Abstract
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.
Highlights
Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) can both form short secondary structural folds known as hairpin loops
We have investigated the temperature-dependent conformation of DNA and RNA hairpin loops by temperature Replica Exchange Molecular Dynamics (REMD)
Both DNA and RNA clearly exhibit two-statelike temperature transitions, as indicated by the radius of gyration and virtual Forster Resonance Energy Transfer (FRET) intensity, the actual conformational ensembles contain significantly different structures, even at room temperature
Summary
Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) can both form short secondary structural folds known as hairpin loops. Hairpin loops form in single-stranded nucleic acids and consist of a base-paired stem and a loop sequence with unpaired nucleotide bases. Hairpins occur when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop.[1] The resulting structure is a key building block of many folded secondary structures found in nature, such as ribozymes (RNA enzymes) and messenger-RNA.[2]. Nucleic acids are ubiquitous in modern biological phenomena. RNA is involved in the building of ribosomes, in protein synthesis, and in regulatory mechanisms. Viruses are primitive entities containing DNA or RNA, while viroids are merely RNA fragments
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