Insulin-linked Polymorphic Region Research Articles

Towards Computational Modeling of Ligand Binding to the ILPR G-Quadruplex.

Using a combination of unconstrained and constrained molecular dynamics simulations, we have evaluated the binding affinities between two porphyrin derivatives (TMPyP4 and TEGPy) and the G-quadruplex (G4) of a DNA fragment modeling the insulin-linked polymorphic region (ILPR). Refining a well-established potential of mean force (PMF) approach to selections of constraints based on root-mean-square fluctuations results in an excellent agreement between the calculated and observed absolute free binding energy of TMPyP4. The binding affinity of IPLR-G4 toward TEGPy is predicted to be higher than that toward TMPyP4 by 2.5 kcal/mol, which can be traced back to stabilization provided by the polyether side chains of TMPyP4 that can nestle into the grooves of the quadruplex and form hydrogen bonds through the ether oxygen atoms. Because our refined methodology can be applied to large ligands with high flexibility, the present research opens an avenue for further ligand design in this important area.

Identification of sugar-containing natural products that interact with i-motif DNA

There are thousands of compounds shown to interact with G-quadruplex DNA, yet very few which target i-motif (iM) DNA. Previous work showed that tobramycin can interact with iM- DNA, indicating the potential for sugar-molecules to target these structures. Computational approaches indicated that the sugar-containing natural products baicalin and geniposidic acid had potential to target iM-DNA. We assessed the DNA interacting properties of these compounds using FRET-based DNA melting and a fluorescence-based displacement assay using iM-DNA structures from the human telomere and the insulin linked polymorphic region (ILPR), as well as complementary G-quadruplex and double stranded DNA. Both baicalin and geniposidic acid show promise as iM-interacting compounds with potential for use in experiments into the structure and function of i-motif forming DNA sequences and present starting points for further synthetic development of these as probes for iM-DNA.

Studies on the Interactions of 3,11-Difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium and Insulin with the Quadruplex-Forming Oligonucleotide Sequence a2 from the Insulin-Linked Polymorphic Region.

Recently, several quadruplex-DNA-forming sequences have been identified in the insulin-linked polymorphic region (ILPR), which is a guanine-rich oligonucleotide sequence in the promoter region of insulin. The formation of this non-canonical quadruplex DNA (G4-DNA) has been shown to be involved in the biological activity of the ILPR, specifically with regard to its interplay with insulin. In this context, this contribution reports on the investigation of the association of the quadruplex-forming ILPR sequence a2 with insulin as well as with the well-known G4-DNA ligand 3,11-difluoro-6,8,13-trimethyl-8H-quino[4,3,2-kl]acridinium (1), also named RHPS4, by optical and NMR spectroscopy. CD- and NMR-spectroscopic measurements confirmed the preferential formation of an antiparallel quadruplex structure of a2 with four stacked guanine quartets. Furthermore, ligand 1 has high affinity toward a2 and binds by terminal π stacking to the G1–G11–G15–G25 quartet. In addition, the spectroscopic studies pointed to an association of insulin to the deoxyribose backbone of the loops of a2.

Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase

Noncanonical DNA structures that stall DNA replication can cause errors in genomic DNA. Here, we investigated how the noncanonical structures formed by sequences in genes associated with a number of diseases impacted DNA polymerization by the Klenow fragment of DNA polymerase. Replication of a DNA sequence forming an i-motif from a telomere, hypoxia-induced transcription factor, and an insulin-linked polymorphic region was effectively inhibited. On the other hand, replication of a mixed-type G-quadruplex (G4) from a telomere was less inhibited than that of the antiparallel type or parallel type. Interestingly, the i-motif was a better inhibitor of replication than were mixed-type G4s or hairpin structures, even though all had similar thermodynamic stabilities. These results indicate that both the stability and topology of structures formed in DNA templates impact the processivity of a DNA polymerase. This suggests that i-motif formation may trigger genomic instability by stalling the replication of DNA, causing intractable diseases.

Quantification of Chemical and Mechanical Effects on the Formation of the G-Quadruplex and i-Motif in Duplex DNA.

