RNA In Aqueous Solution Research Articles

Aqueous Activation of RNA 2'-OH for Conjugation with Amines and Thiols.

Strategies for covalent modification of RNA are important for enabling biological studies of the biopolymer and for enhancing properties of therapeutic RNAs. While a number of electrophiles have been observed to react with RNA, few methods exist for reaction with nucleophiles. Here, we describe new reagents that enable efficient conjugation of amines and other nucleophiles to unmodified RNA postsynthetically via transient activation of 2'-OH groups. Reaction of single-stranded RNA in aqueous solution with phenolic imidazolecarbamates at room temperature results in stoichiometric and superstoichiometric yields of imidazolecarbonyl group adducts, and control experiments with DNA confirm the site of reaction in RNA as 2'-OH. Subsequent incubation of imidazolecarbonyl-activated RNAs with primary or selected secondary amines results in rapid, high-yield conversion to carbamate conjugates. The activation and subsequent nucleophile reaction can be carried out either stepwise or in a one-pot reaction. Thiols and phenol species react to yield (thio)carbonate adducts, and amino acid sidechains also react, suggesting possible future utility for protein conjugates and analysis of protein-RNA interactions. The activation method is found to be selective to unpaired regions of RNA, and can be directed to a specific location in a strand by use of a loop-inducing helper DNA. The results establish novel and efficient reagents and methods for modifying RNA postsynthetically with nucleophiles.

Design and synthesis of a series of OFF-ON near infrared fluorescent probes for nucleic acid in aqueous solution

Five cyanine dyes (6a-e) with aza units were prepared by the reaction of pyridinum or quinolinium with suitable aldehydes. They present several remarkable features including large Stokes shift (235–282 nm), long emission wavelength (640–698 nm) and excellent selectivity. Moreover, probes 6a-b display obvious and sensitive fluorescent response to DNA and RNA in aqueous solution, and the quantum yield of probe 6a response to RNA increases from 0 to 8.9%. More importantly, probes 6c and 6e can effectively avoid DNA interference and only respond to RNA in aqueous solution. In addition, laser confocal cell experiment has showed that probe 6b can image the nucleolus of nucleic acids in HeLa cells.

Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding

Understanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.

The effect of allyl isothiocyanate on RNA

Allyl isothiocyanate (AITC), finds in cruciferous vegetables. AITC shows bactericidal, fungicidal activities and anticancer activity by inhibition of cell proliferation, cell cycle arrest and apoptosis induction and tumor growth inhibition. In this study, the interaction of Allylisothiocyanate with yeast RNA in aqueous solution at physiological conditions using constant RNA concentration and various molar ratios of AITC/RNA complexes are examine. Fourier transform infrared (FTIR) and uv-visible difference spectroscopic methods are used to determine the AITC binding mode, binding constant and stability of RNA in AITC/RNA complexes in aqueous solution. Spectroscopic evidence shows that AITC interacts with RNA. The external binding of AITC to RNA with overall binding constant of K(AITC-RNA)=7.207×10 6 M -1 are also presented. RNA remains in A conformation upon AITC complexation. Keywords : Allyl isothiocyanate; RNA; FTIR; UV-vis; binding constant; conformation.

The use of a near-infrared RNA fluorescent probe with a large Stokes shift for imaging living cells assisted by the macrocyclic molecule CB7

A near-infrared fluorescent dye Hsd was designed and synthesized, which absorbed as hemicyane and emitted as Cy7 and therefore produced a Stokes shift as large as 224 nm. Quantum chemistry calculation demonstrated that the large Stokes shift was produced by the combination of intramolecular charge transfer (ICT) and internal conversion. Significantly, Hsd showed selectively response to RNA in aqueous solution and fixed cells. Moreover, Hsd could be uptaken into the cells under the assistance of cucurbit[7]uril (CB7) and selectively stain RNA in living cells. The introducing of CB7 provides a platform to amplify the application of some cell-impermeant fluorescent stains through the supramolecular chemistry methods.

RNA Secondary Structure Prediction Using High-throughput SHAPE

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.

