Base-paired Duplex Research Articles

Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex.

The structures of two crystal forms of the RNA 16-mer with the sequence GUGGUCUGAUGAGGCC, grown in the presence of a high concentration of sulphate ions, have been determined using synchrotron radiation at 1.4- and 2.0-A resolution. RNA with this sequence is known as one of the two strands of the noncleavable form of the hammerhead ribozyme. In both crystal structures, two G(syn)-G(anti) noncanonical base pairs are observed in the middle of a 14 base-pair (bp) duplex having 5'-dangling GU residues. Both structures contain sulphate anions interacting with the G-G bp stabilizing G in its syn conformation and bridging the two RNA strands. In both cases the interactions take place in the major groove, although the anions are accommodated within different helix geometries, most pronounced in the changing width of the major groove. In one structure, where a single sulphate spans both G-G pairs, the major groove is closed around the anion, while in the other structure, where each of the two G-G pairs is associated with a separate sulphate, the groove is open. This work provides the first examples of a G-G pair in syn-anti conformation, which minimizes the purine-purine clash in the center of the duplex, while utilizing its residual hydrogen bonding potential in specific interactions with sulphate anions.

Ground-State Recovery Following UV Excitation is Much Slower in G·C−DNA Duplexes and Hairpins Than in Mononucleotides

Excited states in double-stranded oligonucleotides containing G.C base pairs were studied by femtosecond transient absorption spectroscopy. Relaxation to the electronic ground state occurs about 10 times more slowly in the duplexes and hairpins studied on average than in the individual mononucleotides of G and C. Detection of long-lived excited states in G.C oligonucleotides complements the earlier observation of slow ground-state recovery in A.T DNA, showing that excited states with picosecond lifetimes are formed in DNAs containing either kind of base pair. The results show further that Watson-Crick G.C base pairs in these base-paired and base-stacked duplexes do not enable subpicosecond relaxation to the electronic ground state. A model is proposed in which fluorescent exciton states decay rapidly and irreversibly to dark exciplex states. This model explains the seemingly contradictory observations of femtosecond fluorescence and slower, picosecond recovery of the ground-state population.

Interaction of Antitumor Drug Aclacinomycin‐A with DNA and Its Specific Sequence Site

Abstract Through UV and fluorescence spectrophotometries, the interaction of aclacinomycin‐A (ACM‐A) with DNA and its specific sequence have been investigated with the aid of circular dichroism spectrophotometry and differential pulse voltammetry method. The results demonstrated that ACM‐A was capable of intercalating DNA double helix, the π‐π electronic overlapping between π‐electrons of ACM‐A and base pair of DNA stabilized the ACM‐A‐DNA adduct, and through electrostatic interaction, the trisaccharide interacted with the minor groove of DNA owing to an amino group at C(3′). Electrochemical and spectroelectrochemical studies revealed that the original form of ACM‐A had higher affinity for DNA than the reduction form in which the trisaccharide group at C(7) was lost. According to the results obtained in this paper, ACM‐A showed preference for AT base pairs of the deoxyribonucleic acid duplex, and it was apt to interact with cytosine and thymine rather than the adenine of oligonucleotide.

Structural effects of internucleotide linkage modification at mismatch site in DNA/RNA duplex: Raman study

Two types of DNA oligonucleotide modifications, namely lengthening of the internucleotide linkage by insertion of CH 2 methylene group and substitution of deoxyribose by deoxyxylose, were studied with respect to their possible impact on the oligonucleotide binding specificity. Structural effects of the modifications at the mismatched site of DNA/RNA hybrid duplex were monitored via Raman spectroscopy by using a molecular model system consisting of a DNA nonamer (5′-GTG A TA TGC-3′) with the modification at the site of the central thymidine and of RNA counterparts with altered central nucleotide (5′-GCA U NU CAC-3′, N = A or U). A novel approach based on single and double difference Raman spectra allowed extraction and analysis of spectroscopic signatures introduced by chemical modification and mismatched basepairs in NA duplexes. The double difference spectra revealed that substitution of 2′-deoxy- d-deoxyribose by 2′-deoxy- d-deoxyxylose supports bending of the modified dA-dT-dA segment in the mismatched duplex, while lengthening of the internucleotide linkage by insertion of the CH 2 methylene group induces irregular distortion of this track. The modifications do not induce a better stacking interaction of the mismatched uracil and thus do not increase the stability of the T·U mismatched duplexes.