The formation of biologically significant tetraplex DNA species, such as G-quadruplexes and i-motifs, is affected by chemical (ions and pH) and mechanical [superhelicity (σ) and molecular crowding] factors. Because of the extremely challenging experimental conditions, the relative importance of these factors on tetraplex folding is unknown. In this work, we quantitatively evaluated the chemical and mechanical effects on the population dynamics of DNA tetraplexes in the insulin-linked polymorphic region using magneto-optical tweezers. By mechanically unfolding individual tetraplexes, we found that ions and pH have the largest effects on the formation of the G-quadruplex and i-motif, respectively. Interestingly, superhelicity has the second largest effect followed by molecular crowding conditions. While chemical effects are specific to tetraplex species, mechanical factors have generic influences. The predominant effect of chemical factors can be attributed to the fact that they directly change the stability of a specific tetraplex, whereas the mechanical factors, superhelicity in particular, reduce the stability of the competing species by changing the kinetics of the melting and annealing of the duplex DNA template in a nonspecific manner. The substantial dependence of tetraplexes on superhelicity provides strong support that DNA tetraplexes can serve as topological sensors to modulate fundamental cellular processes such as transcription.

A comparative study of the interactions of cationic hetarenes with quadruplex-DNA forming oligonucleotide sequences of the insulin-linked polymorphic region (ILPR).

The interactions of the ILPR sequence (ILPR = "insulin-linked polymorphic region") a2 [d(ACAG4TGTG4ACAG4TGTG4)] with [2.2.2]heptamethinecyanine derivatives 1a–e and with the already established quadruplex ligands coralyne (2), 3,3′-[2,6-pyridinediylbis(carbonylimino)]bis[1-methylquinolinium] (3), 4,4′,4′′,4′′′-(21H,23H-porphine-5,10,15,20-tetrayl)tetrakis[1-methylpyridinium] (4), naphtho[2,1-b:3,4-b′:6,5-b′′:7,8-b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences.

An Isothermal Titration and Differential Scanning Calorimetry Study of the G-Quadruplex DNA–Insulin Interaction

The binding of insulin to the G-quadruplexes formed by the consensus sequence of the insulin-linked polymorphic region (ILPR) was investigated with differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). The thermal denaturation temperature of insulin was increased by almost 4 °C upon binding to ILPR G-quadruplex DNA as determined by DSC. The thermodynamic parameters (K(D), ΔH, ΔG, and ΔS) of the insulin-G-quadruplex complex were further investigated by temperature-dependent ITC measurement over the range of 10-37 °C. The binding of insulin to the ILPR consensus sequence displays micromolar affinity in phosphate buffer at pH 7.4, which is mainly driven by entropic factors below 25 °C but by enthalpic terms above 30 °C. The interaction was also examined in several different buffers, and results showed that the observed ΔH is dependent on the ionization enthalpy of the buffer used. This indicates proton release upon the binding of G-quadruplex DNA to insulin. Additionally, the large negative change in heat capacity for this interaction may be associated with the dominant hydrophobicity of the amino acid sequence of insulin's β subunit, which is known to bind to the ILPR G-quadruplex DNA.

A Biophysical Study of the G-Quadruplex-Insulin Interaction

The formation of guanine (G)-quadruplex structures in the guanine-rich tandem repeats of the insulin-linked polymorphic region (ILPR) have potential effects on transcription of the insulin gene. Recent studies demonstrate that the ILPR G-quadruplexes can bind to insulin. The energetics of the binding between insulin and the G-quadruplexes formed by the most common ILPR repeat sequence have also been characterized in prior work. We have studied the proton transfer involved in the interaction between insulin and this DNA sequence by conducting isothermal titration calorimetry (ITC) experiments in various buffers and analyzing the observed enthalpy change. The transcriptional activity of a number of ILPR repeat sequences, including the consensus sequence, have been measured previously. Transcriptional activity for less common repeats is significantly lower than that of the consensus sequence but can be increased substantially by varying only one or two nucleotides. To determine the potential role of G-quadruplex formation and stability in regulating transcription, we have studied the second and third most common ILPR repeats as well as their variant sequences that exhibit increased transcriptional activity. ITC was used to characterize the energetics of the binding interaction between insulin and each of the four ILPR repeat sequences. The bulk thermodynamic measurements performed at various temperatures from 20 - 37 degrees Celsius provide insight into these biomolecular interactions.