RNA Secondary Structure Prediction Using High-throughput SHAPE

Understanding the function of RNA involved in biological processes requires a thorough knowledge of RNA structure. Toward this end, the methodology dubbed "high-throughput selective 2' hydroxyl acylation analyzed by primer extension", or SHAPE, allows prediction of RNA secondary structure with single nucleotide resolution. This approach utilizes chemical probing agents that preferentially acylate single stranded or flexible regions of RNA in aqueous solution. Sites of chemical modification are detected by reverse transcription of the modified RNA, and the products of this reaction are fractionated by automated capillary electrophoresis (CE). Since reverse transcriptase pauses at those RNA nucleotides modified by the SHAPE reagents, the resulting cDNA library indirectly maps those ribonucleotides that are single stranded in the context of the folded RNA. Using ShapeFinder software, the electropherograms produced by automated CE are processed and converted into nucleotide reactivity tables that are themselves converted into pseudo-energy constraints used in the RNAStructure (v5.3) prediction algorithm. The two-dimensional RNA structures obtained by combining SHAPE probing with in silico RNA secondary structure prediction have been found to be far more accurate than structures obtained using either method alone.

RNA adducts with Na2SeO4 and Na2SeO3 – Stability and structural features

Abstract Selenium compounds are widely available in dietary supplements and have been extensively studied for their antioxidant and anticancer properties. Low blood Se levels were found to be associated with an increased incidence and mortality from various types of cancers. Although many in vivo and clinical trials have been conducted using these compounds, their biochemical and chemical mechanisms of efficacy are the focus of much current research. This study was designed to examine the interaction of Na 2 SeO 4 and Na 2 SeO 3 with RNA in aqueous solution at physiological conditions, using a constant RNA concentration (6.25 mM) and various sodium selenate and sodium selenite/polynucleotide (phosphate) ratios of 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared, UV–Visible spectroscopic methods were used to determine the drug binding modes, the binding constants, and the stability of Na 2 SeO 4 and Na 2 SeO 3 –RNA complexes in aqueous solution. Spectroscopic evidence showed that Na 2 SeO 4 and Na 2 SeO 3 bind to the major and minor grooves of RNA ( via G, A and U bases) with some degree of the Se–phosphate (PO 2 ) interaction for both compounds with overall binding constants of K(Na 2 SeO 4 –RNA) = 8.34 × 10 3 and K(Na 2 SeO 3 –RNA) = 4.57 × 10 3 M −1 . The order of selenium salts–biopolymer stability was Na 2 SeO 4 –RNA > Na 2 SeO 3 –RNA. RNA aggregations occurred at higher selenium concentrations. No biopolymer conformational changes were observed upon Na 2 SeO 4 and Na 2 SeO 3 interactions, while RNA remains in the A-family structure.

ANTIOXIDANT SAFFRON CONSTITUENTS BIND DNA AND TRNA

Crocetin (CRT) and dimethylcrocetin (DMCRT) are derived from saffron's carotenoids while safranal is the main component of its essential oil. The antioxidant activity of these compounds was tested by the DPPH antioxidant activity assay. Also the interactions of CRT, DMCRT and safranal with calf-thymus DNA and transfer RNA in aqueous solution at physiological conditions are reported. The structural analysis showed external binding to the major or minor groove and some degree of intercalation of saffron compounds to DNA and RNA. A partial B- to A-DNA transition occurs at high ligand concentration while tRNA remains in the A-family.