RNA silencing and HIV: A hypothesis for the etiology of the severe combined immunodeficiency induced by the virus

A novel intrinsic HIV-1 antisense gene was previously described with RNA initiating from the region of an HIV-1 antisense initiator promoter element (HIVaINR). The antisense RNA is exactly complementary to HIV-1 sense RNA and capable of forming ~400 base-pair (bp) duplex RNA in the region of the long terminal repeat (LTR) spanning the beginning portion of TAR in the repeat (R) region and extending through the U3 region. Duplex or double-stranded RNA of several hundred nucleotides in length is a key initiating element of RNA interference (RNAi) in several species. This HIVaINR antisense RNA is also capable of forming multiple stem-loop or hairpin-like secondary structures by M-fold analysis, with at least one that perfectly fits the criteria for a microRNA (miRNA) precursor. MicroRNAs (miRNAs) interact in a sequence-specific manner with target messenger RNAs (mRNAs) to induce either cleavage of the message or impede translation. Human mRNA targets of the predicted HIVaINR antisense RNA (HAA) microRNAs include mRNA for the human interleukin-2 receptor gamma chain (IL-2RG), also called the common gamma (γc) receptor chain, because it is an integral part of 6 receptors mediating interleukin signalling (IL-2R, IL-4R, IL-7R, IL-9R, IL-15R and IL-21R). Other potential human mRNA targets include interleukin-15 (IL-15) mRNA, the fragile × mental retardation protein (FMRP) mRNA, and the IL-1 receptor-associated kinase 1 (IRAK1) mRNA, amongst others. Thus the proposed intrinsic HIVaINR antisense RNA microRNAs (HAAmiRNAs) of the human immunodeficiency virus form complementary targets with mRNAs of a key human gene in adaptive immunity, the IL-2Rγc, in which genetic defects are known to cause an X-linked severe combined immunodeficiency syndrome (X-SCID), as well as mRNAs of genes important in innate immunity. A new model of intrinsic RNA silencing induced by the HIVaINR antisense RNA in the absence of Tat is proposed, with elements suggestive of both small interfering RNA (siRNA) and miRNA.

Pyrene-modified guanosine as fluorescent probe for DNA modulated by charge transfer

8-(Pyren-1-yl)-2′-deoxyguanosine (Py-G) was incorporated synthetically as a modified DNA base and optical probe into oligonucleotides. A variety of Py-G-modified DNA duplexes have been investigated by methods of optical spectroscopy. The DNA duplex hybridization can be observed by both fluorescence and absorption spectroscopy since the Py-G group exhibits altered properties in single strands versus double strands for both spectroscopy methods. The fluorescence enhancement upon DNA hybridization can be improved significantly by the presence of 7-deazaguanin as an additional modification and charge acceptor three bases away from the Py-G modification site. Moreover, Py-G in DNA can be applied as a photoinducable donor for charge transfer processes when indol is present as an artificial DNA base and charge acceptor. Correctly base-paired duplexes can be discriminated from mismatched ones by comparison of their fluorescence quenching.

Mechanistic Studies of Mini-TAR RNA/DNA Annealing in the Absence and Presence of HIV-1 Nucleocapsid Protein