Characterizing the Biomolecular Interactions between Insulin and G-Quadruplex DNA

The formation of guanine (G)-quadruplex structures in the guanine-rich tandem repeats of the insulin-linked polymorphic region (ILPR) is linked to transcriptional effects on the insulin gene. Recent studies demonstrate that the ILPR G-quadruplexes can bind to insulin while the energetics of this interaction with the most common ILPR repeat sequences have been characterized. Studies have also measured the transcriptional activity of less common ILPR repeats. Transcriptional activity for these repeats is significantly lower than that of the consensus sequence but can be increased substantially by varying only one or two nucleotides. To determine the potential role of G-quadruplex formation and stability in regulating transcription, we have studied the second and third most common ILPR repeats as well as their variant sequences that exhibit increased transcriptional activity. Circular dichroism (CD) spectroscopy, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC) have been used to characterize the binding interaction between insulin and each of the four ILPR repeat sequences. The bulk thermodynamic measurements performed at various temperatures from 20 - 37 degrees Celsius provide insight into these biomolecular interactions. Correction et al.Biophysical JournalApril 16, 2013In Brief2013. Characterizing the Biomolecular Interactions between Insulin and G-Quadruplex DNA. Nicole L. Michmerhuizen, Christine M. Timmer, Kumar Sinniah. Biophys. J. 104(2)s: 419a. Full-Text PDF Open Archive

Development of an electrochemical insulin sensor based on the insulin-linked polymorphicregion

Here we report the design and fabrication of an electrochemical aptamer-based (E-AB) sensor for detection of insulin. The aptamer used in this study is the insulin-linked polymorphic region (ILPR) sequence, a G-rich sequence that presumably undergoes ligand-induced folding to form a G-quadruplex in presence of insulin. Our circular dichroism data, however, suggests that the ILPR sequence, even in absence of the target, is predominantly in a G-quadruplex-like form. Insulin binding, however, has shown to further induce the formation of the G-quadruplex. To evaluate the potential of the ILPR sequence as a biosensing element, we constructed two E-AB insulin sensors that are identical in all aspects but the location of the methylene blue (MB) redox label. We find that the sensor fabricated with internal MB-modified probes (In-IT) shows enhanced sensing behavior when compared to one fabricated using terminal-MB modified probes (In1). The improvements observed with the In-IT sensor could be attributed to the more effective obstruction of electron transfer upon insulin binding. Overall, both sensors perform well, affording a detection limit of 10nM and 50nM for the In-IT and In1 sensors, respectively.

Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures.

G-Quadruplex and i-Motif Are Mutually Exclusive in ILPR Double-Stranded DNA

G-quadruplex has demonstrated its biological functions in vivo. Although G-quadruplex in single-stranded DNA (ssDNA) has been well characterized, investigation of this species in double-stranded DNA (dsDNA) lags behind. Here we use chemical footprinting and laser-tweezers-based single-molecule approaches to demonstrate that a dsDNA fragment found in the insulin-linked polymorphic region (ILPR), 5′-(ACA GGGG TGT GGGG)2 TGT, can fold into a G-quadruplex at pH 7.4 with 100 mM K+, and an i-motif at pH 5.5 with 100 mM Li+. Surprisingly, under a condition that favors the formation of both G-quadruplex and i-motif (pH 5.5, 100 mM K+), a unique determination of change in the free energy of unfolding (ΔGunfold) by laser-tweezers experiments provides compelling evidence that only one species is present in each dsDNA. Under this condition, molecules containing G-quadruplex are more stable than those with i-motif. These two species have mechanical stabilities (rupture force ≥ 17 pN) comparable to the stall force of RNA polymerases, which, from a mechanical perspective alone, could justify a regulatory mechanism for tetraplex structures in the expression of human insulin.

The Binding of G‐Quadruplex DNA to Insulin: From Single Molecule to Bulk‐Methods

The formation of guanine (G)‐quadruplex structures in the guanine‐rich tandem repeats of the insulin‐linked polymorphic region (ILPR) is linked to transcriptional effects on the insulin gene. Recent studies demonstrate that the ILPR G‐quadruplexes can bind to insulin, and while this may impact the transcription of insulin, little is known about the binding mechanism. We have performed single molecule atomic force microscopy (AFM), differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC) and fluorescence quenching spectroscopy to characterize the binding interaction between G‐quadruplex DNA and insulin. In this presentation, I will describe the bulk thermodynamic measurements performed at various temperatures from 10 to 37 °C. The experimental results based on KD demonstrate a moderate affinity by the ILPR consensus sequence to insulin. In addition to thermodynamic measurements, kinetic off‐rates were measured by single molecule force‐pulling measurements and these results will be discussed in relation to kinetic off‐rates measured from the unfolding of G‐quadruplex DNA.