A Comparative Study on the Interaction of Cis- and Trans-Platin with DNA and RNA

Cis-diamminedichloroplatinum(II) is a frequently used and very effective chemotherapeutic drug for treatment of various malignancies; however, the trans isomer is clinically ineffective. Cis-platin exerts its antitumor activity by binding to DNA via intrastrand cross-links to d(GpG) (dG = deoxyguanosine) and to d(ApG) (dA = deoxyadenosine), interfering with DNA replication and transcription and causing cell death. The trans-diamminedichloroplatinum(II) isomer also binds DNA, but is clinically ineffective. This study was designed to examine the interactions of cis- and trans-platin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using a constant DNA and RNA concentration (6.25 mM) and various platin salts/polynucleotide (phosphate) ratios of 1/100, 1/50, 1/25, and 1/12.5. Fourier transform infrared, ultraviolet-visible spectroscopic methods were used to determine the drug binding modes, the binding constants, and the stability of cis- and trans-platin-DNA and -RNA complexes in aqueous solution. Spectroscopic evidence showed that cis- and trans-platin bind to the major and minor grooves of DNA (via G, A, T, and C bases), while RNA binding is through G, U, A, and C bases with some degree of the pt-phosphate (PO(2)) interaction for both isomers and overall binding constants of K((cis-platin-DNA)) = 5.51 x 10(4) M(-1), K((trans-platin-DNA)) = 2.26 x 10(4) M(-1), K((cis-platin-RNA)) = 1.9 x 10(4) M(-1), and K((trans-platin-RNA)) = 1.75 x 10(4) M(-1). DNA and RNA aggregations occurred at high platin concentrations. No biopolymer conformational changes were observed upon cis- and trans-platin interactions, while DNA remains in the B-family, and RNA retains its A-family structure. The order of platin compound-polymer stability was cis-platin-DNA > trans-platin-DNA > cis-platin-RNA > trans-platin-RNA.

Curcumin Binding to DNA and RNA

Curcumin, the yellow pigment from the rhizoma of Curcuma longa, is a widely studied phytochemical with a variety of biological activities. The ongoing research and clinical trials have proved that this natural phenolic compound has great and diverse pharmacological potencies. Beside its effective antioxidant, antiinflammatory, and antimicrobial/antiviral properties, curcumin is also considered as a cancer chemopreventive agent. While the antioxidant activity of curcumin is well documented, its interaction with DNA and RNA is not fully investigated. This study was designed to examine the interactions of curcumin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using constant DNA and RNA concentration (6.25 mM) and various curcumin/polynucleotide (phosphate) ratios of 1/120, 1/80, 1/40, 1/20, and 1/10. Fourier transform infrared (FTIR) and UV-visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of curcumin-DNA and curcumin-RNA complexes in aqueous solution. Spectroscopic evidence showed that curcumin binds to the major and minor grooves of DNA duplex and to RNA bases as well as to the back bone phosphate group with overall binding constants of K(curcumin-DNA) = 4.255 x 10(4) M(-1) and K(curcumin-RNA) = 1.262 x 10(4) M(-1). Major DNA and RNA aggregation occurred at high pigment concentration. No conformational changes were observed upon curcumin interaction with these biopolymers; that is, DNA remains in the B, and RNA retains its A-family structure.

Structural analysis of DNA and RNA interactions with antioxidant flavonoids

Flavonoids are natural polyphynolic compounds with major antioxidant activity that can prevent DNA damage. The anticancer and antiviral activities of these natural products are attributed to their potential biomedical applications. In this review we are examining how the antioxidant flavonoids bind DNA and RNA and what mechanism of action is involved in preventing DNA damage. Detailed spectroscopic data on the interactions of morin (mor), apigenin (api), naringin (nar), quercetin (que), kaempferol (kae) and delphinidin (del) with DNA and transfer RNA in aqueous solution at physiological conditions were analysed. The structural analysis showed flavonoids mainly intercalate into DNA and RNA duplexes with minor external binding to the major or minor groove and the backbone phosphate group with overall binding constants for DNA adducts Kmor═5.99×103 M–1, Kapi═7.10×104 M–1, and Knar═3.10×103 M–1, Kque═7.25×104 M–1, Kkae═3.60×104 M–1 and Kdel═1.66×104 M–1, and for tRNA adducts Kmor═9.15×103 M–1, Kapi═4.96×104 M–1, and Knar═1.14×104 M–1, Kque═4.80×104 M–1, Kkae═4.65×104 M–1 and Kdel═9.47×104 M–1. The stability of adduct formation is in the order of que > api > kae > del >mor > nar for DNA and del > api > que > kae > nar > mor for tRNA. Low flavonoid concentration induces helical stabilization, whereas high pigment content causes helix opening. Flavonoids induce a partial B to A–DNA transition at high pigment concentration, while tRNA remains in A-family structure upon flavonoid complexation. The antioxidant activity of flavonoids changes in the order delphinidin > quercetin > kaempferol > morin > naringin > apigenin. The results show intercalated flavonoid molecule can act as an antioxidant and prevent DNA damage.