HIV-1 reverse transcription involves several nucleic acid rearrangements, which are catalyzed by the nucleocapsid protein (NC). Annealing of the trans-activation response element (TAR) DNA hairpin to a complementary TAR RNA hairpin, resulting in the formation of an extended 98 –base-pair duplex, is an essential step in the minus-strand transfer step of reverse transcription. To elucidate the TAR RNA/DNA annealing reaction pathway, annealing kinetics were studied systematically by gel-shift assays performed in the presence or absence of HIV-1 NC. Truncated 27 nucleotide mini-TAR RNA and DNA constructs were used in this work. In the absence of NC, the annealing is slow, and involves the fast formation of an unstable extended “kissing” loop intermediate, followed by a slower strand exchange between the terminal stems. This annealing is very sensitive to loop–loop complementarity, as well as to nucleic acid concentration, ionic strength and temperature. NC stimulates the annealing ∼ 5000-fold by stabilizing the bimolecular intermediate ∼ 100 to 200-fold, and promoting the subsequent strand exchange reaction ∼ 10 to 20-fold. NC concentration dependence studies suggest that there is a direct correlation between the amount of NC required to stabilize the intermediate and the amount needed to induce mini-TAR aggregation. Whereas saturating levels of NC are required to efficiently aggregate nucleic acids, sub-saturating NC is sufficient to significantly enhance duplex destabilization. Equilibrium levels of mini-TAR RNA/DNA annealing were also measured under a variety of conditions. Taken together, the results presented here provide a quantitative accounting of HIV-1 NC's aggregation and duplex destabilizing activity, and provide insights into the universal nucleic acid chaperone activity of this essential viral protein.

Three-Dimensional Structure of the Human DNA-PKcs/Ku70/Ku80 Complex Assembled on DNA and Its Implications for DNA DSB Repair

DNA-PKcs is a large (approximately 470 kDa) kinase that plays an essential role in the repair of DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ). DNA-PKcs is recruited to DSBs by the Ku70/Ku80 heterodimer, with which it forms the core of a multiprotein complex that promotes synapsis of the broken DNA ends. We have purified the human DNA-PKcs/Ku70/Ku80 holoenzyme assembled on a DNA molecule. Its three-dimensional (3D) structure at approximately 25 Angstroms resolution was determined by single-particle electron microscopy. Binding of Ku and DNA elicits conformational changes in the FAT and FATC domains of DNA-PKcs. Dimeric particles are observed in which two DNA-PKcs/Ku70/Ku80 holoenzymes interact through the N-terminal HEAT repeats. The proximity of the dimer contacts to the likely positions of the DNA ends suggests that these represent synaptic complexes that maintain broken DNA ends in proximity and provide a platform for access of the various enzymes required for end processing and ligation.

Competition between the DNA unwinding and strand pairing activities of the Werner and Bloom syndrome proteins

BackgroundThe premature aging and cancer-prone Werner and Bloom syndromes are caused by defects in the RecQ helicase enzymes WRN and BLM, respectively. Recently, both WRN and BLM (as well as several other RecQ members) have been shown to possess a strand annealing activity in addition to the requisite DNA unwinding activity. Since an annealing function would appear to directly oppose the action of a helicase, we have examined in this study the dynamic equilibrium between unwinding and annealing mediated by either WRN or BLM.ResultsOur investigation into the competition between annealing and unwinding demonstrates that, under standard reaction conditions, WRN- or BLM-mediated annealing can partially or completely mask unwinding as measured in standard helicase assays. Several strategies were employed to suppress the annealing activity so that the actual strength of WRN- or BLM-dependent unwinding could be more accurately assessed. Interestingly, if a DNA oligomer complementary to one strand of the DNA substrate to be unwound is added during the helicase reaction, both WRN and BLM unwinding is enhanced, presumably by preventing protein-mediated re-annealing. This strategy allowed measurement of WRN-catalyzed unwinding of long (80 base pair) duplex regions and fully complementary, blunt-ended duplexes, both of which were otherwise quite refractory to the helicase activity of WRN. Similarly, the addition of trap strand stimulated the ability of BLM to unwind long and blunt-ended duplexes. The stimulatory effect of the human replication protein A (hRPA, the eukaryotic single-stranded DNA binding protein) on both WRN- and BLM-dependent unwinding was also re-examined in light of its possible role in preventing re-annealing. Our results show that hRPA influences the outcome of WRN and BLM helicase assays by both inhibiting re-annealing and directly promoting unwinding, with the larger contribution from the latter mechanism.ConclusionThese findings indicate that measurements of unwinding by WRN, BLM, and probably other RecQ helicases are complicated by their annealing properties. Thus, WRN- and BLM-dependent unwinding activities are significantly stronger than previously believed. Since this broadens the range of potential physiological substrates for WRN and BLM, our findings have relevance for understanding their functions in vitro and in vivo.

Extended Weak Bonding Interactions in DNA: π-Stacking (Base−Base), Base−Backbone, and Backbone−Backbone Interactions

We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.

