Table 2.
LNA 7-mer Oligonucleotide Gapmers with Sequence 5′-ATgtaGC-3′ and Specific Chirality of the Phosphorous Atoms
| LNA Oligonucleotides |
Relative Energya (eV) |
Dipole (Debye) |
Density (0.002 electrons/au3) |
Electrostatic Potential (83.68 kJ/mol) |
Electrostatic Potential (−83.68 kJ/mol) |
Distance (5′-O to 3′-O) (Å) |
Structure |
HOMO (eV) |
LUMO (eV) |
|||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Design and Sequence (5′ to 3′) | Area (Å2) | Accessible Area (Å2) | Area (Å2) | Accessible Area (Å2) | Area (Å2) | Accessible Area (Å2) | ||||||
| ATgtaGC: 6Rp | 0.96 | 33.68 | 1,802 | 876 | 2,159 | 1,040 | 1,135 | 214 | 34.7 | helical | −7.88 (A) | −0.39 |
| A-Sp-TgtaGC: 5Rp | 0.63 | 23.23 | 1,783 | 832 | 2,078 | 942 | 1,157 | 142 | 32.8 | helical | −7.98 (g) | −0.27 |
| AT-Sp-gta GC: 5Rp | 0.01 | 25.06 | 1,775 | 765 | 2,030 | 884 | 1,030 | 115 | 27.8 | helical | −7.97 (A) | −0.19 |
| ATg-Sp-taGC: 5Rp | 1.37 | 36.31 | 1,772 | 821 | 2,113 | 1,024 | 1,241 | 188 | 30.3 | helical | −7.82 (A) | −1.19 |
| ATgt-Sp-aGC: 5Rp | 0.73 | 29.73 | 1,793 | 853 | 2,067 | 971 | 1,102 | 185 | 22.5 | non helical | −7.91 (A) | 0.16 |
| ATgta-Sp-GC: 5Rp | 1.81 | 24.67 | 1,805 | 843 | 2,220 | 1,156 | 1,173 | 209 | 32.3 | helical | −7.69 (G) | −0.65 |
| ATgtaG-Sp-C: 5Rp | 2.39 | 34.35 | 1,812 | 856 | 2,182 | 1,067 | 1,256 | 219 | 32.9 | helical | −7.87 (A) | −0.46 |
| ATgtaGC: 6Sp | 1.26 | 33.16 | 1,659 | 668 | 2,045 | 843 | 1,100 | 240 | 14.5 | non helical | −7.88 (a) | −0.40 |
| A-Rp-TgtaGC: 5Sp | 1.24 | 27.94 | 1,739 | 747 | 2,040 | 941 | 1,166 | 183 | 24.4 | non helical | −8.14 (a) | −0.52 |
| AT-Rp-gtaGC: 5Sp | 0.00 | 61.30 | 1,759 | 820 | 2,172 | 1,140 | 1,447 | 441 | 26.3 | helical | −7.59 (g) | −0.80 |
| ATg-Rp-taGC: 5Sp | 0.68 | 5.81 | 1,734 | 756 | 1,989 | 819 | 1,150 | 116 | 20.4 | helical | −8.13 (G) | −0.27 |
| ATgt-Rp-aGC: 5Sp | 1.87 | 39.63 | 1,729 | 772 | 2,039 | 941 | 1,189 | 177 | 29.4 | helical | −7.99 (A) | −0.54 |
| ATgta-Rp-GC: 5Sp | 2.41 | 26.02 | 1,696 | 731 | 1,990 | 909 | 1,156 | 139 | 29.8 | helical | −8.18 (A) | −0.53 |
| ATgtaG-Rp-C: 5Sp | 1.62 | 30.37 | 1,763 | 762 | 1,997 | 908 | 1,115 | 239 | 30.2 | helical | −7.57 (G) | −0.60 |
The results are derived in HF-SCF calculations, with the basis set as 6-31G∗. The table includes the structures of the oligonucleotides, their relative energies, their dipole moments, and the distances between 5′-O and 3′-O. Also included are the energies of the HOMOs and LUMOs as well as the areas and accessible areas of the charge density and electrostatic potentials. The location of HOMO is indicated following the HOMO value.
a
All energies are relative to that of AT-Rp-gtaGC: 5Sp.