CH3 is in an axial or equatorial conformation. This entry is the cis-5R,6S-TG lesion opposite dG with TG CH3 in an axial conformation
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-1H NOESY
1
2
1
2D 1H-1H COSY
2
3
2
2D 1H-1H NOESY
1
4
1
2D 31P-1H COSY
-
Sample preparation
Details
Solution-ID
Contents
Solvent system
1
20 mM sodium phosphate-1, 100 mM sodium chloride-2, 10 uM sodium azide-3, 50 uM EDTA-4, 100% D2O
100% D2O
2
20 mM sodium phosphate-5, 100 mM sodium chloride-6, 10 uM sodium azide-7, 50 uM EDTA-8, 90% H2O/10% D2O
90% H2O/10% D2O
Sample
Conc. (mg/ml)
Component
Solution-ID
20mM
sodium phosphate-1
1
100mM
sodium chloride-2
1
10uM
sodium azide-3
1
50uM
EDTA-4
1
20mM
sodium phosphate-5
2
100mM
sodium chloride-6
2
10uM
sodium azide-7
2
50uM
EDTA-8
2
Sample conditions
Conditions-ID
Ionic strength
pH
Pressure (kPa)
Temperature (K)
1
0.1
7.0
ambient
303K
2
0.1
7.0
ambient
278K
-
NMR measurement
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker Avance
Bruker
AVANCE
800
1
Bruker Avance
Bruker
AVANCE
600
2
-
Processing
NMR software
Name
Developer
Classification
Amber
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... andKollm
Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 10
+
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