Flexibility of Short-Strand RNA in Aqueous Solution as Revealed by Molecular Dynamics Simulation: Are A-RNA and A´-RNA Distinct Conformational Structures?

We use molecular dynamics simulations to compare the conformational structure and dynamics of a 21-base pair RNA sequence initially constructed according to the canonical A-RNA and A′-RNA forms in the presence of counterions and explicit water. Our study aims to add a dynamical perspective to the solid-state structural information that has been derived from X-ray data for these two characteristic forms of RNA. Analysis of the three main structural descriptors commonly used to differentiate between the two forms of RNA – namely major groove width, inclination and the number of base pairs in a helical twist – over a 30 ns simulation period reveals a flexible structure in aqueous solution with fluctuations in the values of these structural parameters encompassing the range between the two crystal forms and more. This provides evidence to suggest that the identification of distinct A-RNA and A′-RNA structures, while relevant in the crystalline form, may not be generally relevant in the context of RNA in the aqueous phase. The apparent structural flexibility observed in our simulations is likely to bear ramifications for the interactions of RNA with biological molecules (e.g. proteins) and non-biological molecules (e.g. non-viral gene delivery vectors).

Structural analysis of DNA and RNA interactions with antioxidant flavonoids

Flavonoids are natural polyphynolic compounds with major antioxidant activity that can prevent DNA damage. The anticancer and antiviral activities of these natural products are attributed to their potential biomedical applications. In this review we are examining how the antioxidant flavonoids bind DNA and RNA and what mechanism of action is involved in preventing DNA damage. Detailed spectroscopic data on the interactions of morin (mor), apigenin (api), naringin (nar), quercetin (que), kaempferol (kae) and delphinidin (del) with DNA and transfer RNA in aqueous solution at physiological conditions were analysed. The structural analysis showed flavonoids mainly intercalate into DNA and RNA duplexes with minor external binding to the major or minor groove and the backbone phosphate group with overall binding constants for DNA adducts Kmor═5.99×103M–1, Kapi═7.10×104M–1, and Knar═3.10×103M–1, Kque═7.25×104M–1, Kkae═3.60×104M–1and Kdel═1.66×104M–1, and for tRNA adducts Kmor═9.15×103M–1, Kapi═4.96×104M–1, and Knar═1.14×104M–1, Kque═4.80×104M–1, Kkae═4.65×104M–1and Kdel═9.47×104M–1. The stability of adduct formation is in the order of que > api > kae > del >mor > nar for DNA and del > api > que > kae > nar > mor for tRNA. Low flavonoid concentration induces helical stabilization, whereas high pigment content causes helix opening. Flavonoids induce a partial B to A–DNA transition at high pigment concentration, while tRNA remains in A-family structure upon flavonoid complexation. The antioxidant activity of flavonoids changes in the order delphinidin > quercetin > kaempferol > morin > naringin > apigenin. The results show intercalated flavonoid molecule can act as an antioxidant and prevent DNA damage.

RNA binding to antioxidant flavonoids

Flavonoids are an interesting group of natural polyphenolic compounds that exhibit extensive bioactivities such as scavenging free radical, antitumor and antiproliferative effects. The anticancer and antiviral effects of these natural products are attributed to their potential biomedical applications. While flavonoids complexation with DNA is known, their bindings to RNA are not fully investigated. This study was designed to examine the interactions of three flavonoids; morin (Mor), apigenin (Api) and naringin (Nar) with yeast RNA in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various pigment/RNA (phosphate) ratios of 1/120 to 1/1. FTIR, UV–visible spectroscopic methods were used to determine the ligand binding modes, the binding constant and the stability of RNA in flavonoid-RNA complexes in aqueous solution. Spectroscopic evidence showed major binding of flavonoids to RNA with overall binding constants of K morin = 9.150 × 10 3 M −1, K apigenin = 4.967 × 10 4 M −1, and K naringin = 1.144 × 10 4 M −1. The affinity of flavonoid-RNA binding is in the order of apigenin > naringin > morin. No biopolymer secondary structural changes were observed upon flavonoid interaction and RNA remains in the A-family structure in these pigment complexes.