Tetraplatinated Artificial Oligopeptides Afford High Affinity Intercalation into dsDNA

This paper reports the binding of an artificial tetrapeptide to which are tethered four Pt(II) complexes (i.e., [Pt(tpy)(py)]48+) with a 12 base pair duplex DNA oligonucleotide. Isothermal Titration Calorimetry reveals that two tetrametallic peptides stoichiometrically bind to each DNA duplex with a binding constant, KB, of 1.7 x 106 M-1, with a change in free energy of -8.5 kcal/mol. This KB represents an affinity 2 orders of magnitude greater than that of the monometallic analogue [Pt(tpy)(pic)]2+ for the same dsDNA sequence. The metalated peptides bind by intercalation into the DNA, partially unwinding the helix while stabilizing the structure, causing an increase in the dsDNA melting temperature of 25 degrees C.

1H NMR and Optical Spectroscopic Investigation of the Sequence-Dependent Dimerization of a Symmetrical Cyanine Dye in the DNA Minor Groove

A symmetrical cyanine dye was previously shown to bind as a cofacial dimer to alternating A-T sequences of duplex DNA. Indirect evidence suggested that dimerization of the dye occurred in the minor groove. 1H NMR experiments reported here verify this model based on broadening and shifting of signals due to protons on carbon 2 of adenine and imino protons at the central five A-T pairs of the 11 base pair duplex: 5'-GCGTATATGCG-3'/3'-CGCATATACGC-5'. This binding mode is similar to that of distamycin A, even though the dye lacks the hydrogen-bonding groups used by distamycin for sequence-specific recognition. Surprisingly, the third base pair (G-C) was also implicated in the binding site. UV-vis experiments were used to compare the extent of dimerization of the dye for 11 different sequence variants. These experiments verified the importance of a G-C pair at the third position: replacing this pair with A-T suppressed dimerization. These results indicate that the dye binding site spans six base pairs: 5'-GTATAT-3'. The initial G-C pair seems to be important for widening the minor groove rather than for making important contacts with the dye molecules since inverting its orientation to C-G or replacing it with I-C still led to favorable dimerization of the dye.

Stabilizing contributions of sulfur-modified nucleotides: crystal structure of a DNA duplex with 2'-O-[2-(methoxy)ethyl]-2-thiothymidines

Substitution of oxygen atoms by sulfur at various locations in the nucleic acid framework has led to analogs such as the DNA phosphorothioates and 4′-thio RNA. The phosphorothioates are excellent mimics of DNA, exhibit increased resistance to nuclease degradation compared with the natural counterpart, and have been widely used as first-generation antisense nucleic acid analogs for applications in vitro and in vivo. The 4′-thio RNA analog exhibits significantly enhanced RNA affinity compared with RNA, and shows potential for incorporation into siRNAs. 2-Thiouridine (s2U) and 5-methyl-2-thiouridine (m5s2U) are natural nucleotide analogs. s2U in tRNA confers greater specificity of codon–anticodon interactions by discriminating more strongly between A and G compared with U. 2-Thio modification preorganizes the ribose and 2′-deoxyribose sugars for a C3′-endo conformation, and stabilizes heteroduplexes composed of modified DNA and complementary RNA. Combination of the 2-thio and sugar 2′-O-modifications has been demonstrated to boost both thermodynamic stability and nuclease resistance. Using the 2′-O-[2-(methoxy)ethyl]-2-thiothymidine (m5s2Umoe) analog, we have investigated the consequences of the replacement of the 2-oxygen by sulfur for base-pair geometry and duplex conformation. The crystal structure of the A-form DNA duplex with sequence GCGTAT*ACGC (T* = m5s2Umoe) was determined at high resolution and compared with the structure of the corresponding duplex with T* = m5Umoe. Notable changes as a result of the incorporation of sulfur concern the base-pair parameter ‘opening’, an improvement of stacking in the vicinity of modified nucleotides as measured by base overlap, and a van der Waals interaction between sulfur atoms from adjacent m5s2Umoe residues in the minor groove. The structural data indicate only minor adjustments in the water structure as a result of the presence of sulfur. The observed small structural perturbations combined with the favorable consequences for pairing stability and nuclease resistance (when combined with 2′-O-modification) render 2-thiouracil-modified RNA a promising candidate for applications in RNAi.

