Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Å resolution

Abstract

The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of the ribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 Å, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti)·A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.

GC-Content Dependence of Elastic and Overstretching Properties of DNA:RNA Hybrid Duplexes

“…However, the persistent lengths obtained from this new fitting show no clear dependence on GC contents but decrease as the NaCl concentration increases (as expected) within the range of the experimental conditions we explored (see Table S3). Together, these results support that DRH adopts a conformation between Aand B-form helices (15)(16)(17)(18)(19)(20)(21)(22), and its structural and elastic properties do not exhibit an obvious dependence on GC contents when they vary from 40 to 60%. It is also worth mentioning that, in our experiments, the measured persistence lengths for DRH of 52% GC content are larger than that of the control dsDNA with the same length ($2.8 kb) and sequence (Tables 1 and S2).…”

“…To date, most studies have focused on the conformation and thermodynamic stability of DRH through ensemble measurements (15)(16)(17)(18)(19)(20)(21)(22). Several DRH structures were solved by using x-ray diffraction (15,16,22) and NMR (17), suggesting that DRH adopts a conformation between A-and B-form helices, which also varies depending on the specific sequences and relative humidity (1).…”

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

“…The X-ray crystallography shows hybrids closely matching the Aform duplexes, including the C3′-endo pucker and χ anti base conformation for both strands. [8][9][10][11][12][13] In contrast, the NMR solution experiments suggest a population split between A-and Bforms, [14][15] pointing to a mixed population of C2′-endo and C3′-endo sugar puckers in the DNA strand of the hybrids, with concomitant χ anti/high-anti transitions. [16][17][18][19][20] Overall, there is a notable degree of ambiguity in the experimental structural characterization of DNA/RNA hybrids, a situation which could be greatly improved by well-executed computational studies.…”

Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes

“…The hybrids are also formed during CRISPR gene editing , and they have promising applications in nanotechnology. − Structurally, the hybrids form classical right-handed double helices, but the major structural biology methods somewhat disagree on the details of their geometries. The X-ray crystallography shows hybrids closely matching the A-form duplexes, including the C3′-endo pucker and χ anti base conformation for both strands. − In contrast, the NMR solution experiments suggest a population split between A- and B-forms, , pointing to a mixed population of C2′-endo and C3′-endo sugar puckers in the DNA strand of the hybrids, with concomitant χ anti/high-anti transitions. − Overall, there is a notable degree of ambiguity in the experimental structural characterization of DNA/RNA hybrids, a situation which could be greatly improved by well-executed computational studies.…”