An Overview of DNA and RNA Bindings to Antioxidant Flavonoids

In this report we are examining how the antioxidant flavonoids can prevent DNA damage and what mechanism of action is involved in the process. Flavonoids are strong antioxidants that prevent DNA damage. The anticancer and antiviral activities of these natural products are implicated in their mechanism of actions. We study the interactions of quercetin (que), kaempferol (kae), and delphinidin (del) with DNA and transfer RNA in aqueous solution at physiological conditions, using constant DNA or RNA concentration 6.25 mmol (phosphate) and various pigment/polynucleotide(phosphate) ratios of 1/65 to 1 (DNA) and 1/48 to 1/8 (tRNA). The structural analysis showed quercetin, kaempferol, and delphinidin intercalate DNA and RNA duplexes with minor external binding to the major or minor groove and the backbone phosphate group with overall binding constants for DNA adducts K(que) = 7.25 (+/-0.65) x 10(4) M(-1), K(kae) = 3.60 (+/-0.33) x 10(4) M(-1), and K(del) = 1.66 (+/-0.25) x 104 (-1) and for tRNA adducts K(que) = 4.80 (+/-0.50) x 10(4) M(-1), K(kae) = 4.65 (+/-0.45) x 10(4) M(-1), and K(del) = 9.47 (+/-0.70) x 10(4) M(-1). The stability of adduct formation is in the order of del>que>kae for tRNA and que>kae>del for DNA. Low flavonoid concentration induces helical stabilization, whereas high pigment content causes helix opening. A partial B to A-DNA transition occurs at high drug concentration, while tRNA remains in A-family structure. The antioxidant activity of flavonoids changes in order delphinidin>quercetin>kaempferol. The results show intercalated flavonoids can make them strong antioxidants to protect DNA from harmful free radical reactions.

Interaction of Arsenic Trioxide As2O3with DNA and RNA

Arsenic salts have been used for centuries to treat a variety of medical conditions ranging from infectious disease to cancer. More recently, trivalent arsenic trioxide was found to exhibit high antitumor activity towards hematological malignancies. Even though much is known about antitumor activity and DNA damage by As2O3, there has been no report on the interaction of arsenic trioxide with isolated DNA or RNA. Therefore, it was of interest to examine the interaction of As2O3 with DNA and RNA in aqueous solution at physiological pH. FTIR and UV-visible difference spectroscopic methods were used to characterize the nature of drug-DNA and drug-RNA interactions and to determine the As binding site, the binding constant, the sequence selectivity, the helix stability, and the biopolymer secondary structure in the As2O3-polynucleotide complexes in vitro. The FTIR spectroscopic studies were conducted with As2O3-polynucleotide (phosphate) ratios of 1/40, 1/20, 1/10, and 1/5, with a final DNA (P) or RNA (P) concentration of 6.25 mmol/l. Spectroscopic results showed As2O3 binds to DNA and RNA at G-C, A-T, and A-U bases, and no interaction with the backbone PO2 group. As2O3-DNA and -RNA adducts showed one type of binding with overall binding constant of K(As2O3-DNA) = 1.24 x 10(5) M(-1) and K(As2O3-RNA) = 2.60 x 10(5) M(-1). The As2O3-polynucleotide complexation is associated with a partial biopolymer aggregation and no major alterations of B-DNA or A-RNA structure.