The AUUCU Repeats Responsible for Spinocerebellar Ataxia Type 10 Form Unusual RNA Hairpins

Spinocerebellar ataxia type 10 is an autosomal dominant disorder caused by expansion of a pentameric repeat tract (ATTCT.AGAAT)(n) in intron 9 of the gene that encodes ataxin-10. We have analyzed duplex DNA containing the repeat, the individual DNA strands, and the RNA that would be generated by transcription of the repeat. Circular dichroism and UV absorbance measurements suggest that the previously reported tendency of the repeat to unpair when supercoiled is probably related simply to GC content rather than reflecting any unusual property of the duplex. DNA containing d(ATTCT)9 forms a folded structure at relatively low temperatures, whereas the antisense strand, d(AGAAT)9, does not form a structure even at 0 degrees C. In contrast r(AUUCU)9 forms a folded structure under physiologically reasonable conditions. S1 nuclease analysis reveals a single region of hypersensitivity in the middle of the repeat tract, whereas V1 digestion is consistent with a hydrogen bonded or well stacked structure. CD spectroscopy shows that the structure is unimolecular and hydrogen bonded and has a significant amount of A-form helix. NMR spectroscopy demonstrates that these hydrogen bonds comprise an equal number of A.U and U.U base pairs. Our data thus suggest that the repeat forms an unusual RNA hairpin. Thus the ability to form an RNA hairpin seems to be a common property of those Repeat Expansion Diseases that are not recessively inherited and are caused by repeats that are transcribed but not translated.

DNA binding and helicase actions of mouse MCM4/6/7 helicase

Helicases play central roles in initiation and elongation of DNA replication. We previously reported that helicase and ATPase activities of the mammalian Mcm4/6/7 complex are activated specifically by thymine-rich single-stranded DNA. Here, we examined its substrate preference and helicase actions using various synthetic DNAs. On a bubble substrate, Mcm4/6/7 makes symmetric dual contacts with the 5′-proximal 25 nt single-stranded segments adjacent to the branch points, presumably generating double hexamers. Loss of thymine residues from one single-strand results in significant decrease of unwinding efficacy, suggesting that concurrent bidirectional unwinding by a single double hexameric Mcm4/6/7 may play a role in efficient unwinding of the bubble. Mcm4/6/7 binds and unwinds various fork and extension structures carrying a single-stranded 3′-tail DNA. The extent of helicase activation depends on the sequence context of the 3′-tail, and the maximum level is achieved by DNA with 50% or more thymine content. Strand displacement by Mcm4/6/7 is inhibited, as the GC content of the duplex region increases. Replacement of cytosine–guanine pairs with cytosine–inosine pairs in the duplex restored unwinding, suggesting that mammalian Mcm4/6/7 helicase has difficulties in unwinding stably base-paired duplex. Taken together, these findings reveal important features on activation and substrate preference of the eukaryotic replicative helicase.

RNA Guanine Quadruplex Invasion by Complementary and Homologous PNA Probes

Guanine quadruplexes are gaining increasing attention due to their suspected roles in regulating gene expression at the transcriptional and translational levels. This paper describes the ability of short peptide nucleic acid (PNA) probes to disrupt a stable RNA quadruplex and hybridize to their target sequence. In one case, the PNA probe is complementary to the target, resulting in formation of a Watson-Crick base-paired duplex. In the second case, the PNA probe is homologous to the target and forms a hybrid quadruplex structure. The hybrid duplex is formed in a 1:1 stoichiometry, as expected based on the constraints imposed by Watson-Crick pairing. However, the hybrid quadruplex is formed in a PNA2:RNA stoichiometry, due to the ability of the short PNA to hybridize with both halves of the original RNA quadruplex.