Characterizing the Binding of G-Quadruplex DNA to Insulin by Single Molecule and Bulk Ensemble Methods

The formation of guanine (G)-quadruplex structures in the guanine-rich tandem repeats of the insulin-linked polymorphic region (ILPR) is linked to transcriptional effects on the insulin gene. Recent studies demonstrate that the ILPR G-quadruplexes can bind to insulin, and while this may impact the transcription of insulin, little is known about the binding mechanism. We have performed single molecule atomic force microscopy (AFM), differential scanning calorimetry (DSC), isothermal titration calorimetry (ITC) and fluorescence quenching spectroscopy measurements to characterize the binding interaction between G-quadruplex DNA and insulin.

G-Quadruplex Motifs Arranged in Tandem Occurring in Telomeric Repeats and the Insulin-Linked Polymorphic Region

To date, various G-quadruplex structures have been reported in the human genome. There are numerous studies focusing on quadruplex-forming sequences in general, but few studies have focused on two or more quadruplexes in the same molecule, which are most commonly found in telomeric DNA and other tandem repeats, e.g., insulin-linked polymorphic region (ILPR). Although the human telomere consists of a number of repeats, higher-order G-quadruplex structures are discussed less often because of the complexity of the structures. In this study, sequences consisting of 4-12 repeats of d(G(4)TGT), d(G(3)T(2)A), and/or d(G(4)T(2)A) have been studied by circular dichroism, ultraviolet spectroscopy, and temperature-gradient gel electrophoresis. These sequences serve as a model for the arrangement of quadruplexes in the telomere and ILPR in solution. Our major findings are as follows. (i) The number of G-rich repeats has a great influence on G-quadruplex stability. (ii) The evidence of quadruplex-quadruplex interaction is confirmed. (iii) For the first time, we directly observed the melting behavior of different conformers in a single experiment. Our results agree with other calorimetric and spectroscopic data and data obtained by single-molecule studies, atomic force microscopy, and mechanical unfolding by optical tweezers. We propose that the end of telomeres can be formed by only a few tandem quadruplexes (fewer than three). Our findings improve our understanding of the mechanism of G-quadruplex formation in long repeats in G-rich-regulating parts of genes and telomere ends.

Investigating the Binding of Insulin to G-Quadruplex DNA by Differential Scanning Calorimetry

The formation of guanine (G)-quadruplex in the guanine-rich tandem repeats of the insulin-linked polymorphic region (ILPR) is linked to transcriptional effects on the insulin gene. Recent studies demonstrate that these G-quadruplexes can bind insulin, and while this may impact the transcription of insulin, little is known about the binding mechanism. We have performed differential scanning calorimetry to characterize the binding interaction between insulin and G-quadruplex DNA. The consensus quadruplex ILPR sequence shows an unfolding temperature at 93.2 degrees celsius, while this peak is absent in a scrambled version of this sequence. The unfolding temperature of an insulin-G-quadruplex mix showed ∼ 3 degrees celsius change in the Tm for the insulin peak in comparison with the unfolding of insulin alone, and a ∼1 degree celsius change from insulin-scrambled DNA mix. These results provide additional support for the binding of insulin to G-quadruplex DNA. Experiments are currently in progress to measure the binding constant of this interaction by isothermal titration calorimetry.

Coexistence of an ILPR i-Motif and a Partially Folded Structure with Comparable Mechanical Stability Revealed at the Single-Molecule Level

Investigation of i-motif is of high importance to fully understand the biological functions of G quadruplexes in the context of double-stranded DNA. Whereas single-molecule approaches have profiled G quadruplexes from a perspective unavailable by bulk techniques, there is a lack of similar literature on the i-motif in the cytosine (C)-rich region complementary to G quadruplex-forming sequences. Here, we have used laser tweezers to investigate the structures formed in 5'-(TGTCCCCACACCCC)(2), a predominate variant in the insulin-linked polymorphic region (ILPR). We have observed two species with the change in contour length (DeltaL) of 10.4 (+/-0.1) and 5.1 (+/-0.5) nm, respectively. Since DeltaL of 10.4 nm is located within the expected range for an i-motif structure, we assign this species to the i-motif. The formation of the i-motif in the same sequence has been corroborated by bulk experiments such as Br(2) footprinting, circular dichroism, and thermal denaturation. The assignment of the i-motif is further confirmed by decreased formation of this structure (23% to 1.3%) with pH 5.5 --> 7.0, which is a well-established behavior for i-motifs. In contrast to that of the i-motif, the formation of the second species with DeltaL of 5.1 nm remains unchanged (6.1 +/- 1.6%) in the same pH range, implying that pH-sensitive C:CH(+) pairs may not contribute to the structure as significantly as those to the i-motif. Compared to the DeltaG(unfold) of an i-motif (16.0 +/- 0.8 kcal/mol), the decreased free energy in the partially folded structure (DeltaG(unfold) 10.4 +/- 0.7 kcal/mol) may reflect a weakened structure with reduced C:CH(+) pairs. Both DeltaL and DeltaG(unfold) argue for the intermediate nature of the partially folded structure in comparison to the i-motif. In line with this argument, we have directly observed the unfolding of an i-motif through the partially folded structure. The i-motif and the partially folded structure share similar rupture forces of 22-26 pN, which are higher than those that can stall transcription catalyzed by RNA polymerases. This suggests, from a mechanical perspective alone, that either of the structures can stop RNA transcription.

