Comment on "Sequencing-independent delocalization in a DNA-like double chain with base pairing".

نویسندگان

  • A Sedrakyan
  • F Domínguez-Adame
چکیده

In a recent paper [1], Caetano and Schulz (CS) claim that intrinsic DNA-correlations, due to the base pairing (A-T and C-G), lead to electron delocalization. Furthermore, they point out that there is a localization-delocalization transition (LDT) for certain parameter ranges. In this Comment we present analytical and numerical evidences that in their model all states are localized, thus excluding a LDT. The equation for the electron amplitude can be cast in a compact form by using a 4 4 transfer matrix, Tn;ij, belonging to the SU 2; 2 group. Here n runs over the sites of one chain and i; j 2 fA;T;G;Cg. Only four different transfer matrices arise (Tn;AT, Tn;TA, Tn;CG, Tn;GC). The Lyapunov exponents, the eigenvalues of the limiting matrix limN!1 ln Q1 n N T 1=N n;ij , provide information about the localization length of the states, assuming exponential localization. Because of the self-averaging property they can be calculated by taking the product of random transfer matrices over a long system. Similarly, the Landauer exponent La N lnhk Q1 n N Tn;ijki (h. . .i denotes ensemble averages) is twice the largest Lyapunov exponent near the critical region in one-dimensional systems [2] and can be calculated analytically following the technique developed in Ref. [3]. For brevity, here we only provide the main steps: We use the decomposition of the product of two fundamental representations, Tn, of the SU 2; 2 group as Tn 0 Ty n 0 1=4 0 0 n , where ( 0; . . . ; 15) are the generators of the algebra u 2; 2 . The matrix n 1=4 Tr Tn Ty n is the adjoint representation of Tn. It is then straightforward to get h i 1=4 AT TA CG GC . The Landauer exponents are the nonnegative eigenvalues of h i. The condition of the existence of an extended state is equivalent to detjh i Ij 0, and it is a matter of simple algebra to prove that this condition is never met. To provide further support to our claim, we also calculated the localization properties of the system numerically, following the procedure sketched above. The results are collected in Fig. 1 using the same parameters as in Ref. [1]. It becomes clear that neither the largest Lyapunov exponents nor the Landauer one vanish over the whole energy spectrum. Also, the largest Lyapunov exponent for DNAcorrelated (with base pairing) and totally uncorrelated (without base pairing) models overlap. In addition, the second, smaller Lyapunov exponent becomes positive too, as seen in Fig. 1 (set labeled B). Most important, its minimal value is size independent within the numerical accuracy (0:0131 0:0035, 0:0124 0:0028, and 0:0127 0:0025 for N 2000, 3000, and 4000, respectively). There-

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Sequencing-independent delocalization in a DNA-like double chain with base pairing.

The question of whether or not DNA is intrinsically conducting is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing in opposition to correlations along each chain. We show that a disordered base paired double chain presents truly or, at least, effectively delocalized states. This e...

متن کامل

Multiple end joining mechanisms repair a chromosomal DNA break in fission yeast.

Non-homologous end joining (NHEJ) is an important mechanism for repairing DNA double-strand breaks (DSBs). The fission yeast Schizosaccharomyces pombe has a conserved set of NHEJ factors including Ku, DNA ligase IV, Xlf1, and Pol4. Their roles in chromosomal DSB repair have not been directly characterized before. Here we used HO endonuclease to create a specific chromosomal DSB in fission yeast...

متن کامل

Stacked-unstacked equilibrium at the nick site of DNA.

Stability of duplex DNA with respect to separation of complementary strands is crucial for DNA executing its major functions in the cell and it also plays a central role in major biotechnology applications of DNA: DNA sequencing, polymerase chain reaction, and DNA microarrays. Two types of interaction are well known to contribute to DNA stability: stacking between adjacent base-pairs and pairin...

متن کامل

Enhanced fidelity in mismatch extension by DNA polymerase through directed combinatorial enzyme design.

The fidelity of DNA polymerase activity is of central importance for numerous biotechnological applications.r1.21 The imperfect fidelity of DNA polymerases under the unnatural conditions of several techniques such as those of the polymerase chain reaction (PCR) either restricts the application of these enzymes or demands their tedious optimization. Thus, a prime target for the design of DNA pol...

متن کامل

Theoretical Study of Heteroatom Resonance-Assisted Hydrogen Bond: Effect of Substituent on π-delocalization

The concept of Resonance Assisted Hydrogen Bond (RAHB), which usually occurs in b diketons, has a remarkable role in chemistry. These molecules, which contain heteroatom particularly O and N, are species with biological interest in protein folding and DNA pairing. Therefore, the amplification of hydrogen bonds strength by substituents may be important in life scie...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Physical review letters

دوره 96 5  شماره 

صفحات  -

تاریخ انتشار 2006