Table 1:

Frequent protein-oligonucleotide hydrogen bonds made in either the A3Bctd-ssDNA or ssDNA-rC simulations. Colors indicate frequency of hydrogen bonds (% of frames in which bonds occur). Dark red: 0%, light red: 1–33%, yellow: 34–66%, green: 67+%.

Hydrogen Bond	TTCATG	TTrCATG C2’ endo	TTrCATG C3’ endo
−1 T 3-position NH - Asp314 sidechain O	94%	86%	0%
−1 T 3-position NH - Asp316 sidechain O	0%	0%	96%
−1 T 2-position O - Tyr 315 backbone NH	51%	59%	0%
Target C sugar O2’ - Thr214 sidechain OH	N/A	3%	94%
Target C sugar O2’H - His253 sidechain Nε	N/A	18%	0%
Target C sugar O3’ - Asn240 sidechain NH	22%	42%	0%
Target C sugar O4’ - Thr214 sidechain OH	89%	74%	0%
Target C 2-position O - Ala254 backbone NH	95%	76%	0%
Target C 3-position amine - Ser282 backbone C=O	96%	85%	93%
Target C 3-position amine - Glu255 sidechain O	85%	35%	0%
+ 1 A 3-position N - Arg212 sidechain guanidinium	21%	17%	42%