X-Ray Structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase Core and Its Complex with DNA

SWI2/SNF2 ATPases remodel chromatin or other DNA:protein complexes by a poorly understood mechanism that involves ATP-dependent DNA translocation and generation of superhelical torsion. Crystal structures of a dsDNA-translocating SWI2/SNF2 ATPase core from Sulfolobus solfataricus reveal two helical SWI2/SNF2 specific subdomains, fused to a DExx box helicase-related ATPase core. Fully base paired duplex DNA binds along a central cleft via both minor groove strands, indicating that SWI2/SNF2 ATPases travel along the dsDNA minor groove without strand separation. A structural switch, linking DNA binding and the active site DExx motif, may account for the stimulation of ATPase activity by dsDNA. Our results suggest that torque in remodeling processes is generated by an ATP-driven screw motion of DNA along the active site cleft. The structures also redefine SWI2/SNF2 functional motifs and uncover unexpected structural correlation of mutations in Cockayne and X-linked mental retardation syndromes.

How Much π-Stacking Do DNA Termini Seek? Solution Structure of a Self-Complementary DNA Hexamer with Trimethoxystilbenes Capping the Terminal Base Pairs,

The exposed terminal base pairs of DNA duplexes are nonclassical binding sites for small molecules. Instead, small molecules usually prefer intercalation or minor groove binding. Here we report the solution structure of the DNA duplex (TMS-TGCGCA)(2), where TMS denotes trimethoxystilbene carboxamides that are 5'-tethered to the DNA. The stilbenes, for which intercalation is conformationally accessible, stack on the terminal T:A base pairs of an undisturbed B-form duplex. Two conformations, differing by the orientation of the stilbene relative to the terminal base pair, are observed, indicating that the flip rate is slow for the pi-stacked aromatic ring system. The trimethoxystilbene is known to greatly increase base pairing fidelity at the terminus. Here we show that it gauges the size of the T:A base pair by embracing the 2'-methylene group of the terminal dA residue of the unmodified terminus with its methoxy "arms", but that it does not engage the entire base pair in pi-stacking. Mismatched base pairs with their altered geometry will not allow for the same embracing interaction. On the basis of the current structure, a trimethoxychrysene carboxamide is proposed as a ligand with increased pi-stacking surface and possible applications as improved fidelity-enhancing element.

Self-diffusion in solutions of a 20 base pair oligonucleotide: Effects of concentration and ionic strength

The long-time self-diffusion coefficients of a 20 base pair duplex oligonucleotide are measured as functions of 20-mer and added NaCl salt concentrations. The self-diffusion coefficients decrease monotonically with increasing 20-mer concentrations for the high-added salt sample and display non-monotonically decreasing 20-mer concentration dependences at lower added salt concentrations. The non-monotonic behavior is attributed to the opposing effects of the tendency to increase the interactions between 20-mers as the concentration is increased and to a decrease in the extent of the Coulomb forces as counterions from the 20-mer increasingly screen them. Attempts to account for the effect of the Coulomb forces on the self-diffusion coefficients by using effective dimensions in the hard rod theory give good agreement with experiment at the highest salt concentration studied. For the lower salt concentrations there appear to be two scaling regimes--one at low polyion concentration in which the high salt scaling of the rod dimensions by adding the Debye screening to the length and diameter of the rod is appropriate and one at high polyion concentrations where the scaling of the dimensions is the addition of 1/2 the Debye screening length. Estimates of the "overlap" concentration C*=1/L(eff) indicate that the non-monotonic decrease occurs at concentrations lower than C*. Finally, the fluorescence correlation spectroscopy self-diffusion coefficients measured here are compared with the mutual diffusion coefficients measured by dynamic light scattering.

Monte Carlo Backbone Sampling for Nucleic Acids Using Concerted Rotations Including Variable Bond Angles

An efficient concerted rotation algorithm for use in Monte Carlo statistical mechanics simulations of nucleic acids is reported. The corresponding algorithm “concerted rotations with flexible bond angles” (CRA) for sampling polypeptides was found to be superior to local moves that included only flexible dihedral angles by allowing exploration of a larger conformational space as well as facilitating backbone transitions. The performance of the present CRA algorithm for polynucleotides is compared to two alternatives, a simple update of main-chain torsion angles and a previously reported, concerted rotation algorithm with fixed bond angles and a mix of flexible and rigid main-chain dihedral angles. The test system is a 12 base-pair duplex B-form DNA helix, and the performance comparisons are made for the system both in a vacuum and with continuum GB/SA solvation. The results demonstrate the superior efficiency of the CRA method over the alternatives.