Characterization of Insulin Ilpr Sequences for Their Ability to Adopt a G-Quadruplex Structure

A major genetic factor linked to the progression of type 1 diabetes occurs in the insulin-linked polymorphic repeat region (ILPR) located 363 bp upstream of the human insulin gene. Genetic studies have shown that individuals with class I repeats (30–60) are predisposed to the development of type 1 diabetes while individuals with longer repeats are protected. Previous research has suggested that some sequences found within the ILPR can adopt a G-quadruplex structure, and this finding has lead to speculation that G-quadruplexes may control insulin expression in certain circumstances. Unfortunately, relatively little study has been done on whether sequences found in the ILPR can adopt a quadruplex fold. In this study, we have utilized circular dichroism, thermal difference spectroscopy and ultraviolet (UV) melting studies to examine the first seven common repeat sequences (A-G) found in the ILPR. We find that sequences A-E adopt a quadruplex fold while sequences F and G likely do not. Examination of sequence B and a single nucleotide variant, B2, revealed that both folded into a G-quadruplex. This result casts doubt on previous studies suggesting that the formation of a quadruplex was related to the ability of ILPR sequences to regulate transcription.

A Single Molecule Force Spectroscopy Study of the Binding Interaction Between Insulin and G-Quadruplex DNA

The formation of guanine (G)-quadruplex in the guanine-rich tandem repeats of the insulin-linked polymorphic region (ILPR) is linked to transcriptional effects on the insulin gene. Recent studies demonstrate that these G-quadruplexes can bind insulin, and while this may impact the transcription of insulin, little is known about the binding mechanism. A single molecule force spectroscopy study was performed to examine the selective binding of insulin to the ILPR G-quadruplex DNA. In this study, the insulin was covalently attached to a flat gold surface while the quadruplex DNA was attached to an AFM probe. The rupture force between insulin and quadruplex DNA was measured at various force loading rates. To confirm the specificity of the binding, control studies were performed by blocking the tethered G-quadruplex with “free insulin” in solution. Additional control studies were performed with a shorter DNA sequence incapable of forming a G-quadruplex on the AFM tip and a scrambled DNA sequence of the ILPR sequence. Results from the dynamic force-pulling studies are described based on the Bell-Evans and Dudko-Hummer models.

DNA-modified ITO surfaces for affinity MALDI-MS

Indium Tin Oxide (ITO) coated surfaces were compared with fused silica and aluminium probes for conventional MALDI-MS of proteins, followed by experiments to determine if the advantages of ITO over the poorly conducting fused silica surface would carryover to affinity MALDI-MS, in which the probe surface is modified with DNA for protein capture and detection. Improved precision of m/z values and increased detectability by 1 to 2 orders of magnitude were observed for capture and detection of insulin and insulin-like growth factor 2 at surfaces modified with sequences from the insulin-linked polymorphic region (ILPR) of the human insulin gene that have previously been shown to bind with high affinity to these proteins. Results also indicate capture and detection of the insulin β-chain from DTT-treated human serum at the DNA-modified ITO surfaces. The improved performance is accompanied by the same ease of covalent DNA attachment and indefinite reusability of the DNA-modified surfaces previously demonstrated for fused silica probes. The use of ITO-coated surfaces is an important advance toward the routine use of DNA-modified surfaces in affinity MALDI-MS for rapid screening of DNA–protein interactions for applications such as biomarker discovery and detection of low abundance proteins in complex biological samples.