Interaction of antitumor drug Sn(CH3)2Cl2 with DNA and RNA

Sn(CH3)2Cl2 exerts its antitumor activity in a specific way. Unlike anticancer cis-Pt(NH3)2Cl2 drug which binds strongly to the nitrogen atoms of DNA bases, Sn(CH3)2Cl2 shows no major affinity towards base binding. Thus, the mechanism of action by which tinorganometallic compounds exert antitumor activity would be different from that of the cisplatin drug. The aim of this study was to examine the binding of Sn(CH3)2Cl2 with calf thymus DNA and yeast RNA in aqueous solutions at pH 7.1–6.6 with constant concentrations of DNA and RNA and various molar ratios of Sn(CH3)2Cl2/DNA (phosphate) and Sn(CH3)2Cl2/RNA of 1/40, 1/20, 1/10, 1/5. Fourier transform infrared (FTIR) and UV–visible difference spectroscopic methods were used to determine the Sn(CH3)2Cl2 binding mode, binding constant, sequence selectivity and structural variations of Sn(CH3)2Cl2/DNA and Sn(CH3)2Cl2/RNA complexes in aqueous solution. Sn(CH3)2Cl2 hydrolyzes in water to give Sn(CH3)2(OH)2 and [Sn(CH3)2(OH)(H2O)n]+ species. Spectroscopic evidence showed that interaction occurred mainly through (CH3)2Sn(IV) hydroxide and polynucleotide backbone phosphate group with overall binding constant of K(Sn(CH3)2Cl2–DNA)=1.47×105M−1 and K(Sn(CH3)2Cl2–RNA)=7.33×105M−1. Sn(CH3)2Cl2 induced no biopolymer conformational changes with DNA remaining in the B-family structure and RNA in A-conformation upon drug complexation.

AZT Binds RNA at Multiple Sites

Azidothymidine (AZT) is a widely used inhibitor of type I human immunodeficiency virus (HIV) reverse transcriptase that act as a DNA chain terminator. Studies have shown primer unblocking and rescue of DNA synthesis AZT-resistant HIV-1 reverse transcriptase on DNA and RNA templates. Our recent study showed AZT bindings to the G-C, A-T base pairs and the backbone phosphate group of DNA duplex resulting in partial DNA conformational changes. This study was designed to examine the interaction of AZT with RNA in aqueous solution at physiological condition, using different drug/RNA (phosphate) molar ratios of 1/800 to 1/2 and constant RNA concentration of 1.25 or 12.5 mM (phosphate). Capillary electrophoresis, FTIR, and UV-visible difference spectroscopic methods and molecular modeling were used to determine the drug binding sites, binding constants, and the effects of AZT complexation on RNA conformation. Structural analysis showed that AZT binds RNA through G-C and A-U bases with two binding constants of K1=7.3 x 10(5) M(-1) and K2=1.90 x 10(5) M(-1). The drug distributions were 54% with G-C, 36% A-U, and 10% with the backbone phosphate group. RNA remains in A-family structure and drug sugar pucker in the C2'-endo/anti conformation in the AZT-RNA complexes. Molecular modeling studies show hydrogen bondings between RNA and AZT donor groups.

Taxol interaction with DNA and RNA — Stability and structural features

Taxol (paclitaxel) is an anticancer drug that interacts with microtubule proteins in a manner that catalyzes their formation from tubulin and stabilizes the resulting structures. However, in the human lung tumor cell, the concentration of paclitaxel is highest in the nucleus. Therefore, it was of interest to examine the interaction of taxol with DNA and RNA in aqueous solution at physiological pH. Capillary electrophoresis and Fourier transform infrared (FTIR) difference spectroscopic methods were used to characterize the nature of drug–DNA and drug–RNA interactions and to determine the taxol binding site, the binding constant, the sequence selectivity, the helix stability, and the biopolymer secondary structure in the taxol–polynucleotide complexes in vitro. The FTIR spectroscopic studies were conducted with taxol/polynucleotide (phosphate) ratios of 1/80, 1/40, 1/20, 1/10, 1/4, and 1/2 with a final DNA(P) or RNA(P) concentration of 12.5 mmol/L, and capillary electrophoresis was performed after incubation of taxol with polynucleotides at ratios of 1/200 to 1/12 with a final polynucleotide concentration of 1.25 mmol/L. Taxol was shown to bind to DNA and RNA at G–C, A–T, or A–U bases and the backbone PO2group. Two types of binding were observed for taxol–DNA with K1 = 1.3 × 104L mol–1and K2 = 3.5 × 103L mol–1, whereas taxol–RNA complexes showed one type of binding with K = 1.3 × 104L mol–1. The taxol–polynucleotide complexation is associated with a partial helix stabilization and no major alterations of B-DNA or A-RNA structure. Key words: DNA, RNA, taxol, binding site, binding constant, conformation, helix stability, electrophoresis, FTIR spectroscopy.