STRUCTURE SUMMARY FOR B-DNA'S WITH SPECIAL FEATURES ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- BD0006 5'- B DOUBLE HELIX OVERHANGING BASES, N N N D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3' BASE TRIPLET BD0008 CROSSLINKED 5'- B DOUBLE HELIX INTER-STRAND Y N N D(*CP*GP*CP*GP*AP*(SSP)AP*TP*TP*CP* CROSSLINK GP*CP*G)-3' BD0014 5'- B DOUBLE HELIX FLIPPED-OUT BASES N N N D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP *G)-3' BD0016 5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3' B DOUBLE HELIX OVERHANGING BASES, N N N BASE TRIPLET BD0017 5'- B DOUBLE HELIX BASE TRIPLET, Y N N D(*CP*(BRO)UP*CP*CP*(BRO)UP*CP*CP*G FLIPPED-OUT BASES, P*CP*GP*CP*G)-3', 5'- OVERHANGING BASES D(*CP*GP*CP*GP*CP*GP*GP*AP*G)-3' BD0018 5'- B DOUBLE HELIX OVERHANGING BASES N N N D(*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G) -3' BD0019 5'- B DOUBLE HELIX OVERHANGING BASES N N N D(*GP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP *G)-3' BD0020 5'- B DOUBLE HELIX FLIPPED-OUT BASES N N N D(*CP*GP*CP*GP*AP*AP*(TAF)P*TP*CP*G P*CP*G)-3' BD0022 5'- B DOUBLE HELIX SHIFTED BASE PAIRS N N Y D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP *A)-3', 5'- D(*TP*GP*TP*GP*GP*CP*GP*CP*CP*GP*GP *T)-3' BD0027 5'- B DOUBLE HELIX FLIPPED-OUT BASES Y N Y D(*CP*CP*GP*AP*AP*(BRO)UP*GP*AP*GP* G)-3' BD0032 5'- B DOUBLE HELIX FLIPPED-OUT BASES N N N D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP *G)-3' BD0037 5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3' B DOUBLE HELIX OVERHANGING BASES, N N N BASE TRIPLET BD0056 5'- B DOUBLE HELIX OVERHANGING BASES N N N D(*TP*GP*GP*CP*CP*TP*TP*AP*AP*GP*G) -3' BD0061 5'- B DOUBLE HELIX FLIPPED-OUT N N N D(*CP*GP*CP*GP*AP*AP*TP*TP*(EDC)P*G TERMINAL BASES P*CP*G)-3' BD0069 5'-D(*GP*AP*AP*TP*TP*CP*G)-3' B DOUBLE HELIX FLIPPED-OUT BASES, N N N OVERHANGING BASES BD0070 5'- B DOUBLE HELIX FLIPPED-OUT BASES N N N D(*CP*GP*CP*TP*GP*GP*AP*AP*AP*TP*TP *TP*CP*CP*AP*GP*C)-3' BDF062 5'-D(*CP*GP*GP*TP*GP*G)-3', B DOUBLE HELIX OPEN BASE PAIR N N N SPERMINE BDF068 5'-D(*CP*TP*CP*GP*AP*G)-3' B DOUBLE HELIX A-DNA LIKE N N N CONFORMATION AT TERMINI BDL021 5'- B DOUBLE HELIX NICKED N N N D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP *G)-3'/ 5'-D(*CP*GP*CP*GP*TP*T)- 3'+ 5'-D(*TP*TP*CP*GP*CP*G)-3', MODEL A4 BDL032 5'- B DOUBLE HELIX NICKED N N N D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP *G)-3'/ 5'-D(*CP*GP*CP*GP*TP*T*)- 3'+ 5'-D(*TP*TP*CP*GP*CP*G)-3', MODEL T4 ----------------------------------------------------------------------------------------------------------------------------- Page 1 created by the NDB Project on Wed May 26 14:33:02 2004 STRUCTURE SUMMARY FOR B-DNA'S WITH SPECIAL FEATURES ----------------------------------------------------------------------------------------------------------------------------- NDB ID Descriptor Type NA Description Special Features Base Mod. Phosph.Mod. Mispair ----------------------------------------------------------------------------------------------------------------------------- BDL034 5'- B DOUBLE HELIX SHIFTED BASE PAIR N N N D(*AP*CP*CP*GP*GP*CP*GP*CP*CP*AP*CP *A)-3',-15 C DD0062 5'-D(*CP*GP*TP*AP*CP*G)-3', 9- B DOUBLE HELIX FLIPPED-OUT BASES N N N amino-[N-(2-dimethylamino)proply]- acridine-4-carboxamide UD0012 PEPTIDYL-D(CGCAATTGCG) B DOUBLE HELIX FLIPPED-OUT BASES N N N UD0023 5'- B DOUBLE HELIX HOLIDAY JUNCTION N N N D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3' UD0024 CCGGTACCGG B DOUBLE HELIX HOLIDAY JUNCTION, N N N UD0025 5'- B DOUBLE HELIX HOLLIDAY JUNCTION N N N D(*CP*CP*GP*GP*TP*AP*CP*CP*GP*G)-3' UD0026 5'- B DOUBLE HELIX HOLLIDAY JUNCTION N N N D(*TP*CP*GP*GP*TP*AP*CP*CP*GP*A)-3' UD0028 5'- B DOUBLE HELIX FLIPPED-OUT BASES N N N D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3' UD0030 5'- B DOUBLE HELIX OVERHANGING BASES N N N D(*CP*CP*AP*GP*TP*AP*CP*(BRU)P*GP*G )-3' UDH052 5'-CD(*P*AP*TP*TP*CP*AP*TP*TP*C)-3' B QUADRUPLE HELIX CYCLIC, BI-LOOP N N N UDI030 5'-D(*GP*CP*GP*AP*AP*TP*TP*CP*G)-3' B DOUBLE HELIX BASE TRIPLET, N N N OVERHANGING BASE UDI047 5'-D(*GP*CP*GP*TP*AP*CP*GP*CP*G)-3' B DOUBLE HELIX BASE TRIPLET, N N N OVERHANGING BASE UDJ031 5'- B DOUBLE HELIX FLIPPED-OUT BASE, N N N D(*CP*GP*CP*AP*AP*TP*TP*GP*CP*G)-3' BASE TRIPLET UDJ048 5'- B DOUBLE HELIX OVERHANGING BASE, N N N D(*CP*GP*AP*CP*GP*AP*TP*CP*GP*T)-3' CONTINUOUS HELIX UDJ049 5'- B DOUBLE HELIX BASE TRIPLET, N N N D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3' OVERHANGING BASE UDJ060 5'- B DOUBLE HELIX OVERHANGING BASE, N N N D(*CP*GP*AP*CP*GP*AP*TP*CP*GP*T)-3' CONTINUOUS HELIX UDM010 5'- B DOUBLE HELIX BULGE, FLIPPED-OUT N N N D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP BASE *CP*G)-3' UDM017 5'- B DOUBLE HELIX BULGE N N N D(*CP*GP*CP*AP*GP*AP*AP*TP*TP*CP*GP *CP*G)-3', SOAKED W/PROFLAVIN UDO009 5'- B DOUBLE HELIX BULGE N N N D(*CP*GP*CP*GP*AP*AP*AP*TP*TP*TP*AP *CP*GP*CP*G)-3' ----------------------------------------------------------------------------------------------------------------------------- Page 2 created by the NDB Project on Wed May 26 14:33:02 2004